Dataset of historic and modern bread and durum wheat cultivar performance under conventional and reduced tillage with full and reduced irrigation.

Conservation agriculture (CA) is an agronomic management system based on zero tillage and residue retention. Due to its potential for climate change adaptation through the reduction of soil erosion and improved water availability, CA is becoming more important in many regions of the world. However, increased bulk density and large amounts of crop residues may be a constraint for early plant establishment. This holds especially true under irrigated production areas with high yield potential. Genotype × tillage effects on yield are not well understood and it is unclear whether tillage should be an evaluation factor in breeding programs. Fourteen CIMMYT bread (Triticum aestivum) and thirteen durum (Triticum turgidum) wheat genotypes, created between 1964 and 2011, were tested for yield and agronomic performance at CIMMYT's experimental station near Ciudad Obregon, Mexico, during nine seasons. The genotypes were subjected to different tillage and irrigation treatments which consisted of conventional and permanent raised beds with full and reduced irrigation. The dataset includes traits collected during the growing period (days to emergence, days to flowering, maturity, plant height, NDVI, days from flowering to maturity, grain production rate) and at harvest (yield, harvest index, thousand grain weight, spikes/m², grains/m², test weight) and weather data (daily minimum and maximum temperature, rainfall). Six years of data of 26 genotypes were published along with the Honsdorf et al. (2018) paper in Field Crops Research (DOI: s10.1016/j.fcr.2017.11.011). This updated dataset includes three additional seasons of data (harvest years 2016 to 2018) and an additional bread wheat genotype (Borlaug100).

Genome-Wide Association Study of Phytic Acid in Wheat Grain Unravels Markers for Improving Biofortification.

Biofortification of cereal grains offers a lasting solution to combat micronutrient deficiency in developing countries where it poses developmental risks to children. Breeding efforts thus far have been directed toward increasing the grain concentrations of iron (Fe) and zinc (Zn) ions. Phytic acid (PA) chelates these metal ions, reducing their bioavailability in the digestive tract. We present a high-throughput assay for quantification of PA and its application in screening a breeding population. After extraction in 96-well megatiter plates, PA content was determined from the phosphate released after treatment with a commercially available phytase enzyme. In a set of 330 breeding lines of wheat grown in the field over 3 years as part of a HarvestPlus breeding program for high grain Fe and Zn, our assay unraveled variation for PA that ranged from 0.90 to 1.72% with a mean of 1.24%. PA content was not associated with grain yield. High yielding lines were further screened for low molar PA/Fe and PA/Zn ratios for increased metal ion bioavailability, demonstrating the utility of our assay. Genome-wide association study revealed 21 genetic associations, six of which were consistent across years. Five of these associations mapped to chromosomes 1A, 2A, 2D, 5A, and 7D. Additivity over four of these haplotypes accounted for an ∼10% reduction in PA. Our study demonstrates it is possible to scale up assays to directly select for low grain PA in forward breeding programs.

Mining Sources of Resistance to Durum Leaf Rust among Tetraploid Wheat Accessions from CIMMYT's Germplasm Bank.

A collection of 482 tetraploid wheat accessions from the CIMMYT Germplasm Bank was screened in the greenhouse for resistance to leaf rust disease caused by the fungus Puccinia triticina E. The accessions were screened against two races CBG/BP and BBG/BP in the field at two locations: against race CBG/BP at the Norman E. Borlaug Experimental Station (CENEB) located in the Yaqui Valley in the northern state of Sonora in Mexico during the 2014-2015 growing season; and against race BBG/BP at CIMMYT headquarters in El Batan, Texcoco, in the state of Mexico in the summer of 2015. Among the accessions, 79 durum genotypes were identified, of which 68 continued demonstrating their resistance in the field (past the seedling stage) against the two leaf rust races. An additional set of 41 genotypes was susceptible at the seedling stage, but adult plant race-specific resistance was identified in the field. The 79 seedling-resistant genotypes were tested against 15 different leaf rust races at the seedling stage to measure the usefulness of their resistance in a breeding program. Among the 79 accessions tested, 35 were resistant to all races used in the tests. Two sample sources, CIMMYT (18/35) pre-breeding germplasm and Ethiopian landraces (17/35), showed seedling resistance to all races tested except for seven landraces from Ethiopia, which became susceptible to the Cirno race identified in 2017.

