Development and assessment of a coupled crop-climate model

It is well established that crop production is inherently vulnerable to variations in the weather and climate. More recently the influence of vegetation on the state of the atmosphere has been recognized. The seasonal growth of crops can influence the atmosphere and have local impacts on the weather, which in turn affects the rate of seasonal crop growth and development. Considering the coupled nature of the crop-climate system, and the fact that a significant proportion of land is devoted to the cultivation of crops, important interactions may be missed when studying crops and the climate system in isolation, particularly in the context of land use and climate change. To represent the two-way interactions between seasonal crop growth and atmospheric variability, we integrate a crop model developed specifically to operate at large spatial scales (General Large Area Model for annual crops) into the land surface component of a global climate model (GCM; HadAM3). In the new coupled crop-climate model, the simulated environment (atmosphere and soil states) influences growth and development of the crop, while simultaneously the temporal variations in crop leaf area and height across its growing season alter the characteristics of the land surface that are important determinants of surface fluxes of heat and moisture, as well as other aspects of the land-surface hydrological cycle. The coupled model realistically simulates the seasonal growth of a summer annual crop in response to the GCM's simulated weather and climate. The model also reproduces the observed relationship between seasonal rainfall and crop yield. The integration of a large-scale single crop model into a GCM, as described here, represents a first step towards the development of fully coupled crop and climate models. Future development priorities and challenges related to coupling crop and climate models are discussed.

Soil management in relation to sustainable agriculture and ecosystem services

Requirements for research, practices and policies affecting soil management in relation to global food security are reviewed. Managing soil organic carbon (C) is central because soil organic matter influences numerous soil properties relevant to ecosystem functioning and crop growth. Even small changes in total C content can have disproportionately large impacts on key soil physical properties. Practices to encourage maintenance of soil C are important for ensuring sustainability of all soil functions. Soil is a major store of C within the biosphere – increases or decreases in this large stock can either mitigate or worsen climate change. Deforestation, conversion of grasslands to arable cropping and drainage of wetlands all cause emission of C; policies and international action to minimise these changes are urgently required. Sequestration of C in soil can contribute to climate change mitigation but the real impact of different options is often misunderstood. Some changes in management that are beneficial for soil C, increase emissions of nitrous oxide (a powerful greenhouse gas) thus cancelling the benefit. Research on soil physical processes and their interactions with roots can lead to improved and novel practices to improve crop access to water and nutrients. Increased understanding of root function has implications for selection and breeding of crops to maximise capture of water and nutrients. Roots are also a means of delivering natural plant-produced chemicals into soil with potentially beneficial impacts. These include biocontrol of soil-borne pests and diseases and inhibition of the nitrification process in soil (conversion of ammonium to nitrate) with possible benefits for improved nitrogen use efficiency and decreased nitrous oxide emission. The application of molecular methods to studies of soil organisms, and their interactions with roots, is providing new understanding of soil ecology and the basis for novel practical applications. Policy makers and those concerned with development of management approaches need to keep a watching brief on emerging possibilities from this fast-moving area of science. Nutrient management is a key challenge for global food production: there is an urgent need to increase nutrient availability to crops grown by smallholder farmers in developing countries. Many changes in practices including inter-cropping, inclusion of nitrogen-fixing crops, agroforestry and improved recycling have been clearly demonstrated to be beneficial: facilitating policies and practical strategies are needed to make these widely available, taking account of local economic and social conditions. In the longer term fertilizers will be essential for food security: policies and actions are needed to make these available and affordable to small farmers. In developed regions, and those developing rapidly such as China, strategies and policies to manage more precisely the necessarily large flows of nutrients in ways that minimise environmental damage are essential. A specific issue is to minimise emissions of nitrous oxide whilst ensuring sufficient nitrogen is available for adequate food production. Application of known strategies (through either regulation or education), technological developments, and continued research to improve understanding of basic processes will all play a part. Decreasing soil erosion is essential, both to maintain the soil resource and to minimise downstream damage such as sedimentation of rivers with adverse impacts on fisheries. Practical strategies are well known but often have financial implications for farmers. Examples of systems for paying one group of land users for ecosystem services affecting others exist in several parts of the world and serve as a model.

PCR-based markers diagnostic for spring and winter seasonal growth habit in barley

Toward the ultimate goal of replacing field-based evaluation of seasonal growth habit, we describe the design and validation of a multiplex polymerase chain reaction assay diagnostic for allelic status at the barley (Hordeum vulgare ssp. vulgare L.) vernalization locus, VRN-H1 By assaying for the presence of all known insertion–deletion polymorphisms thought to be responsible for the difference between spring and winter alleles, this assay directly tests for the presence of functional polymorphism at VRN-H1 Four of the nine previously recognized VRN-H1 haplotypes (including both winter alleles) give unique profiles using this assay. The remaining five spring haplotypes share a single profile, indicative of function-altering deletions spanning, or adjacent to, the putative “vernalization critical” region of intron 1. When used in conjunction with a previously published PCR-based assay diagnostic for alleles at VRN-H2, it was possible to predict growth habit in all the 100 contemporary UK spring and winter lines analyzed in this study. This assay is likely to find application in instances when seasonal growth habit needs to be determined without the time and cost of phenotypic assessment and during marker-assisted selection using conventional and multicross population analysis.

The sources of phosphorus in the waters of Great Britain

Total phosphorus (TP) and soluble reactive phosphorus (SRP) loads to watercourses of the River Basin Districts (RBDs) of Great Britain (GB) were estimated using inventories of industrial P loads and estimates of P loads from sewage treatment works and diffuse P loads calculated using region-specific export coefficients for particular land cover classes combined with census data for agricultural stocking densities and human populations. The TP load to GB waters was estimated to be 60 kt yr(-1), of which households contributed 73, agriculture contributed 20, industry contributed 3, and 4 came from background sources. The SRP load to GB waters was estimated to be 47 kt yr(-1), of which households contributed 78, agriculture contributed 13, industry contributed 4, and 6 came from background Sources. The 'average' area-normalized TP and SRP loads to GB waters approximated 2.4 kg ha(-1) yr(-1) and 1.8 kg ha(-1) yr(-1), respectively. A consideration of uncertainties in the data contributing to these estimates suggested that the TP load to GB waters might lie between 33 and 68 kt yr(-1), with agriculture contributing between 10 and 28 of the TP load. These estimates are consistent with recent appraisals of annual TP and SRP loads to GB coastal waters and area-normalized TP loads from their catchments. Estimates of the contributions of RBDs to these P loads were consistent with the geographical distribution of P concentrations in GB rivers and recent assessments of surface waters at risk from P Pollution.

