QTLs for water absorption and flour yield identified in the doubled haploid wheat population Lang/QT8766

Two key quality traits in milling wheat are flour yield (FY) and water absorption (WA). Ideally, breeders would prefer to use markers to select promising lines rather than time consuming rheology tests. In this study, we measured FY and WA on a wheat mapping population (Lang/QT8766) of 162 individuals grown in two replicated field experiments at three locations over 2 years. We also carried out near infrared reflectance spectroscopy (NIRS) predictions on the grain for these traits to see if NIRS phenotypic data could provide useful mapping results when compared to the reference phenotypic data. Several common QTLs were identified for FY and WA by both sets of data. The QTL on chromosome 4D was a consistently recurring QTL region for both traits. The QTL on chromosome 2A was positively linked to protein content which was supported by genetic correlation data. The results also indicated it was possible to obtain useful phenotypic data for mapping FY and WA using NIRS data. This would save time and costs as NIRS is quicker and cheaper than current rheology methods.

Implications of geometric plasticity for maximizing photosynthesis in branching corals

Reef-building corals are an example of plastic photosynthetic organisms that occupy environments of high spatiotemporal variations in incident irradiance. Many phototrophs use a range of photoacclimatory mechanisms to optimize light levels reaching the photosynthetic units within the cells. In this study, we set out to determine whether phenotypic plasticity in branching corals across light habitats optimizes potential light utilization and photosynthesis. In order to do this, we mapped incident light levels across coral surfaces in branching corals and measured the photosynthetic capacity across various within-colony surfaces. Based on the field data and modelled frequency distribution of within-colony surface light levels, our results show that branching corals are substantially self-shaded at both 5 and 18 m, and the modal light level for the within-colony surface is 50 mu mol photons m(-2) s(-1). Light profiles across different locations showed that the lowest attenuation at both depths was found on the inner surface of the outermost branches, while the most self-shading surface was on the bottom side of these branches. In contrast, vertically extended branches in the central part of the colony showed no differences between the sides of branches. The photosynthetic activity at these coral surfaces confirmed that the outermost branches had the greatest change in sun- and shade-adapted surfaces; the inner surfaces had a 50 % greater relative maximum electron transport rate compared to the outer side of the outermost branches. This was further confirmed by sensitivity analysis, showing that branch position was the most influential parameter in estimating whole-colony relative electron transport rate (rETR). As a whole, shallow colonies have double the photosynthetic capacity compared to deep colonies. In terms of phenotypic plasticity potentially optimizing photosynthetic capacity, we found that at 18 m, the present coral colony morphology increased the whole-colony rETR, while at 5 m, the colony morphology decreased potential light utilization and photosynthetic output. This result of potential energy acquisition being underutilized in shallow, highly lit waters due to the shallow type morphology present may represent a trade-off between optimizing light capture and reducing light damage, as this type morphology can perhaps decrease long-term costs of and effect of photoinhibition. This may be an important strategy as opposed to adopting a type morphology, which results in an overall higher energetic acquisition. Conversely, it could also be that maximizing light utilization and potential photosynthetic output is more important in low-light habitats for Acropora humilis.

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16-45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.

A physiological framework to explain genetic and environmental regulation of tillering in sorghum

Tillering determines the plant size of sorghum (Sorghum bicolor) and an understanding of its regulation is important to match genotypes to prevalent growing conditions in target production environments. The aim of this study was to determine the physiological and environmental regulation of variability in tillering among sorghum genotypes, and to develop a framework for this regulation. * Diverse sorghum genotypes were grown in three experiments with contrasting temperature, radiation and plant density to create variation in tillering. Data on phenology, tillering, and leaf and plant size were collected. A carbohydrate supply/demand (S/D) index that incorporated environmental and genotypic parameters was developed to represent the effects of assimilate availability on tillering. Genotypic differences in tillering not explained by this index were defined as propensity to tiller (PTT) and probably represented hormonal effects. * Genotypic variation in tillering was associated with differences in leaf width, stem diameter and PTT. The S/D index captured most of the environmental effects on tillering and PTT most of the genotypic effects. * A framework that captures genetic and environmental regulation of tillering through assimilate availability and PTT was developed, and provides a basis for the development of a model that connects genetic control of tillering to its phenotypic consequences.