Harnessing translational research in wheat for climate resilience.

Despite being the world's most widely grown crop, research investments in wheat (Triticum aestivum and Triticum durum) fall behind those in other staple crops. Current yield gains will not meet 2050 needs, and climate stresses compound this challenge. However, there is good evidence that heat and drought resilience can be boosted through translating promising ideas into novel breeding technologies using powerful new tools in genetics and remote sensing, for example. Such technologies can also be applied to identify climate resilience traits from among the vast and largely untapped reserve of wheat genetic resources in collections worldwide. This review describes multi-pronged research opportunities at the focus of the Heat and Drought Wheat Improvement Consortium (coordinated by CIMMYT), which together create a pipeline to boost heat and drought resilience, specifically: improving crop design targets using big data approaches; developing phenomic tools for field-based screening and research; applying genomic technologies to elucidate the bases of climate resilience traits; and applying these outputs in developing next-generation breeding methods. The global impact of these outputs will be validated through the International Wheat Improvement Network, a global germplasm development and testing system that contributes key productivity traits to approximately half of the global wheat-growing area.

Screening and Mapping for Head Blast Resistance in a Panel of CIMMYT and South Asian Bread Wheat Germplasm.

Wheat blast (WB) is a destructive disease in South America and its first outbreak in Bangladesh in 2016 posed a great risk to food security of South Asian countries. A genome wide association study (GWAS) was conducted on a diverse panel of 184 wheat genotypes from South Asia and CIMMYT. Phenotyping was conducted in eight field experiments in Bolivia and Bangladesh and a greenhouse experiment in the United States. Genotypic data included 11,401 SNP markers of the Illumina Infinium 15K BeadChip and four additional STS markers on the 2NS/2AS translocation region. Accessions with stable WB resistance across experiments were identified, which were all 2NS carriers. Nevertheless, a dozen moderately resistant 2AS lines were identified, exhibiting big variation among experiments. Significant marker-trait associations (MTA) were detected on chromosomes 1BS, 2AS, 6BS, and 7BL; but only MTAs on 2AS at the 2NS/2AS translocation region were consistently significant across experiments. The resistant accessions identified in this study could be used in production in South Asian countries as a preemptive strategy to prevent WB outbreak.

Genome-wide association mapping for wheat blast resistance in CIMMYT's international screening nurseries evaluated in Bolivia and Bangladesh.

Wheat blast caused by the fungus Magnaporthe oryzae pathotype Triticum (MoT) is an emerging threat to wheat production. To identify genomic regions associated with blast resistance against MoT isolates in Bolivia and Bangladesh, we performed a large genome-wide association mapping study using 8607 observations on 1106 lines from the International Maize and Wheat Improvement Centre's International Bread Wheat Screening Nurseries (IBWSNs) and Semi-Arid Wheat Screening Nurseries (SAWSNs). We identified 36 significant markers on chromosomes 2AS, 3BL, 4AL and 7BL with consistent effects across panels or site-years, including 20 markers that were significant in all the 49 datasets and tagged the 2NS translocation from Aegilops ventricosa. The mean blast index of lines with and without the 2NS translocation was 2.7 ± 4.5 and 53.3 ± 15.9, respectively, that substantiates its strong effect on blast resistance. Furthermore, we fingerprinted a large panel of 4143 lines for the 2NS translocation that provided excellent insights into its frequency over years and indicated its presence in 94.1 and 93.7% of lines in the 2019 IBWSN and SAWSN, respectively. Overall, this study reinforces the effectiveness of the 2NS translocation for blast resistance and emphasizes the urgent need to identify novel non-2NS sources of blast resistance.

Disease Resistance Evaluation of Elite CIMMYT Wheat Lines Containing the Coupled Fhb1 and Sr2 Genes.