Options for support to agriculture and food security under climate change

Agriculture and food security are key sectors for intervention under climate change. Agricultural production is highly vulnerable even to 2C (low-end) predictions for global mean temperatures in 2100, with major implications for rural poverty and for both rural and urban food security. Agriculture also presents untapped opportunities for mitigation, given the large land area under crops and rangeland, and the additional mitigation potential of aquaculture. This paper presents a summary of current knowledge on options to support farmers, particularly smallholder farmers, in achieving food security through agriculture under climate change. Actions towards adaptation fall into two broad overlapping areas: (1) accelerated adaptation to progressive climate change over decadal time scales, for example integrated packages of technology, agronomy and policy options for farmers and food systems, and (2) better management of agricultural risks associated with increasing climate variability and extreme events, for example improved climate information services and safety nets. Maximization of agriculture’s mitigation potential will require investments in technological innovation and agricultural intensification linked to increased efficiency of inputs, and creation of incentives and monitoring systems that are inclusive of smallholder farmers. Food systems faced with climate change need urgent, broad-based action in spite of uncertainties.

Integrating science into humanitarian and development planning and practice to enhance community resilience

There has been an increased emphasis upon the application of science for humanitarian and development planning, decision-making and practice; particularly in the context of understanding, assessing and anticipating risk (e.g. HERR, 2011). However, there remains very little guidance for practitioners on how to integrate sciences they may have had little contact with in the past (e.g. climate). This has led to confusion as to which ‘science’ might be of use and how it would be best utilised. Furthermore, since this integration has stemmed from a need to be more predictive, agencies are struggling with the problems associated with uncertainty and probability. Whilst a range of expertise is required to build resilience, these guidelines focus solely upon the relevant data, information, knowledge, methods, principles and perspective which scientists can provide, that typically lie outside of current humanitarian and development approaches. Using checklists, real-life case studies and scenarios the full guidelines take practitioners through a five step approach to finding, understanding and applying science. This document provides a short summary of the five steps and some key lessons for integrating science.

The science case for an orbital mission to Uranus: Exploring the origins and evolution of ice giant planets

Giant planets helped to shape the conditions we see in the Solar System today and they account for more than 99% of the mass of the Sun’s planetary system. They can be subdivided into the Ice Giants (Uranus and Neptune) and the Gas Giants (Jupiter and Saturn), which differ from each other in a number of fundamental ways. Uranus, in particular is the most challenging to our understanding of planetary formation and evolution, with its large obliquity, low self-luminosity, highly asymmetrical internal field, and puzzling internal structure. Uranus also has a rich planetary system consisting of a system of inner natural satellites and complex ring system, five major natural icy satellites, a system of irregular moons with varied dynamical histories, and a highly asymmetrical magnetosphere. Voyager 2 is the only spacecraft to have explored Uranus, with a flyby in 1986, and no mission is currently planned to this enigmatic system. However, a mission to the uranian system would open a new window on the origin and evolution of the Solar System and would provide crucial information on a wide variety of physicochemical processes in our Solar System. These have clear implications for understanding exoplanetary systems. In this paper we describe the science case for an orbital mission to Uranus with an atmospheric entry probe to sample the composition and atmospheric physics in Uranus’ atmosphere. The characteristics of such an orbiter and a strawman scientific payload are described and we discuss the technical challenges for such a mission. This paper is based on a white paper submitted to the European Space Agency’s call for science themes for its large-class mission programme in 2013.

Children's misconceptions and the teaching of early years science: a case study

The aim of this paper is to examine how teachers’ awareness of children’s misconceptions can affect children’s acquisition of scientific concepts. In other words, this paper is aimed at examining whether teaching is altered when teachers are aware of pupils’ misconceptions of a specific science concept. This paper details a case study focused on two kindergarten classes of five year-old children and their teachers and took place in Cyprus. Two lessons were observed and three children from each class were interviewed. Through the analysis of children’s responses it was possible to identify specific misconceptions related to the concept of rain. The results indicate that it is very important for teachers to be aware of what misconceptions children have, because this can help them plan lessons for children to overcome their misconceptions. It seems that it is more likely for children to overcome their misconceptions when teachers take these misconceptions into account as they plan and teach science lessons.

Interactive effect of cowpea variety, dose and exposure time on bruchid tolerance to botanical pesticides

Callosobruchus maculatus has for years remained a serious menace in cowpea in Sub-Sahara Africa. The objective of this study was to investigate the effect of genotypic cowpea (Vigna unguiculata (L.) Walp) varieties, time and dose on C. maculatus exposed to powders of Piper guineense and Eugenia aromatica. Irrespective of duration and botanicals, bruchid reared on KDV showed the highest tolerance to both plant materials; while their counterparts from IAR48V were the most susceptible. Median lethal time (LT50) also varied according to the plant materials; with the highest in KDV reared bruchid [P. guineense: KDV (18.31), IAR48V (9.27), IFBV (13.17); E. aromatica: KDV (76.01), IAR48V (5.59), IFBV (6.49)]. There was a significant impact of cowpea variety (V), exposure time (T) and dose (D) on the tolerance of C. maculatus to both plant materials. The effect of all two-way (VxT, VxD, DxT) and three way interactions (V×T×D) on the tolerance of C. maculatus to both plant materials was also significant. Varietal effect was more pronounced in bruchids exposed to E. aromatica; while exposure time was more pronounced in bruchids exposed to P. guineense.

