High-throughput phenotyping platforms enhance genomic selection for wheat grain yield across populations and cycles in early stage.

Genomic selection (GS) models have been validated for many quantitative traits in wheat (Triticum aestivum L.) breeding. However, those models are mostly constrained within the same growing cycle and the extension of GS to the case of across cycles has been a challenge, mainly due to the low predictive accuracy resulting from two factors: reduced genetic relationships between different families and augmented environmental variances between cycles. Using the data collected from diverse field conditions at the International Wheat and Maize Improvement Center, we evaluated GS for grain yield in three elite yield trials across three wheat growing cycles. The objective of this project was to employ the secondary traits, canopy temperature, and green normalized difference vegetation index, which are closely associated with grain yield from high-throughput phenotyping platforms, to improve prediction accuracy for grain yield. The ability to predict grain yield was evaluated reciprocally across three cycles with or without secondary traits. Our results indicate that prediction accuracy increased by an average of 146% for grain yield across cycles with secondary traits. In addition, our results suggest that secondary traits phenotyped during wheat heading and early grain filling stages were optimal for enhancing the prediction accuracy for grain yield.

Genome-wide association mapping for resistance to leaf rust, stripe rust and tan spot in wheat reveals potential candidate genes.

KEY MESSAGE: Genome-wide association mapping in conjunction with population sequencing map and Ensembl plants was used to identify markers/candidate genes linked to leaf rust, stripe rust and tan spot resistance in wheat. Leaf rust (LR), stripe rust (YR) and tan spot (TS) are some of the important foliar diseases in wheat (Triticum aestivum L.). To identify candidate resistance genes for these diseases in CIMMYT's (International Maize and Wheat Improvement Center) International bread wheat screening nurseries, we used genome-wide association studies (GWAS) in conjunction with information from the population sequencing map and Ensembl plants. Wheat entries were genotyped using genotyping-by-sequencing and phenotyped in replicated trials. Using a mixed linear model, we observed that seedling resistance to LR was associated with 12 markers on chromosomes 1DS, 2AS, 2BL, 3B, 4AL, 6AS and 6AL, and seedling resistance to TS was associated with 14 markers on chromosomes 1AS, 2AL, 2BL, 3AS, 3AL, 3B, 6AS and 6AL. Seedling and adult plant resistance (APR) to YR were associated with several markers at the distal end of chromosome 2AS. In addition, YR APR was also associated with markers on chromosomes 2DL, 3B and 7DS. The potential candidate genes for these diseases included several resistance genes, receptor-like serine/threonine-protein kinases and defense-related enzymes. However, extensive LD in wheat that decays at about 5 × 107 bps, poses a huge challenge for delineating candidate gene intervals and candidates should be further mapped, functionally characterized and validated. We also explored a segment on chromosome 2AS associated with multiple disease resistance and identified seventeen disease resistance linked genes. We conclude that identifying candidate genes linked to significant markers in GWAS is feasible in wheat, thus creating opportunities for accelerating molecular breeding.

Determinants of Virulence and In Vitro Development Colocalize on a Genetic Map of Setosphaeria turcica.

Generating effective and stable strategies for resistance breeding requires an understanding of the genetics of host-pathogen interactions and the implications for pathogen dynamics and evolution. Setosphaeria turcica causes northern leaf blight (NLB), an important disease of maize for which major resistance genes have been deployed. Little is known about the evolutionary dynamics of avirulence (AVR) genes in S. turcica. To test the hypothesis that there is a genetic association between avirulence and in vitro development traits, we (i) created a genetic map of S. turcica, (ii) located candidate AVRHt1 and AVRHt2 regions, and (iii) identified genetic regions associated with several in vitro development traits. A cross was generated between a race 1 and a race 23N strain, and 221 progeny were isolated. Genotyping by sequencing was used to score 2,078 single-nucleotide polymorphism markers. A genetic map spanning 1,981 centimorgans was constructed, consisting of 21 linkage groups. Genetic mapping extended prior evidence for the location and identity of the AVRHt1 gene and identified a region of interest for AVRHt2. The genetic location of AVRHt2 colocalized with loci influencing radial growth and mycelial abundance. Our data suggest a trade-off between virulence on Ht1 and Ht2 and the pathogen's vegetative growth rate. In addition, in-depth analysis of the genotypic data suggests the presence of significant duplication in the genome of S. turcica.

