Sorghum pre-breeding contributions to genetic advancement

The sorghum core breeding program has had a long history of contributing to the productivity of the industry particularly through its contributions to traits such as midge resistance and stay-green and also through its contribution to grain yield per se. 100% of the commercial hybrids on the market have some genetics from the program. In this presentation we will provide an overview of what the program does, how the benefits of its research get to industry and the future directions of the program. With respect to the latter we will focus on opportunities to increase grain yield.

Genetic diversity of the Australian National Mango Genebank

Assessment of genetic diversity is an essential component in germplasm characterisation and utilisation. In this study the genetic diversity of mango was determined among 254 Mangifera indica L. accessions and related Mangifera species originating from 12 diverse geographic areas using eleven known simple sequence repeat (SSR) markers from mango. A total of 133 alleles were detected, ranging from eight (LMMA12) to 16 (MIAC-5) alleles per locus with a mean value of 12.36 and an average polymorphism information content (PLC) of 0.72. The mean number of alleles (8.45) was highest in the South East Asian accessions (Indonesia/Malesia) and lowest in the accessions from the Philippines (2.55). Diversity analysis divided the accessions into four major nodes broadly representing their geographical origins. The genetic diversity of 'Kensington Pride' was confirmed as being very low and no parents for this cultivar were identified. No association could be established between SSR markers analysed and embryony. Ten synonymous accessions were identified with matching genetic identity with at least one other accession at all SSR loci examined. Twenty-two unique genotypes were identified for 50 trees previously assigned different accession names. The remaining accessions were genetically distinct from each other. This increased understanding of genetic diversity in the Australian National Mango Genebank will assist breeders to better select parents with the potential to contribute desired genes to the progeny and thus more rapidly deliver improved cultivars to industry to meet consumer demand. Crown Copyright (C) 2012 Published by Elsevier B.V. All rights reserved.

Estimates of genetic parameters for growth and wood properties in Eucalyptus pellita F. Muell. to support tree breeding in Vietnam

Key message Eucalyptus pellita demonstrated good growth and wood quality traits in this study, with young plantation grown timber being suitable for both solid and pulp wood products. All traits examined were under moderate levels of genetic control with little genotype by environment interaction when grown on two contrasting sites in Vietnam. Context Eucalyptus pellita currently has a significant role in reforestation in the tropics. Research to support expanded of use of this species is needed: particularly, research to better understand the genetic control of key traits will facilitate the development of genetically improved planting stock. Aims This study aimed to provide estimates of the heritability of diameter at breast height over bark, wood basic density, Kraft pulp yield, modulus of elasticity and microfibril angle, and the genetic correlations among these traits, and understand the importance of genotype by environment interactions in Vietnam. Methods Data for diameter and wood properties were collected from two 10-year-old, open-pollinated progeny trials of E. pellita in Vietnam that evaluated 104 families from six native range and three orchard sources. Wood properties were estimated from wood samples using near-infrared (NIR) spectroscopy. Data were analysed using mixed linear models to estimate genetic parameters (heritability, proportion of variance between seed sources and genetic correlations). Results Variation among the nine sources was small compared to additive variance. Narrow-sense heritability and genetic correlation estimates indicated that simultaneous improvements in most traits could be achieved from selection among and within families as the genetic correlations among traits were either favourable or close to zero. Type B genetic correlations approached one for all traits suggesting that genotype by environment interactions were of little importance. These results support a breeding strategy utilizing a single breeding population advanced by selecting the best individuals across all seed sources. Conclusion Both growth and wood properties have been evaluated. Multi-trait selection for growth and wood property traits will lead to more productive populations of E. pellita both with improved productivity and improved timber and pulp properties.