Soil phosphorus supply affects nodulation and N:P ratio in 11 perennial legume seedlings

Developing new perennial pasture legumes for low-P soils is a priority for Australian Mediterranean agro-ecosystems, where soil P availability is naturally low. As legumes tend to require higher P inputs than non-legumes, the ability of these plants to fix N2 under varying soil P levels must be determined. Therefore, the objective of this study was to investigate the influence of soil P supply on plant N status and nodule formation in 11 perennial legumes, including some novel pasture species. We investigated the effect of applying soil P, ranging from 0 to 384 μg P/g dry soil, on plant N status and nodulation in a glasshouse. Without exogenous P supply, shoot N concentration and N : P ratio were higher than at 6 μg P/g soil. Shoot N concentration and N : P ratio then changed little with further increase in P supply. There was a close positive correlation between the number of nodules and shoot P concentration in 7 of the 11 species. Total nodule dry weight and the percentage of plant dry weight that consisted of nodules increased when P supply increased from 6 to 48 μg P/g. Without exogenous P addition, N : P ratios partitioned into a two-group distribution, with species having a N : P ratio of either >70 or <50 g/g. We suggest that plants with a high N : P ratio may take up N from the soil constitutively, while those with a low N : P ratio may regulate their N uptake in relation to internal P concentration. The flexibility of the novel pasture legumes in this study to adjust their leaf N concentrations under different levels of soil P supplements other published evidence of good growth and high P uptake and P-use efficiency under low soil P supply and suggests their potential as pasture plants in low-P soils in Australian Mediterranean agro-ecosystems warrants further attention.