Resistance to Fusarium oxysporum f. sp fragariae and Predicted Breeding Values in Strawberry

Fusarium wilt of strawberry, incited by Fusarium oxysporum f. sp. fragariae (Fof), is a major disease of the cultivated strawberry (Fragaria xananassa) worldwide. An increase in disease outbreaks of the pathogen in Western Australia and Queensland plus the search for alternative disease management strategies place emphasis on the development of resistant cultivars. In response, a partial incomplete diallel cross involving four parents was performed for use in glasshouse resistance screenings. The resulting progeny were evaluated for their susceptibility to Fof. Best-performing progeny and suitability of progenies as parents were determined using data from disease severity ratings and analyzed using a linear mixed model incorporating a pedigree to produce best linear unbiased predictions of breeding values. Variation in disease response, ranging from highly susceptible to resistant, indicates a quantitative effect. The estimate of the narrow-sense heritability was 0.49 +/- 0.04 (SE), suggesting the population should be responsive to phenotypic recurrent selection. Several progeny genotypes have predicted breeding values higher than any of the parents. Knowledge of Fof resistance derived from this study can help select best parents for future crosses for the development of new strawberry cultivars with Fof resistance.

Coordination and plasticity in leaf anatomical traits of invasive and native vine species

Premise of the study: Plant invasiveness can be promoted by higher values of adaptive traits (e.g., photosynthetic capacity, biomass accumulation), greater plasticity and coordination of these traits, and by higher and positive relative influence of these functionalities on fitness, such as increasing reproductive output. However, the data set for this premise rarely includes linkages between epidermal–stomatal traits, leaf internal anatomy, and physiological performance.• Methods: Three ecological pairs of invasive vs. noninvasive (native) woody vine species of South-East Queensland, Australia were investigated for trait differences in leaf morphology and anatomy under varying light intensity. The linkages of these traits with physiological performance (e.g., water-use efficiency, photosynthesis, and leaf construction cost) and plant adaptive traits of specific leaf area, biomass, and relative growth rates were also explored.• Key results: Except for stomatal size, mean leaf anatomical traits differed significantly between the two groups. Plasticity of traits and, to a very limited extent, their phenotypic integration were higher in the invasive relative to the native species. ANOVA, ordination, and analysis of similarity suggest that for leaf morphology and anatomy, the three functional strategies contribute to the differences between the two groups in the order phenotypic plasticity > trait means > phenotypic integration.• Conclusions: The linkages demonstrated in the study between stomatal complex/gross anatomy and physiology are scarce in the ecological literature of plant invasiveness, but the findings suggest that leaf anatomical traits need to be considered routinely as part of weed species assessment and in the worldwide leaf economic spectrum.

Induced Variations in Brassinosteroid Genes Define Barley Height and Sturdiness, and Expand the Green Revolution Genetic Toolkit

Reduced plant height and culm robustness are quantitative characteristics important for assuring cereal crop yield and quality under adverse weather conditions. A very limited number of short-culm mutant alleles were introduced into commercial crop cultivars during the Green Revolution. We identified phenotypic traits, including sturdy culm, specific for deficiencies in brassinosteroid biosynthesis and signaling in semidwarf mutants of barley (Hordeum vulgare). This set of characteristic traits was explored to perform a phenotypic screen of near-isogenic short-culm mutant lines from the brachytic, breviaristatum, dense spike, erectoides, semibrachytic, semidwarf, and slender dwarf mutant groups. In silico mapping of brassinosteroid-related genes in the barley genome in combination with sequencing of barley mutant lines assigned more than 20 historic mutants to three brassinosteroid-biosynthesis genes (BRASSINOSTEROID-6-OXIDASE, CONSTITUTIVE PHOTOMORPHOGENIC DWARF, and DIMINUTO) and one brassinosteroid-signaling gene (BRASSINOSTEROID-INSENSITIVE1 [HvBRI1]). Analyses of F2 and M2 populations, allelic crosses, and modeling of nonsynonymous amino acid exchanges in protein crystal structures gave a further understanding of the control of barley plant architecture and sturdiness by brassinosteroid-related genes. Alternatives to the widely used but highly temperature-sensitive uzu1.a allele of HvBRI1 represent potential genetic building blocks for breeding strategies with sturdy and climate-tolerant barley cultivars.