Resistance to gray leaf spot of maize: genetic architecture and mechanisms elucidated through nested association mapping and near-isogenic line analysis.

Gray leaf spot (GLS), caused by Cercospora zeae-maydis and Cercospora zeina, is one of the most important diseases of maize worldwide. The pathogen has a necrotrophic lifestyle and no major genes are known for GLS. Quantitative resistance, although poorly understood, is important for GLS management. We used genetic mapping to refine understanding of the genetic architecture of GLS resistance and to develop hypotheses regarding the mechanisms underlying quantitative disease resistance (QDR) loci. Nested association mapping (NAM) was used to identify 16 quantitative trait loci (QTL) for QDR to GLS, including seven novel QTL, each of which demonstrated allelic series with significant effects above and below the magnitude of the B73 reference allele. Alleles at three QTL, qGLS1.04, qGLS2.09, and qGLS4.05, conferred disease reductions of greater than 10%. Interactions between loci were detected for three pairs of loci, including an interaction between iqGLS4.05 and qGLS7.03. Near-isogenic lines (NILs) were developed to confirm and fine-map three of the 16 QTL, and to develop hypotheses regarding mechanisms of resistance. qGLS1.04 was fine-mapped from an interval of 27.0 Mb to two intervals of 6.5 Mb and 5.2 Mb, consistent with the hypothesis that multiple genes underlie highly significant QTL identified by NAM. qGLS2.09, which was also associated with maturity (days to anthesis) and with resistance to southern leaf blight, was narrowed to a 4-Mb interval. The distance between major leaf veins was strongly associated with resistance to GLS at qGLS4.05. NILs for qGLS1.04 were treated with the C. zeae-maydis toxin cercosporin to test the role of host-specific toxin in QDR. Cercosporin exposure increased expression of a putative flavin-monooxygenase (FMO) gene, a candidate detoxification-related gene underlying qGLS1.04. This integrated approach to confirming QTL and characterizing the potential underlying mechanisms advances the understanding of QDR and will facilitate the development of resistant varieties.

Genomic and pedigree-based prediction for leaf, stem, and stripe rust resistance in wheat.

KEY MESSAGE: Genomic prediction for seedling and adult plant resistance to wheat rusts was compared to prediction using few markers as fixed effects in a least-squares approach and pedigree-based prediction. The unceasing plant-pathogen arms race and ephemeral nature of some rust resistance genes have been challenging for wheat (Triticum aestivum L.) breeding programs and farmers. Hence, it is important to devise strategies for effective evaluation and exploitation of quantitative rust resistance. One promising approach that could accelerate gain from selection for rust resistance is 'genomic selection' which utilizes dense genome-wide markers to estimate the breeding values (BVs) for quantitative traits. Our objective was to compare three genomic prediction models including genomic best linear unbiased prediction (GBLUP), GBLUP A that was GBLUP with selected loci as fixed effects and reproducing kernel Hilbert spaces-markers (RKHS-M) with least-squares (LS) approach, RKHS-pedigree (RKHS-P), and RKHS markers and pedigree (RKHS-MP) to determine the BVs for seedling and/or adult plant resistance (APR) to leaf rust (LR), stem rust (SR), and stripe rust (YR). The 333 lines in the 45th IBWSN and the 313 lines in the 46th IBWSN were genotyped using genotyping-by-sequencing and phenotyped in replicated trials. The mean prediction accuracies ranged from 0.31-0.74 for LR seedling, 0.12-0.56 for LR APR, 0.31-0.65 for SR APR, 0.70-0.78 for YR seedling, and 0.34-0.71 for YR APR. For most datasets, the RKHS-MP model gave the highest accuracies, while LS gave the lowest. GBLUP, GBLUP A, RKHS-M, and RKHS-P models gave similar accuracies. Using genome-wide marker-based models resulted in an average of 42% increase in accuracy over LS. We conclude that GS is a promising approach for improvement of quantitative rust resistance and can be implemented in the breeding pipeline.

Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat.