CGIAR research program on grain legumes

EXECUTIVE SUMMARY Background and context The Grain Legumes CRP was established to bring all research and development work on grain legumes within the CGIAR system under one umbrella. It was set up to provide public goods outcomes to serve the needs of the sustainable production and consumption of grain legumes in the developing world, capitalising upon their properties that enhance the natural resource base upon which production so unequivocally depends. The choice of species and research foci were finalised following extensive consultation with all stakeholders (though perhaps fewer end users), and cover all disciplines that contribute to long-lasting solutions to the issues of developing country production and consumption. ICRISAT leads Grain Legumes and is partnered by the CGIAR centers ICARDA, IITA and CIAT and a number of other important partners, both public and private, and of course farmers in the developed and developing world. Originally in mid-2012 Grain Legumes was structured around eight Product Lines (PL) (i.e. technological innovations) intersecting five Strategic Components (SC) (i.e. arranged as components along the value chain). However, in 2015, it was restructured along a more R4D output model leading to Intermediate Development Outcomes (IDOs). Thus five Flagship Projects (FP) more closely reflecting a systematic pipeline of progression from fundamental science, implementation of interventions and the development of capacity and partnerships to promote and adopt impactful outcomes: FP1) Managing Productivity through crop interactions with biotic and abiotic constraints; FP2) Determination of traits that address production constraints and opportunities; FP3) Trait Deployment of those traits through breeding; FP4) Seed Systems, post-harvest processing and nutrition; FP5) Capacity-Building and Partnerships. Another three cross-cutting FPs analyse the broader environment surrounding the adoption of outputs, the capitalising of investments in genomics research, and a focus on the Management and Governance of Grain Legumes: FP6) Knowledge, impacts, priorities and gender organisation; FP7) Tools and platforms for high throughput genotyping and bioinformatics; and FP8) Management and Governance. Five FPs focus on R4D; FPs 5 and 6 are considered cross-cutting; FP 7 has a technical focus and FP 8 has an overarching objective. Over the three year period since its inception in July 1012, Grain Legumes has had a total budget of $140 million, with $62M originally to come from W1/W2 and the remaining $78M to come from W3/bilateral. In actuality only $45M came from W1/W2 but $106M from W3/bilateral corresponding to 106% of expectation. Purpose, scope and objectives of the external evaluation Principally, the evaluation of Grain Legumes is to ensure that the program is progressing in an effective manner towards addressing the system-level outcomes of the CGIAR as they relate to grain legumes. In essence, the evaluation aims to provide essential evaluative information for decision-making by Program Management and its funders on issues such as extension, expansion and structuring of the program and adjustments in relevant parts of the program. Subsequent to the formal signing of the agreed terms of reference, the evaluation team was also invited to comment upon the mooted options for merging and/or disaggregating of Grain Legumes. The audiences are therefore manifold, from the CGIAR Fund Council and Consortium, the Boards of Trustees of the four component CGIAR centres, the Grain Legumes Steering, Management and Independent Advisory Committees, to the researchers and others involved in the delivery of R4D outcomes and their partner organisations. The evaluation was not only summative in measuring results from Grain Legumes at arm’s length; it was also formative in promoting learning and improvements, and developmental in nurturing adaption to transformational change with time. The evaluation report was written in a manner that allows for engagement of key partners and funders in a dialogue as to how to increase ownership and a common understanding of how the goals are to be achieved. We reviewed research undertaken before the CRPs but leading to impacts during Grain Legumes, and research commenced over the past 2.5 years. For related activities pre- and post-commencement of Grain Legumes, we reviewed the relevance of activities and their relation to CGIAR and the Grain Legumes goals, whether they were likely to lead to the outcomes and impacts as documented in the Grain Legumes proposal, and the quality of the science underpinning the likelihood to deliver outcomes. Throughout, we were cognisant of the extent of the reach of CGIAR centres’ activities, and those of stakeholders upon which the impact of CGIAR R4D depends. Within our remit we evaluated the original and modified management and governance structures, and all the processes/responsibilities managed within those structures. Besides the evaluation of the technical and managerial issues of Grain Legumes, we addressed cross-cutting issues of gender sensitivity, capacity building and the creation and nurturing of partnerships. The evaluation also has the objective to provide information relating to the development of full proposals for the new CRP funding cycle. The evaluation addressed six overarching questions developed from the TOR questions (listed in the Inception Report, 2015 [http://1drv.ms/1POQSZh] and others including cross-cutting issues, phrasing them within the context of traditional evaluation criteria: 1. Relevance: Global development, urbanisation and technological innovation are progressing rapidly, are the aims and focus of Grain Legumes coherent, robust, fit for purpose and relevant to the global community? 2. Efficiency: Is the structure and effectiveness of leadership across Grain Legumes developing efficient partnership management and project management across PLs? 3. Quality of science: Is Grain Legumes utilising a wide range of technologies in a way that will increase our fundamental understanding of the biology that underpins several PLs; and are collected data used in the most effective way? 4. Effectiveness: Are Product Lines strategic contributors to the overarching aims and vision for Grain Legumes? 5. Impact: Are the impact pathways that underlie each PL well defined, measureable and achievable; and are they sufficiently defined in terms of beneficiaries? Does progress towards achieving outputs and outcomes from the major research areas indicate a lasting benefit for CGIAR and the communities it serves? 6. Sustainability: Is Grain Legumes managing the increasing level of restricted funding in terms of program quality and effectiveness, including attracting and retaining quality staff? Questions for the evaluation of governance and management focused on accountability, transparency, the effectiveness and success of program execution, change management processes and communication methods, taking account of the effects of CGIAR reform. The three crosscutting issues were considered as follows: i) gender balance in program delivery, e.g. whether each PL is able to contribute to the increased income, food security, nutrition, environmental and resource conservation for resource-poor women and men existing in rural livelihoods; ii) are internal and external capacity gaps identified/met, is capacity effectively developed within each product line, and are staff at all levels engaged in contributing ideas towards capacity building; and iii) is there effective involvement of partners in research and activity programming, what are the criteria for developing partnerships, how they are formalised and how is communication between partners and within Grain Legumes managed? It was not in remit to search for output, outcomes or impact, however as highlighted later, much of our time was spent on searching for information to support claims of impact, since Grain Legumes had no effective dedicated M&E in place at the time of undertaking the review. Approach and methodology The evaluation was conducted when Grain Legumes had been operational for approximately 3 years. The approach and methodology followed that outlined in the Inception Report [http://1drv.ms/1POQSZh]. The CCEE Team based its findings, conclusions and recommendations on data collection from several sources:  review of program documents, communications with the CO, minutes and presentations from all management and governance committee meetings  review of previous assessments and evaluations  sampling of Grain Legume projects in 7 countries1  more than 66 face to face interviews, a further 133 persons in groups and 4 phone/Skype conversations: ICRISAT, ICARDA, CIAT and IITA staff, partners and stakeholders. Meetings with one Independent Science and Partnership Council (ISPC) member.  