Fusarium head blight (FHB) and stem rust are among the most devastating diseases of wheat worldwide. Fhb1 is the most widely utilized and the only isolated gene for FHB resistance, while Sr2 is a durable stem rust resistance gene used in rust-prone areas. The two loci are closely linked on the short arm of chromosome 3B and the two genes are in repulsion phase among cultivars. With climate change and the shift in Fusarium populations, it is imperative to develop wheat cultivars resistant to both diseases. The present study was dedicated to developing wheat germplasm combining Fhb1 and Sr2 resistance alleles in the International Maize and Wheat Improvement Center (CIMMYT)'s elite cultivars' backgrounds. Four recombinant inbred lines (RILs) in Hartog background that have the resistant Fhb1 and Sr2 alleles in coupled phase linkage were crossed with seven CIMMYT bread wheat lines, resulting in 208 lines. Molecular markers for both genes were employed in addition to the use of pseudo-black chaff (PBC) as a phenotypic marker for the selection of Sr2. At various stages of the selection process, progeny lines were assessed for FHB index, Fusarium damaged kernels (FDK), stem rust, and PBC expression as well as other diseases of interest (stripe rust and leaf spotting diseases). The 25 best lines were selected for CIMMYT's wheat breeding program. In addition to expressing resistance to FHB, most of these 25 lines have an acceptable level of resistance to other tested diseases. These lines will be useful for wheat breeding programs worldwide and potentially speed up the resistance breeding efforts against FHB and stem rust.

Quantitative Trait Loci Mapping for Spot Blotch Resistance in Two Biparental Mapping Populations of Bread Wheat.

Spot blotch (SB), caused by Bipolaris sorokiniana, is a major fungal disease of wheat in South Asia and South America. Two biparental mapping populations with 232 F2:7 progenies each were generated, with CIMMYT breeding lines CASCABEL and KATH as resistant parents and CIANO T79 as the common susceptible parent. The two populations were evaluated for field SB resistance in CIMMYT's Agua Fria station for three consecutive cropping seasons, with artificial inoculation. Genotyping was done with the DArTseq platform and approximately 1,500 high quality and nonredundant markers were used for quantitative trait loci (QTL) mapping. In both populations, a major QTL was found on chromosome 5A in the Vrn-A1 region, explaining phenotypic variations of 13.5 to 25.9%, which turned up to be less- or nonsignificant when days to heading and plant height were used as covariates in the analysis, implying a disease escape mechanism. Another major QTL was located on chromosome 5B in CASCABEL, accounting for 8.9 to 21.4% of phenotypic variation. Minor QTL were found on 4A and 4B in CASCABEL; 1B, 4B, and 4D in KATH; and 1B, 2B, and 4B in CIANO T79. Through an analysis of QTL projection onto the IWGSC Chinese Spring reference genome, the 5B QTL in CASCABEL was mapped in the Sb2 region, delimited by the single nucleotide polymorphism marker wsnp_Ku_c50354_55979952 and the simple sequence repeat marker gwm213, with a physical distance of about 14 Mb to the Tsn1 locus.

Novel Sources of Wheat Head Blast Resistance in Modern Breeding Lines and Wheat Wild Relatives.

Wheat head blast (WHB), caused by the fungus Magnaporthe oryzae pathotype triticum, is a devastating disease affecting South America and South Asia. Despite 30 years of intensive effort, the 2NVS translocation from Aegilops ventricosa contains the only useful source of resistance to WHB effective against M. oryzae triticum isolates. The objective of this study was to identify non-2NVS sources of resistance to WHB among elite cultivars, breeding lines, landraces, and wild-relative accessions. Over 780 accessions were evaluated under field and greenhouse conditions in Bolivia, greenhouse conditions in Brazil, and at two biosafety level-3 laboratories in the United States. The M. oryzae triticum isolates B-71 (2012), 008 (2015), and 16MoT001 (2016) were used for controlled experiments, while isolate 008 was used for field experiments. Resistant and susceptible checks were included in all experiments. Under field conditions, susceptible spreaders were inoculated at the tillering stage to guarantee sufficient inoculum. Disease incidence and severity were evaluated as the average rating for each 1-m-row plot. Under controlled conditions, heads were inoculated after full emergence and individually rated for percentage of diseased spikelets. The diagnostic marker Ventriup-LN2 was used to test for the presence of the 2NVS translocation. Four non-2NVS spring wheat International Maize and Wheat Improvement Center breeding lines (CM22, CM49, CM52, and CM61) and four wheat wild-relatives (A. tauschii TA10142, TA1624, TA1667, and TA10140) were identified as resistant (<5% of severity) or moderately resistant (5 to <25% severity) to WHB. Experiments conducted at the seedling stage showed little correlation with disease severity at the head stage. M. oryzae triticum isolate 16MoT001 was significantly more aggressive against 2NVS-based varieties. The low frequency of WHB resistance and the increase in aggressiveness of newer M. oryzae triticum isolates highlight the threat that the disease poses to wheat production worldwide and the urgent need to identify and characterize new resistance genes that can be used in breeding for durably resistant varieties.