BACKGROUND: Wild relatives of wheat play a significant role in wheat improvement as a source of genetic diversity. Stem rust disease of wheat causes significant yield losses at the global level and stem rust pathogen race TTKSK (Ug99) is virulent to most previously deployed resistance genes. Therefore, the objective of this study was to identify loci conferring resistance to stem rust pathogen races including Ug99 in an Aegilops umbelluata bi-parental mapping population using genotype-by-sequencing (GBS) SNP markers. RESULTS: A bi-parental F2:3 population derived from a cross made between stem rust resistant accession PI 298905 and stem rust susceptible accession PI 542369 was used for this study. F2 individuals were evaluated with stem rust race TTTTF followed by testing F2:3 families with races TTTTF and TTKSK. The segregation pattern of resistance to both stem rust races suggested the presence of one resistance gene. A genetic linkage map, comprised 1,933 SNP markers, was created for all seven chromosomes of Ae. umbellulata using GBS. A major stem rust resistance QTL that explained 80% and 52% of the phenotypic variations for TTTTF and TTKSK, respectively, was detected on chromosome 2U of Ae. umbellulata. CONCLUSION: The novel resistance gene for stem rust identified in this study can be transferred to commercial wheat varieties assisted by the tightly linked markers identified here. These markers identified through our mapping approach can be a useful strategy to identify and track the resistance gene in marker-assisted breeding in wheat.

Quantifying variety-specific heat resistance and the potential for adaptation to climate change.

The impact of climate change on crop yields has become widely measured; however, the linkages for winter wheat are less studied due to dramatic weather changes during the long growing season that are difficult to model. Recent research suggests significant reductions under warming. A potential adaptation strategy involves the development of heat resistant varieties by breeders, combined with alternative variety selection by producers. However, the impact of heat on specific wheat varieties remains relatively unstudied due to limited data and the complex genetic basis of heat tolerance. Here, we provide a novel econometric approach that combines field-trial data with a genetic cluster mapping to group wheat varieties and estimate a separate extreme heat impact (temperatures over 34 °C) across 24 clusters spanning 197 varieties. We find a wide range of heterogeneous heat resistance and a trade-off between average yield and resistance. Results suggest that recently released varieties are less heat resistant than older varieties, a pattern that also holds for on-farm varieties. Currently released - but not yet adopted - varieties do not offer improved resistance relative to varieties currently grown on farm. Our findings suggest that warming impacts could be significantly reduced through advances in wheat breeding and/or adoption decisions by producers. However, current adaptation-through-adoption potential is limited under a 1 °C warming scenario as increased heat resistance cannot be achieved without a reduction in average yields.

Fine mapping of the stem rust resistance gene SrTA10187.

KEY MESSAGE: SrTA10187 was fine-mapped to a 1.1 cM interval, candidate genes were identified in the region of interest, and molecular markers were developed for marker-assisted selection and Sr gene pyramiding. Stem rust (Puccinia graminis f. sp. tritici, Pgt) races belonging to the Ug99 (TTKSK) race group pose a serious threat to global wheat (Triticum aestivum L.) production. To improve Pgt host resistance, the Ug99-effective resistance gene SrTA10187 previously identified in Aegilops tauschii Coss. was introgressed into wheat, and mapped to the short arm of wheat chromosome 6D. In this study, high-resolution mapping of SrTA10187 was done using a population of 1,060 plants. Pgt resistance was screened using race QFCSC. PCR-based SNP and STS markers were developed from genotyping-by-sequencing tags and SNP sequences available in online databases. SrTA10187 segregated as expected in a 3:1 ratio of resistant to susceptible individuals in three out of six BC3F2 families, and was fine-mapped to a 1.1 cM region on wheat chromosome 6DS. Marker context sequence was aligned to the reference Ae. tauschii genome to identify the physical region encompassing SrTA10187. Due to the size of the corresponding region, candidate disease resistance genes could not be identified with confidence. Comparisons with the Ae. tauschii genetic map developed by Luo et al. (PNAS 110(19):7940-7945, 2013) enabled identification of a discrete genetic locus and a BAC minimum tiling path of the region spanning SrTA10187. Annotation of pooled BAC library sequences led to the identification of candidate genes in the region of interest-including a single NB-ARC-LRR gene. The shorter genetic interval and flanking KASP™ and STS markers developed in this study will facilitate marker-assisted selection, gene pyramiding, and positional cloning of SrTA10187.

Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling.