meetings with over 100 people in 16 external groups, such as farmers’ groups  online survey completed by 126 (33.4%) scientists who contribute to Grain Legumes and a number of non-CGIAR partners and Management representatives  bibliometric review of 10 publications within each PL to qualitatively assess the design, conduct, analysis and presentation of results  quantitative and qualitative self-assessment of the contributions of each of the PLs to the six criteria and 3 cross-cutting issues of evaluation mentioned above completed by PLCs (see below). We reviewed the Logical Framework that underpins the desired Goals, or Impacts of Grain Legumes, and the links between the outputs and inputs as they related to the organisational units of Grain Legumes. The logical framework approach to planning and management of Grain Legumes activities implies a linear process, leading from activities, outputs, outcomes, to impacts, but within such an approach there may be room for a more systems dynamics approach allowing for feedback at every step and within every step, in order to refine and improve upon the respective activities as new results, ideas, and directions come to light. We then developed a matrix that summarised quantitatively and qualitatively the contributions of each of the PLs to the six criteria and 3 cross-cutting issues of evaluation mentioned above. Main findings and conclusions Grain legume production and consumption remain of great importance to the food security of not inconsiderable populations in the developing world, and merit sustained research investment. We conclude that Grain Legumes continues to contribute significant returns to research investments by the CGIAR, and such investment should continue. The global research community looks to the CGIAR for leadership in Grain legumes, but needs to be assured of value adding when bringing CGIAR centres under the expected umbrella of synergy. However, there is considerable scope for improving the efficiency with which outcomes are achieved. We note that an absence of an effective M&E has hampered the assessment of the effectiveness of proposed impact pathways. Likewise progress has been hampered by the limited numbers of research partnerships with Advanced Institutes and by budgetary constraints (lamented for their stifling effects on continuation of ongoing exciting research). The unworkable management structure constrains the CRP Director’s leadership role; responsibility without authority will never lead to effective outcomes. Good fortune is responsible for many of the successes of Grain Legumes, underpinned by a devoted work force across the participating CGIAR centres and partners. The quality of the science is not uniformly high, and we believe that mentoring of scientists should be given priority where quality is poor. Simplified yet informative reporting is an imperative to this. World class science underpins the identification of, and molecular basis for, traits important for yield improvement and this expertise should be extended to all grain legume species, capitalising upon the germplasm collections. The linking of Grain Legumes with regional research and development consortia has been very successful, with outcomes aligning with those of Grain Legumes. We see that with declining funding consolidation of research effort based on likely successes will be necessary, and welcome the move afoot to incorporate grain legumes into an agri-food system focused on successful value chains that deliver sustainable outcomes. Relevance and Strategy Grain Legumes has geographic and disciplinary relevance, addressing the major supply chain issues of variety development seed system and agronomy, with some attention to quality and postharvest marketing systems. The CRP has provided the opportunity to cut ongoing and to initiate new research. Research funded by the Gates Foundation (Anon, 2014) suggests that the need for improvement is greatest in Africa and advocates reducing the number of crop by country combinations when resources are sparse. The lesser research investment in Latin America, however, is not in line with the regions’ dependency on legumes. In spite of the fact that there is no evidence of strong inter-partner CGIAR centre or internal synergy, the program is still moving ahead on most fronts in line with the overall project logframe. This is in spite of continual pushing and pulling by in particular donors and the CO. However, to quantify real impact, we believe Grain Legumes must have access to reliable baseline data on production and consumption, and this is missing. Similarly, there is little evidence of the proposed ‘Inclusive Market Oriented Development’ (IMOD) framework being used to assist with priority setting. The product lines, eight of which cover most of the historical programmes in place in the partner CGIAR centres at the commencement of the Grain Legumes, do not cover all the constraints for formal constraints analysis was not undertaken at the inception of the Grain Legumes, and some of this additionally identified research is undertaken under the umbrella of the FPs; this needs to be rationalised. We found the PLs to be isolated in activity, even with minimally-integrated activities within each PL, with little evidence of synergy between PLs. Even though the SCs should ensure a systems approach, as with the new FPs, we did not get a feel that this is so. The underplaying of agronomy, and production practices may be one reason for this. We believe that treating legume crops as if they were horticultural crops will increase farmer returns from investment. The choice of Flagship Projects makes sense, with the flow of activity firstly around crop management and agronomy followed by the logical sequence of trait discovery, incorporation into improved varieties, dissemination of those varieties through appropriate seed chains leading to market impacts, and the capacity building required at all steps. One obvious omission, however, is the lack of a central and strategic policy on the role of transgenics in Grain Legumes. We found four notable comparative advantages for Grain Legumes: the access to germplasm of component species, the use of the phenotyping facility at ICRISAT, the approach for village level industry for IPM, and the emphasis on hybrid pigeonpea. Efficiency Each centre has strong control of, and emphasis on, their ‘species’ domains, and ownership of the same detracts from possible synergy. Without synergy or value add, the Grain Legumes brings with it no comparative advantage over each centre continuing their own pre-CRP research agendas. We found little evidence of integration of programmes between centres and almost no cross-centre authorship of publications, such as could have occurred with the integrated cross-centre approaches to stress tolerance including crop modelling: the one publication (Gaur et al., 2015) on heat tolerance by ICRISAT, CIAT and ICARDA does not provide any keys to inter-centre collaboration. The integration of each centre with NARS and university research programmes is good, but the cross-centre links with NARS are poor. A better coordinated integration with Grain Legumes, , rather than through the individual centres, may reduce transactions costs for NARS, Monitoring and evaluation is, as noted throughout our report, one area of Grain Legumes research management that has not been given the attention it should have received. If it had have received proper attention, some of the issues of poor efficiency might have been nipped in the bud. A strong monitoring and evaluation system would have provided the baseline data and set the milestones that would have allowed both efficiency and effectiveness to be better appraised. We found no attempt to define comparative advantages of the CGIAR centres and their R4D activities, although practice showed the better grasp of CIAT in developing innovative seed distribution systems. During field visits and interviews, the CCEE Team observed shortcomings in the communication processes within Grain Legumes and with the broader scientific community and the public. For example, the public face of the program on the internet is out of date. Survey findings, however, suggest that information is shared freely and routinely within the PL within which scientists work. Some external issues, such as those with funding, low W1/W2 and poor sustainability of funding (especially if funding is top heavy with a few agencies), undermine research investment and confidence of partners in the system (e.g. as voiced by researchers working on crops and countries not included in TL III and the cessation of ongoing competitively-funded projects especially in India), but other issues attributable to the governance and management of the Grain Legumes, such as opaque integration of W3/bilaterals with W1/W2 funding require attention. Offsetting this, the existence of the Grain Legumes did mobilise additional funding [that it would not have if Grain Legumes did not exist]. We were concerned that Grain Legumes is simply not recognised outside of the CRP, with a limited www presence and centres promote themselves, rather than Grain Legumes (with exception in IITA). This is not a good move if one wishes to increase investment in the Grain Legumes. Although funding agencies require cost:benefit ratios, for example for each PL we faced difficulty in determining comparative value for money between investment in different types of research, and in being able to clearly attribute research and development outcomes to financial investment. There was also a time CCEE frame issue too. There is poor interaction with the private sector, notably in areas where they have a comparative financial advantage. We questioned in particular the apparent lack of interaction with the major agro-chemical companies, with respect to the development of herbicide tolerant (HT) grain legumes and the lack of evidence that the regulatory and trade aspects related to herbicide tolerant crops had been considered. Quality of science The quality of the science is highly variable across Grain Legumes, with pockets of real excellence that are linked to good levels of productivity, whereas other PLs are struggling to deliver quality publications, and outputs and outcomes that are based on these. There is much evidence of gradualism in terms of research output and outcomes, i.e. essentially the same activities that were ongoing at the time of the launch of Grain Legumes are still in place. However, there are examples of game changers including those from valuable investments in genomics, phenotyping, and bio-control. We were pleased to see large proportions of collaboration on publications with non-CGIAR centres, reflecting cooperation with partners in developed and developing countries. The value of collaboration when ensuring quality of science cannot be stressed highly enough both within the CRP, and with other global and national partners. PLs should be given incentives to collaborate with other CRPs and external