Four Consistent Loci Confer Adult Plant Resistance to Leaf Rust in the Durum Wheat Lines Heller#1 and Dunkler.

The durum wheat lines Heller#1 and Dunkler from the International Maize and Wheat Improvement Center Global Wheat Program showed moderate and stable adult plant resistance to leaf rust under high disease pressure over field environments in northwestern Mexico. Leaf rust phenotyping was performed on two recombinant inbred line (RIL) populations derived from crosses of Heller#1 and Dunkler with the susceptible parent Atred#2, conducted under artificially induced Puccinia triticina epidemics in 2013, 2014, 2015, and 2016. The Atred#2 × Heller#1 and Atred#2 × Dunkler populations were genotyped by single nucleotide polymorphism (SNP) platforms and diversity arrays technology markers, respectively. Four leaf rust resistance quantitative trait loci were detected simultaneously in the two RIL populations: Lr46, QLr.cim-2BC, QLr.cim-5BL, and QLr.cim-6BL based on phenotypic data across all four crop seasons. They explained 11.7 to 46.8%, 7.2 to 26.1%, 8.4 to 24.1%, and 12.4 to 28.5%, respectively, of the phenotypic variation for leaf rust resistance in Atred#2 × Heller#1 and 16.3 to 56.6%, 6.7 to 15.7%, 4.1 to 10.1%, and 5.1 to 20.2% of the variation in the Atred#2 × Dunkler population. Only the resistance allele of QLr.cim-2BC was from the susceptible parent Atred#2, and resistance alleles at other loci came from the resistant parents Heller#1 and Dunkler. The SNP markers closely linked to Lr46 and QLr.cim-2BC were converted to kompetitive allele specific PCR markers for use in marker-assisted selection to improve leaf rust resistance through crosses with Heller#1 and Dunkler sources.

Genetics of Greenbug Resistance in Synthetic Hexaploid Wheat Derived Germplasm.

The greenbug, Schizaphis graminum Rondani, significantly reduces wheat, Triticum aestivum L., grain yields if not controlled. Host plant resistance (HPR) can protect yield, is environmentally friendly and easy to use. Our objectives were to: (1) identify genomic regions associated with S. graminum resistance in a recombinant inbred line (RIL) population derived from a cross of "Sokoll" (resistant) and "Weebill1" (moderately susceptible), (2) evaluate Sokoll derived breeding germplasm for resistance, and (3) conduct allelism tests between Sokoll and sources carrying resistance genes Gba, Gbb, and Gbd. Resistance was measured quantitatively and qualitatively using a SPAD meter and visual assessments, respectively. We identified a large effect resistance gene on chromosome arm 7DL of Sokoll, herein referred as GbSkl, which contributed up to 24% of the phenotypic variation. Other minor QTL on chromosomes 2B, 3A, and 7B were also identified. The QTL on 2B and 3A originated from Weebill1. Of the Sokoll derived germplasm, 13% displayed resistance. Allelism tests indicated that GbSkl could be allelic or tightly linked to the temporarily designated genes Gba, Gbb, and Gbd. Utility of SPAD to determine quantitative variation in resistance phenotyping is demonstrated and breeding efforts are underway to transfer the resistance from Sokoll to new CIMMYT elite germplasm.

Genetics for low correlation between Fusarium head blight disease and deoxynivalenol (DON) content in a bread wheat mapping population.