BACKGROUND: In plant breeding, there are two primary applications for DNA markers in selection: 1) selection of known genes using a single marker assay (marker-assisted selection; MAS); and 2) whole-genome profiling and prediction (genomic selection; GS). Typically, marker platforms have addressed only one of these objectives. RESULTS: We have developed spiked genotyping-by-sequencing (sGBS), which combines targeted amplicon sequencing with reduced representation genotyping-by-sequencing. To minimize the cost of targeted assays, we utilize a small percent of sequencing capacity available in runs of GBS libraries to "spike" amplified targets of a priori alleles tagged with a different set of unique barcodes. This open platform allows multiple, single-target loci to be assayed while simultaneously generating a whole-genome profile. This dual-genotyping approach allows different sets of samples to be evaluated for single markers or whole genome-profiling. Here, we report the application of sGBS on a winter wheat panel that was screened for converted KASP markers and newly-designed markers targeting known polymorphisms in the leaf rust resistance gene Lr34. CONCLUSIONS: The flexibility and low-cost of sGBS will enable a range of applications across genetics research. Specifically in breeding applications, the sGBS approach will allow breeders to obtain a whole-genome profile of important individuals while simultaneously targeting specific genes for a range of selection strategies across the breeding program.

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).

Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.

Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize.

Quantitative resistance to plant pathogens, controlled by multiple loci of small effect, is important for food production, food security, and food safety but is poorly understood. To gain insights into the genetic architecture of quantitative resistance in maize, we evaluated a 5,000-inbred-line nested association mapping population for resistance to northern leaf blight, a maize disease of global economic importance. Twenty-nine quantitative trait loci were identified, and most had multiple alleles. The large variation in resistance phenotypes could be attributed to the accumulation of numerous loci of small additive effects. Genome-wide nested association mapping, using 1.6 million SNPs, identified multiple candidate genes related to plant defense, including receptor-like kinase genes similar to those involved in basal defense. These results are consistent with the hypothesis that quantitative disease resistance in plants is conditioned by a range of mechanisms and could have considerable mechanistic overlap with basal resistance.

Simultaneous transfer, introgression, and genomic localization of genes for resistance to stem rust race TTKSK (Ug99) from Aegilops tauschii to wheat.

Wheat production is currently threatened by widely virulent races of the wheat stem rust fungus, Puccinia graminis f. sp. tritici, that are part of the TTKSK (also known as 'Ug99') race group. The diploid D genome donor species Aegilops tauschii (2n = 2x = 14, DD) is a readily accessible source of resistance to TTKSK and its derivatives that can be transferred to hexaploid wheat, Triticum aestivum (2n = 6x = 42, AABBDD). To expedite transfer of TTKSK resistance from Ae. tauschii, a direct hybridization approach was undertaken that integrates gene transfer, mapping, and introgression into one process. Direct crossing of Ae. tauschii accessions with an elite wheat breeding line combines the steps of gene transfer and introgression while development of mapping populations during gene transfer enables the identification of closely linked markers. Direct crosses were made using TTKSK-resistant Ae. tauschii accessions TA1662 and PI 603225 as males and a stem rust-susceptible T. aestivum breeding line, KS05HW14, as a female. Embryo rescue enabled recovery of F1 (ABDD) plants that were backcrossed as females to the hexaploid recurrent parent. Stem rust-resistant BC1F1 plants from each Ae. tauschii donor source were used as males to generate BC2F1 mapping populations. Bulked segregant analysis of BC2F1 genotypes was performed using 70 SSR loci distributed across the D genome. Using this approach, stem rust resistance genes from both accessions were located on chromosome arm 1DS and mapped using SSR and EST-STS markers. An allelism test indicated the stem rust resistance gene transferred from PI 603225 is Sr33. Race specificity suggests the stem rust resistance gene transferred from TA1662 is unique and this gene has been temporarily designated SrTA1662. Stem rust resistance genes derived from TA1662 and PI 603225 have been made available with selectable molecular markers in genetic backgrounds suitable for stem rust resistance breeding.

Introgression of stem rust resistance genes SrTA10187 and SrTA10171 from Aegilops tauschii to wheat.

Aegilops tauschii, the diploid progenitor of the wheat D genome, is a readily accessible germplasm pool for wheat breeding as genes can be transferred to elite wheat cultivars through direct hybridization followed by backcrossing. Gene transfer and genetic mapping can be integrated by developing mapping populations during backcrossing. Using direct crossing, two genes for resistance to the African stem rust fungus race TTKSK (Ug99), were transferred from the Ae. tauschii accessions TA10187 and TA10171 to an elite hard winter wheat line, KS05HW14. BC2 mapping populations were created concurrently with developing advanced backcross lines carrying rust resistance. Bulked segregant analysis on the BC2 populations identified marker loci on 6DS and 7DS linked to stem rust resistance genes transferred from TA10187 and TA10171, respectively. Linkage maps were developed for both genes and closely linked markers reported in this study will be useful for selection and pyramiding with other Ug99-effective stem rust resistance genes. The Ae. tauschii-derived resistance genes were temporarily designated SrTA10187 and SrTA10171 and will serve as valuable resources for stem rust resistance breeding.