QTL analysis in multiple sorghum populations facilitates the dissection of the genetic and physiological control of tillering

Tillering in sorghum can be associated with either the carbon supply–demand (S/D) balance of the plant or an intrinsic propensity to tiller (PTT). Knowledge of the genetic control of tillering could assist breeders in selecting germplasm with tillering characteristics appropriate for their target environments. The aims of this study were to identify QTL for tillering and component traits associated with the S/D balance or PTT, to develop a framework model for the genetic control of tillering in sorghum. Four mapping populations were grown in a number of experiments in south east Queensland, Australia. The QTL analysis suggested that the contribution of traits associated with either the S/D balance or PTT to the genotypic differences in tillering differed among populations. Thirty-four tillering QTL were identified across the populations, of which 15 were novel to this study. Additionally, half of the tillering QTL co-located with QTL for component traits. A comparison of tillering QTL and candidate gene locations identified numerous coincident QTL and gene locations across populations, including the identification of common non-synonymous SNPs in the parental genotypes of two mapping populations in a sorghum homologue of MAX1, a gene involved in the control of tiller bud outgrowth through the production of strigolactones. Combined with a framework for crop physiological processes that underpin genotypic differences in tillering, the co-location of QTL for tillering and component traits and candidate genes allowed the development of a framework QTL model for the genetic control of tillering in sorghum.

The Genetic Architecture of Climatic Adaptation of Tropical Cattle

Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity.

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.

Phenotyping novel stay-green traits to capture genetic variation in senescence dynamics

Stay-green plants retain green leaves longer after anthesis and can have improved yield, particularly under water limitation. As senescence is a dynamic process, genotypes with different senescence patterns may exhibit similar final normalised difference vegetative index (NDVI). By monitoring NDVI from as early as awn emergence to maturity, we demonstrate that analysing senescence dynamics improves insight into genotypic stay-green variation. A senescence evaluation tool was developed to fit a logistic function to NDVI data and used to analyse data from three environments for a wheat (Triticum aestivum L.) population whose lines contrast for stay-green. Key stay-green traits were estimated including, maximum NDVI, senescence rate and a trait integrating NDVI variation after anthesis, as well as the timing from anthesis to onset, midpoint and conclusion of senescence. The integrative trait and the timing to onset and mid-senescence exhibited high positive correlations with yield and a high heritability in the three studied environments. Senescence rate was correlated with yield in some environments, whereas maximum NDVI was associated with yield in a drought-stressed environment. Where resources preclude frequent measurements, we found that NDVI measurements may be restricted to the period of rapid senescence, but caution is required when dealing with lines of different phenology. In contrast, regular monitoring during the whole period after flowering allows the estimation of senescence dynamics traits that may be reliably compared across genotypes and environments. We anticipate that selection for stay-green traits will enhance genetic progress towards high-yielding, stay-green germplasm.

Increased virulence of rabbit haemorrhagic disease virus associated with genetic resistance in wild Australian rabbits (Oryctolagus cuniculus)

The release of myxoma virus (MYXV) and Rabbit Haemorrhagic Disease Virus (RHDV) in Australia with the aim of controlling overabundant rabbits has provided a unique opportunity to study the initial spread and establishment of emerging pathogens, as well as their co-evolution with their mammalian hosts. In contrast to MYXV, which attenuated shortly after its introduction, rapid attenuation of RHDV has not been observed. By studying the change in virulence of recent field isolates at a single field site we show, for the first time, that RHDV virulence has increased through time, likely because of selection to overcome developing genetic resistance in Australian wild rabbits. High virulence also appears to be favoured as rabbit carcasses, rather than diseased animals, are the likely source of mechanical insect transmission. These findings not only help elucidate the co-evolutionary interaction between rabbits and RHDV, but reveal some of the key factors shaping virulence evolution.