KEY MESSAGE: Two QTL with major effects on DON content reduction were identified on chromosomes 3BL and 3DL, with the former showing minor and the latter showing no effects on FHB resistance. Deoxynivalenol (DON) contamination in food and feed is a major concern regarding Fusarium head blight (FHB) infection in wheat. However, relatively less attention has been paid on DON compared to FHB. In this study, a FHB-susceptible cultivar 'NASMA' was hybridized with a FHB-resistant CIMMYT breeding line 'IAS20*5/H567.71' to generate 197 recombinant inbred lines. The population was phenotyped for FHB and associated traits including DON accumulation in spray-inoculated field experiments at CIMMYT-Mexico across four years. Genotyping was performed by using the Illumina Infinium 15 K Beadchip and SSR markers. QTL mapping results indicated that the field FHB resistance was mainly controlled by QTL at Rht-D1 and Vrn-A1, along with a few minor QTL. For DON content, two major QTL were identified: the first located on chromosome 3BL (R2 of 16-24%), showing minor effects on FHB, and the second was on chromosome 3DL (R2 of 10-15%), exhibiting no effect on FHB resistance. It is likely that both DON QTL are new based on comparison with previous studies. This study indicates that resistance to DON accumulation and FHB disease could involve different genes, and the utilization of the two DON QTL in breeding could be helpful in further reducing DON contamination in food and feed.

Hyperspectral Reflectance-Derived Relationship Matrices for Genomic Prediction of Grain Yield in Wheat.

Hyperspectral reflectance phenotyping and genomic selection are two emerging technologies that have the potential to increase plant breeding efficiency by improving prediction accuracy for grain yield. Hyperspectral cameras quantify canopy reflectance across a wide range of wavelengths that are associated with numerous biophysical and biochemical processes in plants. Genomic selection models utilize genome-wide marker or pedigree information to predict the genetic values of breeding lines. In this study, we propose a multi-kernel GBLUP approach to genomic selection that uses genomic marker-, pedigree-, and hyperspectral reflectance-derived relationship matrices to model the genetic main effects and genotype × environment (G × E) interactions across environments within a bread wheat (Triticum aestivum L.) breeding program. We utilized an airplane equipped with a hyperspectral camera to phenotype five differentially managed treatments of the yield trials conducted by the Bread Wheat Improvement Program of the International Maize and Wheat Improvement Center (CIMMYT) at Ciudad Obregón, México over four breeding cycles. We observed that single-kernel models using hyperspectral reflectance-derived relationship matrices performed similarly or superior to marker- and pedigree-based genomic selection models when predicting within and across environments. Multi-kernel models combining marker/pedigree information with hyperspectral reflectance phentoypes had the highest prediction accuracies; however, improvements in accuracy over marker- and pedigree-based models were marginal when correcting for days to heading. Our results demonstrate the potential of using hyperspectral imaging to predict grain yield within a multi-environment context and also support further studies on the integration of hyperspectral reflectance phenotyping into breeding programs.

Integrating genomic-enabled prediction and high-throughput phenotyping in breeding for climate-resilient bread wheat.

Genomic selection and high-throughput phenotyping (HTP) are promising tools to accelerate breeding gains for high-yielding and climate-resilient wheat varieties. Hence, our objective was to evaluate them for predicting grain yield (GY) in drought-stressed (DS) and late-sown heat-stressed (HS) environments of the International maize and wheat improvement center's elite yield trial nurseries. We observed that the average genomic prediction accuracies using fivefold cross-validations were 0.50 and 0.51 in the DS and HS environments, respectively. However, when a different nursery/year was used to predict another nursery/year, the average genomic prediction accuracies in the DS and HS environments decreased to 0.18 and 0.23, respectively. While genomic predictions clearly outperformed pedigree-based predictions across nurseries, they were similar to pedigree-based predictions within nurseries due to small family sizes. In populations with some full-sibs in the training population, the genomic and pedigree-based prediction accuracies were on average 0.27 and 0.35 higher than the accuracies in populations with only one progeny per cross, indicating the importance of genetic relatedness between the training and validation populations for good predictions. We also evaluated the item-based collaborative filtering approach for multivariate prediction of GY using the green normalized difference vegetation index from HTP. This approach proved to be the best strategy for across-nursery predictions, with average accuracies of 0.56 and 0.62 in the DS and HS environments, respectively. We conclude that GY is a challenging trait for across-year predictions, but GS and HTP can be integrated in increasing the size of populations screened and evaluating unphenotyped large nurseries for stress-resilience within years.