Discussion: Prioritize perennial grain development for sustainable food production and environmental benefits.

Perennial grains have potential to contribute to ecological intensification of food production by enabling the direct harvest of human-edible crops without requiring annual cycles of disturbance and replanting. Studies of prototype perennial grains and other herbaceous perennials point to the ability of agroecosystems including these crops to protect water quality, enhance wildlife habitat, build soil quality, and sequester soil carbon. However, genetic improvement of perennial grain candidates has been hindered by limited investment due to uncertainty about whether the approach is viable. As efforts to develop perennial grain crops have expanded in past decades, critiques of the approach have arisen. With a recent report of perennial rice producing yields equivalent to those of annual rice over eight consecutive harvests, many theoretical concerns have been alleviated. Some valid questions remain over the timeline for new crop development, but we argue these may be mitigated by implementation of recent technological advances in crop breeding and genetics such as low-cost genotyping, genomic selection, and genome editing. With aggressive research investment in the development of new perennial grain crops, they can be developed and deployed to provide atmospheric greenhouse gas reductions.

In the eye of the beholder: the effect of rater variability and different rating scales on QTL mapping.

The agronomic importance of developing durably resistant cultivars has led to substantial research in the field of quantitative disease resistance (QDR) and, in particular, mapping quantitative trait loci (QTL) for disease resistance. The assessment of QDR is typically conducted by visual estimation of disease severity, which raises concern over the accuracy and precision of visual estimates. Although previous studies have examined the factors affecting the accuracy and precision of visual disease assessment in relation to the true value of disease severity, the impact of this variability on the identification of disease resistance QTL has not been assessed. In this study, the effects of rater variability and rating scales on mapping QTL for northern leaf blight resistance in maize were evaluated in a recombinant inbred line population grown under field conditions. The population of 191 lines was evaluated by 22 different raters using a direct percentage estimate, a 0-to-9 ordinal rating scale, or both. It was found that more experienced raters had higher precision and that using a direct percentage estimation of diseased leaf area produced higher precision than using an ordinal scale. QTL mapping was then conducted using the disease estimates from each rater using stepwise general linear model selection (GLM) and inclusive composite interval mapping (ICIM). For GLM, the same QTL were largely found across raters, though some QTL were only identified by a subset of raters. The magnitudes of estimated allele effects at identified QTL varied drastically, sometimes by as much as threefold. ICIM produced highly consistent results across raters and for the different rating scales in identifying the location of QTL. We conclude that, despite variability between raters, the identification of QTL was largely consistent among raters, particularly when using ICIM. However, care should be taken in estimating QTL allele effects, because this was highly variable and rater dependent.

Shades of gray: the world of quantitative disease resistance.

A thorough understanding of quantitative disease resistance (QDR) would contribute to the design and deployment of durably resistant crop cultivars. However, the molecular mechanisms that control QDR remain poorly understood, largely due to the incomplete and inconsistent nature of the resistance phenotype, which is usually conditioned by many loci of small effect. Here, we discuss recent advances in research on QDR. Based on inferences from analyses of the defense response and from the few isolated QDR genes, we suggest several plausible hypotheses for a range of mechanisms underlying QDR. We propose that a new generation of genetic resources, complemented by careful phenotypic analysis, will produce a deeper understanding of plant defense and more effective utilization of natural resistance alleles.

Implementing within-cross genomic prediction to reduce oat breeding costs.

A barrier to the adoption of genomic prediction in small breeding programs is the initial cost of genotyping material. Although decreasing, marker costs are usually higher than field trial costs. In this study we demonstrate the utility of stratifying a narrow-base biparental oat population genotyped with a modest number of markers to employ genomic prediction at early and later generations. We also show that early generation genotyping data can reduce the number of lines for later phenotyping based on selections of siblings to progress. Using sets of small families selected at an early generation could enable the use of genomic prediction for adaptation to multiple target environments at an early stage in the breeding program. In addition, we demonstrate that mixed marker data can be effectively integrated to combine cheap dominant marker data (including legacy data) with more expensive but higher density codominant marker data in order to make within generation and between lineage predictions based on genotypic information. Taken together, our results indicate that small programs can test and initiate genomic predictions using sets of stratified, narrow-base populations and incorporating low density legacy genotyping data. This can then be scaled to include higher density markers and a broadened population base.