Spot form of net blotch resistance in barley is under complex genetic control

Key message: Evaluation of resistance toPyrenophora teresf.maculatain barley breeding populations via association mapping revealed a complex genetic architecture comprising a mixture of major and minor effect genes. Abstract: In the search for stable resistance to spot form of net blotch (Pyrenophora teres f. maculata, SFNB), association mapping was conducted on four independent barley (Hordeum vulgare L.) breeding populations comprising a total of 898 unique elite breeding lines from the Northern Region Barley Breeding Program in Australia for discovery of quantitative trait loci (QTL) influencing resistance at seedling and adult plant growth stages. A total of 29 significant QTL were validated across multiple breeding populations, with 22 conferring resistance at both seedling and adult plant growth stages. The remaining 7 QTL conferred resistance at either seedling (2 QTL) or adult plant (5 QTL) growth stages only. These 29 QTL represented 24 unique genomic regions, of which five were found to co-locate with previously identified QTL for SFNB. The results indicated that SFNB resistance is controlled by a large number of QTL varying in effect size with large effects QTL on chromosome 7H. A large proportion of the QTL acted in the same direction for both seedling and adult responses, suggesting that phenotypic selection for SFNB resistance performed at either growth stage could achieve adequate levels of resistance. However, the accumulation of specific resistance alleles on several chromosomes must be considered in molecular breeding selection strategies.

Two distinct classes of QTL determine rust resistance in sorghum

Background: Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments. Results: In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust. Conclusions: The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect rust resistance QTL. The distinction of disease resistance QTL hot-spots, enriched with defence-related gene families from QTL which impact on development and partitioning, provides plant breeders with knowledge which will allow for fast-tracking varieties with both durable pathogen resistance and appropriate adaptive traits.

Growth analysis and biomass partitioning of Cyperus iria in response to rice planting density and nitrogen rate

Cyperus iria is a weed of rice with widespread occurrence throughout the world. Because of concerns about excessive and injudicious use of herbicides, cultural weed management approaches that are safe and economical are needed. Developing such approaches will require a better understanding of weed biology and ecology, as well as of weed response to increases in crop density and nutrition. Knowledge of the effects of nitrogen (N) fertilizer on crop-weed competitive interactions could also help in the development of integrated weed management strategies. The present study was conducted in a screenhouse to determine the effects of rice planting density (0, 5, 10, and 20 plants pot−1) and N rate (0, 50, 100, and 150 kg ha−1) on the growth of C. iria. Tiller number per plant decreased by 73–88%, leaf number by 85–94%, leaf area by 85–98%, leaf biomass by 92–99%, and inflorescence biomass by 96–99% when weed plants were grown at 20 rice plants pot−1 (i.e., 400 plants m−2) compared with weed plants grown alone. All of these parameters increased when N rates were increased. On average, weed biomass increased by 118–389% and rice biomass by 121–275% with application of 50–150 kg N ha−1, compared to control. Addition of N favored weed biomass production relative to rice biomass. Increased N rates reduced the root-to-shoot weight ratio of C. iria. Rice interference reduced weed growth and biomass and completely suppressed C. iria when no N was applied at high planting densities (i.e., 20 plants pot−1). The weed showed phenotypic plasticity in response to N application, and the addition of N increased the competitive ability of the weed over rice at densities of 5 and 10 rice plants pot−1 compared with 20 plants pot−1. The results of the present study suggest that high rice density (i.e., 400 plants m−2) can help suppress C. iria growth even at high N rates (150 kg ha−1).