institutions. There is little cohesion between PLs and with other CRPs as evidenced by publications, although there are some exceptions. We suspect the reasons for this are driven by funding. Productivity from the different PLs is also highly variable and it is not clear what other activities staff are engaged in since, in some PLs, they do not appear to lead to quality publications. Effectiveness Grain Legumes has been very effective in addressing component issues of research, but not the continuum from variety development to legumes on someone’s dinner plate. Our overall assessment of the effectiveness of Grain Legumes in stimulating synergy, innovation and impact indicate that gradualism is more prevalent than innovation. It also shows, as do publications, that there is little integration of disciplines or a focus on ‘systems’. The absence of socio-economists from research teams is evident in the general lack of an end user focus. However, research on genomics, plant breeding and seed systems have made great strides forward, on the brink of delivering impact. Agronomy has been a poor sister, but some of the competitive grants within Grain Legumes have unearthed some potential game changers, such as objective use of transplanting as an agronomic practice. As mentioned earlier, the lack of effective M&E (however, this was part of some major projects such as TL II/TL III), and therefore the ability to monitor impact pathways and achievement of impact, implies no systematic management of data. This creates difficulty when attempting to evaluate the achievement of the Grain Legumes objectives. One might have expected at least one attempt to try to develop publications between centres arguing for similar biologies/research approaches, bringing species together under one umbrella, but we did not find any evidence for this. It is most unfortunate that, due to budgetary cuts, the new ‘schemes’, e.g. competitive grants and scholarships, were cut off before gaining a foothold. With 8 species addressed by Grain Legumes, it is not unexpected that there will be little evidence of shared protocols across centres/species. One rare example was that hosted by the United States Department of Agriculture (USDA) on shared methods for phenotyping of legume germplasm. Researchers from CIAT, IITA, ICRISAT and three USDA stations attended, focusing in simple canopy temperature and root morphology measurements. It is our belief that as a set of research centres, the CGIAR centres should be focusing on the research for which they have a comparative advantage. While imposing the restructure to FPs, which is fine for development objectives and outcomes (funded through W3/bilateral), it is less so for a research institute, and the structure should not detract from the more basic work expected of an international CGIAR centre (or set of centres as in a CRP). Impact It is well known that research does not always lead to scientific breakthroughs. Also, activities such as plant breeding are long term; making impacts difficult to assess. We believe that sufficient progress with genomics and associated research has been made to warrant impact, but we are unable to quantify the levels of impact, or the timeframe for the same. Work in Grain Legumes has enormous potential for real impact in scientific research, commercial, farming, smallholder and household communities, much of which is being realised. However, the PLs need to become more adept at providing convincing cases that are strongly evidenced for these impacts, as this is likely to be a key factor in leveraging future funding. Claimed gains must be referenced against baseline data, and these are not always readily available. The CCEE Team realises that such impact evaluation represents a significant drain on resources, and Grain Legumes should determine whether the balance of costs to benefits favours such investment. Interviews conducted by the CCEE during site visits showed that PLs are quantifying the area of adoption of varieties, but in most cases they are not measuring the impact on environment, health/nutrition. Since the health and nutritional benefits and the environmental gains from growing legumes are major arguments for supporting grain legume research, the community is currently missing substantial opportunities to strengthen its own case for continued support. Whilst there are some impressive examples of considering the whole value chain, e.g. white beans from production through to export; in the main, the pipeline to end user is somewhat piece-meal, with no clear definition of the end user nor differential responsibility of Grain Legumes and of partners. The lack of robust time-defined impact pathways is highlighted in Section 7.4, and even though developed for PL5, timeframes are essential for measuring progress against prediction. Sustainability In summary, there is general acknowledgement that future funding is likely to become more limited, specifically in W1&2 and there is understandable concern over the support for the staff and basic infrastructure that underpin the Grain Legumes programme. For example, it is reported that staffing in parts of CIAT has been dependent on W1&2 and that this is too unstable to re-establish a critical mass. The present system whereby W3 and bilateral projects do not pay a realistic level of overheads means that such projects are being effectively subsidised by W1&2. This position is not sustainable in the long term as there will be a progressive but definite loss of basic skills and resources in the core centres. The only obvious options to prevent this outcome include a severe reduction in the fixed costs of the centres and/or a refusal to accept W3 and bilateral funding with an inadequate overhead component. In the latter case, there is an obvious danger that funders will move their resources away from the CGIAR system towards other, perhaps less expensive, suppliers of research, and possibly more relevant development expertise. This issue must be addressed. As the Grain Legumes moves into the future, and if sustainable funding cannot be assured, decisions must be made concerning a reduction in activities, keeping some caretaker breeding maintenance, and focus (as has TL III) on fewer species and a reduced geographic focus. Cross cutting issues: Gender, capacity building and partnerships Gender is not mainstreamed, but there is some evidence that this is improving, especially with dedicated gender specialists and the slow integration of gender across CRPs. There is a need to approach gender through the vision of agriculture as a social practice, with recognition of what changes will be acceptable culturally and what not, and capitalising upon the perceived and actual features of production and processing that grain legumes are primarily women-based crops. Gender awareness may be high among Scientists, but it appears to be a predominantly passive attribute with few proactively seeking opportunities for gender equity. It is, however, a sound sensitivity base on which to build. Nevertheless, examples of notable gender initiatives were identified during field visits. For example, in Benin, the development of biocontrol technologies has enthusiastically integrated diversity, engaging with women farmers’ and youths while maintaining cultural norms. Women are gathering and processing, youths are taking the product to market. The implication is that several groups benefit, rather than domination by the majority group. In Malawi, innovative approaches have been developed to improving nutrition for children, such as incorporating nutrient enriched bean flour products into snacks. In India, scientists collaborating with gender scientists and socio-economists are identifying the impact of mechanical harvesting on agricultural labour and the potential displacement of female labourers. In Kenya, a novel initiative is improving the accessibility of certified seed for new varieties. Seed suppliers have introduced small packs of grain legume seed at low unit cost, which are being purchased by young people and women. Capacity building efforts for external partners are not clearly aligned with the research mandate and delivery of Grain Legumes. However, there are a number of training activities that are being undertaken by Grain Legumes, largely through the W3/bilateral project. Gender balance never reaches parity, but it appears that efforts are made to include female participants. Within the evaluation timeframe it was not possible to conduct external surveys to further validate or review external capacity building efforts in Grain Legumes. Training of scientists is significant, with >40 benefiting. Postgraduate training is varied across PLs, and there is some opportunity to increase the numbers being supervised. We consider that support for postgraduates at ICRISAT could be better coordinated, satisfying more of the students’ needs. It is important, however, to follow up investments in capacity building by monitoring effectiveness, career progressions and so on. Training activities appear to be rather centre-specific, not following a coordinated programme managed by, nor at the level of, the Grain Legumes. Numbers of persons trained and their gender are important, but a measure of the effectiveness of the training is more important. Although optimism is expressed by the great majority of Research Managers that partnerships were working well to leverage knowledge and research capacities, scientists have a less favourable view, particularly in terms of their incentives to participate. It seems likely that the activities taking place within Grain Legumes were, in the most part, continuations of previous collaborations. This is not surprising in light of the reduction in the emphasis on partnerships as Grain Legumes evolved to a funded project, and the consequent lack of opportunity and ambition for establishing novel partnerships. Where they exist, partnerships are