Biological control of prickly acacia: Current research and future prospects

Prickly acacia, Vachellia nilotica subsp. indica (syn. Acacia nilotica subsp. indica) (Fabaceae), a major weed in the natural grasslands of western Queensland, has been a target of biological control since the 1980s with limited success to date. Surveys in India, based on genetic and climate matching, identified five insects and two rust pathogens as potential agents. Host-specificity tests were conducted for the insects in India and under quarantine conditions in Australia, and for the rust pathogens under quarantine conditions at CABI in the UK. In no-choice tests, the brown leaf-webber, Phycita sp. A, (Lepidoptera: Pyralidae) completed development on 17 non-target plant species. Though the moth showed a clear preference for prickly acacia in oviposition choice trials screening of additional test-plant species was terminated in view of the potential non-target risk. The scale insect Anomalococcus indicus (Hemiptera: Lecanodiaspididae) developed into mature gravid females on 13 out of 58 non-target plant species tested. In the majority of cases very few female scales matured but development was comparable to that on prickly acacia on four of the non-target species. In multiple choice tests, the scale insect showed a significant preference for the target weed over non-target species tested. In a paired-choice trial under field conditions in India, crawler establishment occurred only on prickly acacia and not on the non-target species tested. Further choice trials are to be conducted under natural field conditions in India. A colony of the green leaf-webber Phycita sp. B has been established in quarantine facilities in Australia and host-specificity testing has commenced. The gall-rust Ravenelia acaciae-arabicae and the leaf-rust Ravenelia evansii (Puccineales: Raveneliaceae) both infected and produced viable urediniospores on Vachellia sutherlandii (Fabaceae), a non-target Australian native plant species. Hence, no further testing with the two rust species was pursued. Inoculation trials using the gall mite Aceria liopeltus (Acari: Eriophyidae) from V. nilotica subsp. kraussiana in South Africa resulted in no gall induction on V. nilotica subsp. indica. Future research will focus on the leaf-weevil Dereodus denticollis (Coleoptera: Curculionidae) and the leaf-beetle Pachnephorus sp. (Coleoptera: Chrysomelidae) under quarantine conditions in Australia. Native range surveys for additional potential biological control agents will also be pursued in northern and western Africa.

Genetic control of flowering in spotted gum, Corymbia citriodora subsp. variegata and C. maculata

Genetically controlled asynchrony in anthesis is an effective barrier to gene flow between planted and native forests. We investigated the degree of genetically controlled variation in the timing of key floral developmental stages in a major plantation species in subtropical Australia, Corymbia citriodora subsp. variegata K.D. Hill and L.A.S Johnson, and its relative C. maculata K.D. Hill and L.A.S. Johnson. Flowering observations were made in a common garden planting at Bonalbo in northern New South Wales in spring on 1855 trees from eight regions over three consecutive years, and monthly on a subset of 208 trees for 12 months. Peak anthesis time was stable over years and observations from translocated trees tended to be congruent with the observations in native stands, suggesting strong genetic control of anthesis time. A cluster of early flowering provenances was identified from the north-east of the Great Dividing Range. The recognition of a distinct flowering race from this region accorded well with earlier evidence of adaptive differentiation of populations from this region and geographically-structured genetic groupings in C. citriodora subsp. variegata. The early flowering northern race was more fecund, probably associated with its disease tolerance and greater vigour. Bud abundance fluctuated extensively at the regional level across 3 years suggesting bud abundance was more environmentally labile than timing of anthesis. Overall the level of flowering in the planted stand (age 12 years) was low (8–12% of assessed trees with open flowers), and was far lower than in nearby native stands. Low levels of flowering and asynchrony in peak anthesis between flowering races of C. citriodora subsp. variegata may partially mitigate a high likelihood of gene flow where the northern race is planted in the south of the species range neighbouring native stands