Fine mapping of qGW1, a major QTL for grain weight in sorghum

Key message We detected seven QTLs for 100-grain weight in sorghum using an F 2 population, and delimited qGW1 to a 101-kb region on the short arm of chromosome 1, which contained 13 putative genes. Abstract Sorghum is one of the most important cereal crops. Breeding high-yielding sorghum varieties will have a profound impact on global food security. Grain weight is an important component of grain yield. It is a quantitative trait controlled by multiple quantitative trait loci (QTLs); however, the genetic basis of grain weight in sorghum is not well understood. In the present study, using an F2 population derived from a cross between the grain sorghum variety SA2313 (Sorghum bicolor) and the Sudan-grass variety Hiro-1 (S. bicolor), we detected seven QTLs for 100-grain weight. One of them, qGW1, was detected consistently over 2 years and contributed between 20 and 40 % of the phenotypic variation across multiple genetic backgrounds. Using extreme recombinants from a fine-mapping F3 population, we delimited qGW1 to a 101-kb region on the short arm of chromosome 1, containing 13 predicted gene models, one of which was found to be under purifying selection during domestication. However, none of the grain size candidate genes shared sequence similarity with previously cloned grain weight-related genes from rice. This study will facilitate isolation of the gene underlying qGW1 and advance our understanding of the regulatory mechanisms of grain weight. SSR markers linked to the qGW1 locus can be used for improving sorghum grain yield through marker-assisted selection.

Polyphasic characterization of four new plant pathogenic Phyllosticta species from China, Japan, and the United States

The black rot disease of Vitis species and other host genera of Vitacease is caused by Phyllosticta ampelicida and allied taxa which is considered to be a species complex. In this paper, we introduce four new species of Phyllosticta, including two from the P. ampelicida complex, based on a polyphasic characterization including disease symptoms and host association, morphology, and molecular phylogeny. The phylogenetic analysis was conducted based on the ribosomal internal transcribed spacer (ITS) region and a combined multi-locus alignment of the ITS, actin (ACT), partial translation elongation factor 1-alpha (TEF-1), and glyceraldehydes 3-phosphate dehydrogenase (GPDH) gene regions. Our study confirms the phylogenetic distinctions of the four new species, as well as their phenotypic differences with known species in the genus.

Genetic characterization of field-evolved resistance to phosphine in the rusty grain beetle, Cryptolestes ferrugineus (Laemophloeidae: Coleoptera)

Inheritance of resistance to phosphine fumigant was investigated in three field-collected strains of rusty grain beetle, Cryptolestes ferrugineus, Susceptible (S-strain), Weakly Resistant (Weak-R) and Strongly Resistant (Strong-R). The strains were purified for susceptibility, weak resistance and strong resistance to phosphine, respectively, to ensure homozygosity of resistance genotype. Crosses were established between S-strain × Weak-R, S-strain × Strong-R and Weak-R × Strong-R, and the dose mortality responses to phosphine of these strains and their F1, F2 and F1-backcross progeny were obtained. The fumigations were undertaken at 25 °C and 55% RH for 72 h. Weak-R and Strong-R showed resistance factors of 6.3 × and 505 × compared with S-strain at the LC50. Both weak and strong resistances were expressed as incompletely recessive with degrees of dominance of − 0.48 and − 0.43 at the LC50, respectively. Responses of F2 and F1-backcross progeny indicated the existence of one major gene in Weak-R, and at least two major genes in Strong-R, one of which was allelic with the major factor in Weak-R. Phenotypic variance analyses also estimated that the number of independently segregating genes conferring weak resistance was 1 (nE = 0.89) whereas there were two genes controlling strong resistance (nE = 1.2). The second gene, unique to Strong-R, interacted synergistically with the first gene to confer a very high level of resistance (~ 80 ×). Neither of the two major resistance genes was sex linked. Despite the similarity of the genetics of resistance to that previously observed in other pest species, a significant proportion (~ 15 to 30%) of F1 individuals survived at phosphine concentrations higher than predicted. Thus it is likely that additional dominant heritable factors, present in some individuals in the population, also influenced the resistance phenotype. Our results will help in understanding the process of selection for phosphine resistance in the field which will inform resistance management strategies. In addition, this information will provide a basis for the identification of the resistance genes.