good on the whole, especially with US. They could be expanded where comparative advantages exist (for example with Canada and Australia for machine harvestable legumes), but some earlier identified partnerships, e.g. with Turkey, have not been capitalised upon. Others experience problems of variety access (the embargo on exports of some sources of materials from India), yet others do have relevance e.g. imported Brazilian varieties in pre-release in Ethiopia (even though two of the three are from CIAT materials). Governance and Management The standard format of committee structure and responsibilities is common to other CRPs, as are the attendant problems. One of the major problems is that the Grain Legumes Director has responsibility but no authority; hence, even with the support of the RMC, the Director is unable to ‘direct’ in the literal sense of the work the activities of Grain Legumes. We also see the same sense of helplessness with the role of the PLCs. They have responsibility but no authority in managing the affairs of their PL, and they have no access to funds with which to promote intellectual collaboration and cooperation. Minutes from governance and management meetings do not reflect the compromised weak position of the Director and the associated difficulties in the management of Grain Legumes. Nor do the minutes reflect concerns about the amount of time spent by scientists in meetings for planning, integration, evaluation and reporting. Many scientists reported significant opportunity costs in participating in the ongoing imposed [by the CO] evolution of Grain Legumes and CRPs in general. The changes brought in by the CO have not helped promote any greater authority and capacity of the Grain Legumes Director to direct. Likewise, they do not address any of the issues with the conflict of interest in having the Lead Centre chair the Steering Committee. Indeed, we believe that the combining of the Steering Committee with the Independent Advisory Committee, besides becoming unwieldy in number, annuls any sense of independence in advice offered to the Grain Legumes management. We have concerns with the declining proportion of W1/W2 funds (as expressed in the section on Sustainability), and believe that when basic financial planning takes place, integration of W1/W2 and W3/bilateral sources must occur, and be linked to anticipated outcomes and impacts. This will ensure a close alignment of collaborators’ and partners’ objectives and contributions to that of the Grain Legumes. We also queried the process for, and the formality, or lack of, surrounding, the approval of annual budgets, and the level of priority setting when budgets are cut. Recommendations for Grain Legumes The CCEE Team makes the following recommendations, critical issues are highlighted in bold, and those that require action by an entity other than the Grain Legumes Research Management Committee or Project Management united are identified in a footnote. Relevance and Strategy Recommendation 1: A period of consistency is necessary to raise confidence, morale and trust across scientists, managers and partners to foster the assembly of enduring Grain Legumes outcomes2.  There needs to be a concerted effort to undertake baseline studies and to implement a robust M&E activity during this period. Without these data the foundation for integrated research in grain legumes is jeopardised.  There is a strong need to link more closely with the private sector, especially where there are financial and other comparative advantages to do so. Recommendation 2: The agronomic and physiological trait targets of Grain Legumes (tolerance to changing climate patterns, to the pests and diseases of today and of the future, incorporation of quality traits and adaptations to intensive production systems [machine-harvestability and herbicide tolerance], and short season high yielding characters) are all worthy of continued investment when selecting for improved varieties.  There needs to be a common strategy, implemented across centres and species, as to how to address these trait targets through conventional and modern breeding approaches, but only if adequate funding is assured and secured and if a consistency and unity of purpose can be achieved across a large-scale. This should take the form of cross-species coordinated research programmes to address these breeding targets that cooperate across centres and make efficient use of facilities and other resources.  The CRP should undertake a detailed strategic review of the role of transgenics across the range of targets in the mandate crops. Efficiency Recommendation 3: The lack of an effective M&E process is a significant omission, not least in terms of more efficient use of resources and the lack of baseline data with which to measure impact, and must be rectified.  Reinforcing Recommendation 1, an effective M&E system initially directed towards baseline studies must be implemented.  Transaction costs may be reduced through bilateral projects, which are seen as more cost effective than W1/W2 where transaction costs are disproportionately higher. Recommendation 4: To improve communication and coordination within the CRP, and with a broader audience:  There is a priority need for a central database containing, names of staff associated with Grain Legumes and their time commitments, their responsibilities, and involvement in CRP activities, their progress and achievements, their publications, plans of training, travel, and other opportunities for interaction.  Regular global meetings of staff involved in managing PLs, the entire CRP management staff and the IAC are essential for effective coordination of all activity within Grain Legumes.  The website must be given a complete overhaul and improvement and then regular maintenance must be provided to keep it current. Quality of Science Recommendation 5: It is essential to continue investment in good science and to institute a change from gradualism in research output and outcomes to an expectation of innovative and concrete achievements that can be attributed clearly to people, centres and core facilities.  A cost:benefit analysis and subsequent strategic planning must be undertaken to justify further investment in the genomics and phenotyping facilities at ICRISAT especially as such technologies advance rapidly. Strategic planning and coordination must also be implemented for capitalising on the investment in crop simulation modelling. (The phenotyping facility of ICRISAT needs to focus on delivering some outcomes, not only outputs.)  PLs should be given incentives to collaborate with other CRPs and external institutions. The CCEE recommends special recognition of high quality collaborative papers, thereby encouraging increased quality of the research programmes and widening the penetration of research impacts.  More importance should be placed on the quality of publication, rather than quantity of outputs and there should be recognition of other types of outputs from Grain Legumes. The CRP Director must be party to this.  If staff are engaged in activities that relate more to impact than publication then this needs to be monitored and recorded and a clearer understanding developed of what constitutes a pathway to impact and how success of such activities can be evaluated. A system must be devised and incorporated into the M&E to enable recognition of other types of outputs (non- publication based) from Grain Legumes, e.g. varieties for breeders. Effectiveness Recommendation 6: To develop greater synergy, Grain Legumes should review management processes and the direction of research activities. In particular, far more extensive integration of research and knowledge exchange should take place across both African and Asian continents so that the best aspects of both can be shared. A multidisciplinary approach is recommended that considers processing solutions, as well as breeding solutions, to capitalise upon the nutritional benefits of the grain legume crops. We recommend:  A better collaboration with social scientists at the design stage of experiments in order to improve the utility of the work carried out and to understand its reach.  Supporting3 the adoption of best practice electronic data collection, central storage and open access, particularly of genomic data, for public use.  Given the focus on the link between phenotyping and genotyping, we note that there is a lack of congruence between the populations that are being phenotyped and those being genotyped, and therefore these could be better aligned within each species.  Concentrating investment external to Grain Legumes on scaling up production of varieties with the most promising trait profiles to meet the basic seed requirement.  Developing a more holistic approach that coordinates an understanding of the disease pathology and epidemiology, and of new chemicals before they become commercially available, together with agronomic practice such that recommendations can be made for growers. Continuing work to establish whether agronomic factors hold true in different environments and to assess GxE effects within breeding programmes. Such rigorous trial practices should be used to inform the evaluation of breeding lines and to provide phenotype data to associate with markers for traits such as heat, drought and herbicide tolerance.  Considering grain legumes as if they were vegetable crops in terms of the strategy for intensification of production, both from the management perspective and for seed systems, will be a useful development objective into the future. This will bring about more rapid intensification and is likely to increase farmer returns from investment. Recommendation 7: The CGIAR centres should focus in on the research for which they have a comparative advantage. While imposing the restructure to FPs, which is fine for development objectives and outcomes (funded through W3/bilateral) it is less so for a research institute, and should not detract from the more basic work expected of an international CGIAR centre (or set of centres in a CRP).  