Genomic Analysis and Prediction within a US Public Collaborative Winter Wheat Regional Testing Nursery.

The development of inexpensive, whole-genome profiling enables a transition to allele-based breeding using genomic prediction models. These models consider alleles shared between lines to predict phenotypes and select new lines based on estimated breeding values. This approach can leverage highly unbalanced datasets that are common to breeding programs. The Southern Regional Performance Nursery (SRPN) is a public nursery established by the USDA-ARS in 1931 to characterize performance and quality of near-release wheat ( L.) varieties from breeding programs in the US Central Plains. New entries are submitted annually and can be re-entered only once. The trial is grown at >30 locations each year and lines are evaluated for grain yield, disease resistance, and agronomic traits. Overall genetic gain is measured across years by including common check cultivars for comparison. We have generated whole-genome profiles via genotyping-by-sequencing (GBS) for 939 SPRN entries dating back to 1992 to explore the potential use of the nursery as a genomic selection (GS) training population (TP). The GS prediction models across years (average = 0.33) outperformed year-to-year phenotypic correlation for yield ( = 0.27) for a majority of the years evaluated, suggesting that genomic selection has the potential to outperform low heritability selection on yield in these highly variable environments. We also examined the predictability of programs using both program-specific and whole-set TPs. Generally, the predictability of a program was similar with both approaches. These results suggest that wheat breeding programs can collaboratively leverage the immense datasets that are generated from regional testing networks.

Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program.

One of the biggest challenges for genetic studies on natural or unstructured populations is the unbalanced datasets where individuals are measured at different times and environments. This problem is also common in crop and animal breeding where many individuals are only evaluated for a single year and large but unbalanced datasets can be generated over multiple years. Many wheat breeding programs have focused on increasing bread wheat (Triticum aestivum L.) yield, but processing and end-use quality are critical components when considering its use in feeding the rising population of the next century. The challenges with end-use quality trait improvements are high cost and seed amounts for testing, the latter making selection in early breeding populations impossible. Here we describe a novel approach to identify marker-trait associations within a breeding program using a meta-genome wide association study (GWAS), which combines GWAS analysis from multi-year unbalanced breeding nurseries, in a manner reflecting meta-GWAS in humans. This method facilitated mapping of processing and end-use quality phenotypes from advanced breeding lines (n = 4,095) of the CIMMYT bread wheat breeding program from 2009 to 2014. Using the meta-GWAS we identified marker-trait associations, allele effects, candidate genes, and can select using markers generated in this process. Finally, the scope of this approach can be broadly applied in 'breeding-assisted genomics' across many crops to greatly increase our functional understanding of plant genomes.

Multitrait, Random Regression, or Simple Repeatability Model in High-Throughput Phenotyping Data Improve Genomic Prediction for Wheat Grain Yield.

High-throughput phenotyping (HTP) platforms can be used to measure traits that are genetically correlated with wheat ( L.) grain yield across time. Incorporating such secondary traits in the multivariate pedigree and genomic prediction models would be desirable to improve indirect selection for grain yield. In this study, we evaluated three statistical models, simple repeatability (SR), multitrait (MT), and random regression (RR), for the longitudinal data of secondary traits and compared the impact of the proposed models for secondary traits on their predictive abilities for grain yield. Grain yield and secondary traits, canopy temperature (CT) and normalized difference vegetation index (NDVI), were collected in five diverse environments for 557 wheat lines with available pedigree and genomic information. A two-stage analysis was applied for pedigree and genomic selection (GS). First, secondary traits were fitted by SR, MT, or RR models, separately, within each environment. Then, best linear unbiased predictions (BLUPs) of secondary traits from the above models were used in the multivariate prediction models to compare predictive abilities for grain yield. Predictive ability was substantially improved by 70%, on average, from multivariate pedigree and genomic models when including secondary traits in both training and test populations. Additionally, (i) predictive abilities slightly varied for MT, RR, or SR models in this data set, (ii) results indicated that including BLUPs of secondary traits from the MT model was the best in severe drought, and (iii) the RR model was slightly better than SR and MT models under drought environment.