Two Main Stripe Rust Resistance Genes Identified in Synthetic-Derived Wheat Line Soru#1.

Stripe rust is a major disease constraint of wheat production worldwide. Resistance to stripe rust was analyzed using 131 F6 recombinant inbred lines (RILs) derived from a cross between synthetic derived wheat line Soru#1 and wheat cultivar Naxos. The phenotype was evaluated in Mexico and Norway at both seedling and adult plant stages. Linkage groups were constructed based on 90K single-nucleotide polymorphism (SNP), sequence-tagged site, and simple sequence repeat markers. Two major resistance loci conferred by Soru#1 were detected and located on chromosomes 1BL and 4DS. The 1BL quantitative trait loci explained 15.8 to 40.2 and 51.1% of the phenotypic variation at adult plant and seedling stages, respectively. This locus was identified as Yr24/Yr26 based on the flanking markers and infection types. Locus 4DS was flanked by molecular markers D_GB5Y7FA02JMPQ0_238 and BS00108770_51. It explained 8.4 to 27.8 and 5.5% of stripe rust variation at the adult plant and seedling stages, respectively. The 4DS locus may correspond to known resistance gene Yr28 based on the resistance source. All RILs that combine Yr24/Yr26 and Yr28 showed significantly reduced stripe rust severity in all four environments compared with the lines with only one of the genes. SNP marker BS00108770_51 was converted into a breeder-friendly kompetitive allele-specific polymerase chain reaction marker that will be useful to accelerate Yr28 deployment in wheat breeding programs.

Genetic Mapping of Resistance in Hexaploid Wheat for a Quarantine Disease: Karnal Bunt.

Karnal bunt (KB) of wheat, caused by Tilletia indica, is one of the greatest challenges to grain industry, not because of yield loss, but quarantine regulations that restrict international movement and trade of affected stocks. Genetic resistance is the best way to manage this disease. Although several different sources of resistance have been identified to date, very few of those have been subjected to genetic analyses. Understanding the genetics of resistance, characterization and mapping of new resistance loci can help in development of improved germplasm. The objective of this study was to identify and characterize resistance loci (QTL) in two independent recombinant inbred lines (RILs) populations utilizing different wheat lines as resistance donors. Elite CIMMYT wheat lines Blouk#1 and Huirivis#1 were used as susceptible female parents and WHEAR/KUKUNA/3/C80.1/3∗BATAVIA//2∗WBLL1 (WKCBW) and Mutus as moderately resistant male parents in Pop1 and Pop2 populations, respectively. Populations were evaluated for KB resistance in 2015-16 and 2016-17 cropping seasons at two seeding dates (total four environments) in Cd. Obregon, Mexico. Two stable QTL from each population were identified in each environment: QKb.cim-2B and QKb.cim-3D (Pop1), QKb.cim-3B1 and QKb.cim-5B2 (Pop2). Other than those four QTL, other QTL were detected in each population which were specific to environments: QKb.cim-5B1, QKb.cim-6A, and QKb.cim-7A (Pop1), QKb.cim-3B2, QKb.cim-4A1, QKb.cim-4A2, QKb.cim-4B, QKb.cim-5A1, QKb.cim-5A2, and QKb.cim-7A2 (Pop2). Among the four stable QTL, all but QKb.cim-3B1 were derived from the resistant parent. QKb.cim-2B and QKb.cim-3D in Pop1 and QKb.cim-3B1 and QKb.cim-5B2 in Pop2 explained 5.0-11.4% and 3.3-7.1% phenotypic variance, respectively. A combination of two stable QTL in each population reduced KB infection by 24-33%, respectively. Transgressive resistant segregants lines derived with resistance alleles from both parents in each population were identified. Single nucleotide polymorphism (SNP) markers flanking these QTL regions may be amenable to marker-assisted selection. The best lines from both populations (in agronomy, end-use quality and KB resistance) carrying resistance alleles at all identified loci, may be used for inter-crossing and selection of improved germplasm in future. Markers flanking these QTL may assist in selection of such lines.