ScreeningCorymbiapopulations for resistance toPuccinia psidii

Disease screening to determine the threat Puccinia psidii poses to plantation and native eucalypts in Australia was undertaken in half-sib families of two contrasting eucalypt species, Eucalyptus cloeziana and E. argophloia. Artificial inoculation with a single-lesion isolate of P. psidii was used to screen these species for resistance to the biotype of P. psidii established in Australia. The objective was to characterize resistance to P. psidii within these two distinct species: E. argophloia, a vulnerable species with a narrow distribution, and E. cloeziana, a species with a broad and extensive distribution in Queensland. Results for E. cloeziana indicate that inland provenances are more resistant to P. psidii infection than provenances from coastal regions. Heritability estimates for the two assessment systems used (resistance on a 1-to-5 ordinal scale verses resistance on a 0-to-1 binomial scale) were low to high (0.24 to 0.63) for E. argophloia and moderate to high (0.4 to 0.91) for E. cloeziana, indicating a significant level of additive genetic variance for rust resistance within the populations. This study demonstrates the potential to select resistant families within the tested populations and indicates that P. psidii could detrimentally affect these species in native forests, nurseries, and plantations.

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.

Genetic differentiation analysis for the identification of complementary parental pools for sorghum hybrid breeding in Ethiopia

Key message The potential for exploiting heterosis for sorghum hybrid production in Ethiopia with improved local adaptation and farmers preferences has been investigated and populations suitable for initial hybrid development have been identified. Abstract Hybrids in sorghum have demonstrated increased productivity and stability of performance in the developed world. In Ethiopia, the uptake of hybrid sorghum has been limited to date, primarily due to poor adaptation and absence of farmer’s preferred traits in existing hybrids. This study aimed to identify complementary parental pools to develop locally adapted hybrids, through an analysis of whole genome variability of 184 locally adapted genotypes and introduced hybrid parents (R and B). Genetic variability was assessed using genetic distance, model-based STRUCTURE analysis and pair-wise comparison of groups. We observed a high degree of genetic similarity between the Ethiopian improved inbred genotypes and a subset of landraces adapted to lowland agro-ecology with the introduced R lines. This coupled with the genetic differentiation from existing B lines, indicated that these locally adapted genotype groups are expected to have similar patterns of heterotic expression as observed between introduced R and B line pools. Additionally, the hybrids derived from these locally adapted genotypes will have the benefit of containing farmers preferred traits. The groups most divergent from introduced B lines were the Ethiopian landraces adapted to highland and intermediate agro-ecologies and a subset of lowland-adapted genotypes, indicating the potential for increased heterotic response of their hybrids. However, these groups were also differentiated from the R lines, and hence are different from the existing complementary heterotic pools. This suggests that although these groups could provide highly divergent parental pools, further research is required to investigate the extent of heterosis and their hybrid performance.

Cereal cultivars can be ranked consistently for resistance to root-lesion nematodes (Pratylenchus thornei & P. neglectus) using diverse procedures

The root-lesion nematodes (RLN) Pratylenchus thornei and P. neglectus are widely distributed in Australian grain producing regions and can reduce the yield of intolerant wheat cultivars by up to 65 , costing the industry ~123 M AUD/year. Consequently, researchers in the northern, southern and western regions have independently developed procedures to evaluate the resistance of cereal cultivars to RLN. To compare results, each of the three laboratories phenotyped a set of 26 and 36 cereal cultivars for relative resistance/susceptibility to P. thornei and P. neglectus respectively. The northern and southern regions also investigated the effects of planting time and experiment duration on RLN reproduction and cultivar ranking. Results show the genetic correlation between cultivars tested using the northern and southern procedures evaluating P. thornei resistance was 0.93. Genetic correlations between experiments using the same procedure, but with different planting times, were 0.99 for both northern and southern procedures. The genetic correlation between cultivars tested using the northern, southern and western procedures evaluating P. neglectus resistance ranged from 0.71 to 0.95. Genetic correlations between experiments using the same procedure but with different planting times ranged from 0.91 to 0.99. This study established that, even though experiments were conducted in different geographic locations and with different trial management practices, the diverse nematode resistance screening procedures ranked cultivars similarly. Consequently, RLN resistance data can be pooled across regions to provide national consensus ratings of cultivars.