Genetic characterization of field-evolved resistance to phosphine in the rusty grain beetle, Cryptolestes ferrugineus (Laemophloeidae: Coleoptera)

Inheritance of resistance to phosphine fumigant was investigated in three field-collected strains of rusty grain beetle, Cryptolestes ferrugineus, Susceptible (S-strain), Weakly Resistant (Weak-R) and Strongly Resistant (Strong-R). The strains were purified for susceptibility, weak resistance and strong resistance to phosphine, respectively, to ensure homozygosity of resistance genotype. Crosses were established between S-strain × Weak-R, S-strain × Strong-R and Weak-R × Strong-R, and the dose mortality responses to phosphine of these strains and their F1, F2 and F1-backcross progeny were obtained. The fumigations were undertaken at 25 °C and 55% RH for 72 h. Weak-R and Strong-R showed resistance factors of 6.3 × and 505 × compared with S-strain at the LC50. Both weak and strong resistances were expressed as incompletely recessive with degrees of dominance of − 0.48 and − 0.43 at the LC50, respectively. Responses of F2 and F1-backcross progeny indicated the existence of one major gene in Weak-R, and at least two major genes in Strong-R, one of which was allelic with the major factor in Weak-R. Phenotypic variance analyses also estimated that the number of independently segregating genes conferring weak resistance was 1 (nE = 0.89) whereas there were two genes controlling strong resistance (nE = 1.2). The second gene, unique to Strong-R, interacted synergistically with the first gene to confer a very high level of resistance (~ 80 ×). Neither of the two major resistance genes was sex linked. Despite the similarity of the genetics of resistance to that previously observed in other pest species, a significant proportion (~ 15 to 30%) of F1 individuals survived at phosphine concentrations higher than predicted. Thus it is likely that additional dominant heritable factors, present in some individuals in the population, also influenced the resistance phenotype. Our results will help in understanding the process of selection for phosphine resistance in the field which will inform resistance management strategies. In addition, this information will provide a basis for the identification of the resistance genes.

High-throughput Phenotyping of Wheat Seminal Root Traits in a Breeding Context

Water availability is a major limiting factor for wheat (Triticum aestivum L.) in rain-fed agricultural systems worldwide. Root architecture has important functional implications for the timing and extent of soil water extraction, yet selection for root traits in wheat breeding programs has been largely limited due to the lack of suitable phenotyping methods. The aim of this research was to develop a low-cost high-throughput phenotyping method to facilitate selection for desirable root traits. We developed a method to assess ‘seminal root angle’ and ‘seminal root number’ in seedlings – two proxy traits associated to root architecture of mature wheat plants (1). The method involves measuring the angle between the first pair of seminal roots and the number of roots of wheat seedlings grown in transparent pots (Figure 1). Images captured at 5 to 10 days after sowing are analyzed to calculate seminal root angle and number. Performing this technique under “speed breeding” conditions (plants grown at a density of 600 plants / m2, under controlled temperature and constant light) allows the selection based on the desired root traits of up to 5 consecutive generations within 12 months. Alternatively, when focusing only on germplasm screening, up to 52 successive phenotypic assays can be conducted within 12 months. This approach has been shown to be highly reproducible, it requires little resource (time, space, and labour) and can be used to rapidly enrich breeding populations with desirable alleles for narrow root angle and a high number of seminal roots to indirectly target the selection of deeper root system with higher branching at depth. Such root characteristics are highly desirable in wheat to cope with the climate model projections, especially in summer rainfall dominant regions including some Australian, Indian, South American and African cropping regions, where winter crops mainly rely on deep stored water.