Collaborative approaches should be explored within Grain Legumes, e.g. similar biologies/research approaches, bringing species together under one umbrella. Similarly better alignment is needed to address the lack of congruence between the populations that are being phenotyped and those being genotyped.  Despite positive impacts from research in genomics, plant breeding and seed systems, the lack of an effective M&E, already mentioned elsewhere, has reduced the ability to monitor impact pathways. This must be addressed.  The absence of socio-economists from research teams is evident in the general lack of an end user focus. Responsibilities of the different actors in the whole value chain must be considered and identified when developing impact targets, and the pathway leading to them, for individual projects. People with socio-economist skills must be part of the team from project inception so that appropriate frameworks are incorporated for measuring and influencing sociological and economic changes brought about by Grain Legumes research. Impact Recommendation 8: PLs need to become more adept at providing convincing cases in which impact is strongly evidenced, as this is likely to be a key factor in leveraging future funding.  Claimed gains must be referenced against baseline data, and these are not always readily available. The CCEE Team realises that such impact evaluation represents a significant drain on resources, and Grain Legumes should determine whether the balance of costs to benefits favours such investment.  It is essential that Grain Legumes provides training to staff on what constitutes impact and how it can be recorded.  Specific, rather than generalised, potential impacts arising from activity within Grain Legumes should be defined at the time of justifying the programme of work and a pathway to impact should form part of the documentation prepared ahead of a piece of research commencing. . In other words, centres should submit work plans to Grain Legumes before they are undertaken using W1/W2 funds Recommendation 9: The reporting activity must be streamlined to a single (brief) format that can be used to report to Grain Legumes, Centres and to donors for special project activities4. Sustainability Recommendation 10: As Grain Legumes moves into the future, and if sustainable funding cannot be assured, decisions must be made concerning a reduction in activities, keeping some caretaker breeding maintenance, and focus (as has TL III) on fewer species and a reduced geographic focus. Zeigler (Director General of IRRI) states “…time and effort would be better spent … making tough decisions about which programs deserve the precious support.”  The present system whereby W3 and bilateral projects do not pay a realistic level of overheads means that such projects are being effectively subsidised by W1&2 and there will be a progressive but definite loss of basic skills and resources in the core centres. To prevent this outcome it is necessary to significantly reduce the fixed costs of the centres and/or refuse to accept W3 and bilateral funding without an adequate overhead component.  In the absence of long term certainty, the scale of the budget allocated to each of the new CRPs should be very conservative, a feature that can only be achieved by restricting/reducing the scope, probably quite significantly. Cross cutting issues: Gender, capacity building and partnerships Recommendation 11: The challenge for Grain Legumes is to achieve pro-active gender mainstreaming, which facilitates opportunities for gender diversity within all activities, from employment processes through research to end users.  Strategic measurable gender indicators need to be embedded in research design, for instance, through specific IDOs for each of the flagships projects. Accurate baseline data are also required to facilitate M&E reviews of progress.  Implementation of the Gender Strategy is the responsibility of everyone, not solely the Gender Team. Thus, ownership could be encouraged by setting personal development for key personnel objectives with specific outcomes, e.g. employment practices or research outcomes.  Recognising the positive gender initiatives in progress or planned, feedback must be communicated and integrated into broader research planning to share opportunities, methods and outcomes.  In addition to promoting gender equity in research, Grain Legumes also needs to ensure that working environments are gender sensitive and that recruitment processes, including promotion opportunities are equitable. Gender imbalance in management should be actively examined to identify further opportunities for developing female leadership. Recommendation 12: It is recommended that a training plan be devised to ensure that capacity building efforts are more clearly aligned with the research mandate, delivery and timeframe of Grain Legumes. Moreover, we recommend that ICRISAT develop a strategy to treat their new cohort of researchers more equitably in the future. Recommendation 13: To develop a more coherent strategic programme designed to eliminate overlap and promote synergy between programmes with common aims, Grain Legumes should hold a meeting with a range of partners. Governance Recommendation 14: Governance processes should be re-assessed and the structure altered to ensure that the Grain Legumes Director has the authority and budget control to drive the execution of strategy.  The ISC should be truly independent and given the power to influence strategic decisions before they become final. We also recommend that PLCs are provided with the authority to manage the direction and finances of their PL; and that ring-fenced funds are provided for the promotion of collaboration, coordination and staff training5. The way ahead In our view, having seen the ineffectiveness of much of the attempts [or lack of attempts] to harness synergies between multiple centres, and of the strength in few or sole centre partnerships, we believe that there is little to justify a full retention of the 8 legume species and 4 CGIAR centres in a CRP. TL I and II and PABRA have shown to be reasonably good cross-centre and single centre integrated programmes, but even they suffer from incomplete value chain approaches to increasing rural incomes while increasing food and nutritional security; they both need multi-faceted solutions which are not immediately forthcoming from Grain Legumes. It is important to embed Grain Legumes research within the agri-food systems these crops serve. Figure ES1 broadly shows the perceived current and potential degrees of synergy between centres, PLs and species, and is discussed more in the text. It is clear that the value chains for individual species from trait determination to nutritional impact have more cohesion than do the individual activities (e.g. trait deployment) across species. For this reason we believe that the future for research in Grain Legumes is best addressed by focusing on each of the species separately, and within an ecosystem framework; any synergy for research across species can be effected through communication and not necessarily through obligatory cooperative research. The ecosystem framework will allow for strengthening of agronomy type systems research, the arguments for benefits of inclusion of grain legumes in cropping systems, which is notable by its absence in much of what Grain Legumes currently undertakes. Figure ES1. Current and potential degrees of synergy between centres, PLs and crop species We therefore agree with the innovation in agri-food systems approach of the CG, and believe that Grain Legumes rightly belongs in the Dryland Cereals and Legumes Agri-food Systems. We believe that the option of combining the crops of dryland cereals and legumes in the cereal-legume-livestock systems of subsistence farming communities for whole-farm productivity is closest to the best way forward. Indeed the inclusion of grain legumes may not warrant even a CRP alone, rather the legume components should fit in with the major crops that determine the production systems. Legumes will always be subservient to the major cereals, as necessary adjuncts to the whole production system, providing both nutritional diversity and environmental services, neither achievable from cereals alone. Figure ES2. Most suitable option for integration of Grain Legumes and Dryland Cereals into an Agri-Food Systems CRP Most suitable option for integration of Grain Legumes and Dryland Cereals into an Agri-Food Systems CRP, which  Incorporates ex-Dryland Systems, Dryland Cereals, Grain Legumes, some HumidTropics, some ex-Livestock &Fisheries into a new CRP  Will cover full agri-food system VC for all 8 legumes in all ecologies, but must interact (dock) with the relevant AFS-CRPs for the dominant cereal in the relevant ecology  Hence, will need to negotiate with other Agrifood Systems-CRPs on who does what for legumes  In addition, responsible for sorghum and millet in the mixed dryland crop-livestock agro-ecologies For major game changers to be effected, we believe that the game has to change, and there is little evidence of this. The direction of CRPs is the correct route, but the journey has not yet come to its destination. A major change of game [such as the adoption of a Flagship Project approach as exemplified by the Australian CSIRO – where flagships contract services from centres of research excellence] would be painful to implant. The CGIAR system is going down the right pathway but it has not gone far enough.

Identification and validation of candidate genes associated with domesticated and improved traits in soybean

Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 traitassociated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 (GmZTL3). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.