Combining High-Throughput Phenotyping and Genomic Information to Increase Prediction and Selection Accuracy in Wheat Breeding.

Genomics and phenomics have promised to revolutionize the field of plant breeding. The integration of these two fields has just begun and is being driven through big data by advances in next-generation sequencing and developments of field-based high-throughput phenotyping (HTP) platforms. Each year the International Maize and Wheat Improvement Center (CIMMYT) evaluates tens-of-thousands of advanced lines for grain yield across multiple environments. To evaluate how CIMMYT may utilize dynamic HTP data for genomic selection (GS), we evaluated 1170 of these advanced lines in two environments, drought (2014, 2015) and heat (2015). A portable phenotyping system called 'Phenocart' was used to measure normalized difference vegetation index and canopy temperature simultaneously while tagging each data point with precise GPS coordinates. For genomic profiling, genotyping-by-sequencing (GBS) was used for marker discovery and genotyping. Several GS models were evaluated utilizing the 2254 GBS markers along with over 1.1 million phenotypic observations. The physiological measurements collected by HTP, whether used as a response in multivariate models or as a covariate in univariate models, resulted in a range of 33% below to 7% above the standard univariate model. Continued advances in yield prediction models as well as increasing data generating capabilities for both genomic and phenomic data will make these selection strategies tractable for plant breeders to implement increasing the rate of genetic gain.

Assessing Genetic Diversity to Breed Competitive Biofortified Wheat With Enhanced Grain Zn and Fe Concentrations.

Breeding wheat with enhanced levels of grain zinc (Zn) and iron (Fe) is a cost-effective, sustainable solution to malnutrition problems. Modern wheat varieties have limited variation in grain Zn and Fe, but large-scale screening has identified high levels of Zn and Fe in wild relatives and progenitors of cultivated wheat. The most promising sources of high Zn and Fe are einkorn (Triticum monococcum), wild emmer (T. dicoccoides), diploid progenitors of hexaploid wheat (such as Aegilops tauschii), T. spelta, T. polonicum, and landraces of T. aestivum. This study evaluate the effects of translocations from rye and different Aegilops species in a "Pavon-76" wheat genetic background and utilized in the wheat biofortification breeding program at CIMMYT that uses diverse genetic resources, including landraces, recreated synthetic hexaploids, T. spelta and pre-breeding lines. Four translocations were identified that resulted significantly higher Zn content in "Pavon 76" genetic background than the check varieties, and they had increased levels of grain Fe as well-compared to "Pavon 76." These lines were also included in the breeding program aimed to develop advanced high Zn breeding lines. Advanced lines derived from diverse crosses were screened under Zn-enriched soil conditions in Mexico during the 2017 and 2018 seasons. The Zn content of the grain was ranging from 35 to 69 mg/kg during 2017 and 38 to 72 mg/kg during 2018. Meanwhile grain Fe ranged from 30 to 43 mg/kg during 2017 and 32 to 52 mg/kg during 2018. A highly significant positive correlation was found between Zn and Fe (r = 0.54; P < 0.001) content of the breeding lines, therefore it was possible to breed for both properties in parallel. Yield testing of the advanced lines showed that 15% (2017) and 24% (2018) of the lines achieved 95-110% yield potential of the commercial checks and also had 12 mg/kg advantage in the Zn content suggesting that greater genetic gains and farmer-preferred wheat varieties were developed and deployed. A decade of research and breeding efforts led to the selection of "best-bet" breeding lines and the release of eight biofortified wheat varieties in target regions of South Asia and in Mexico.

Genetic impact of Rht dwarfing genes on grain micronutrients concentration in wheat.

Wheat is a major staple food crop providing about 20% of dietary energy and proteins, and food products made of whole grain wheat are a major source of micronutrients like Zinc (Zn), Iron (Fe), Manganese (Mn), Magnesium (Mg), Vitamin B and E. Wheat provides about 40% intake of essential micronutrients by humans in the developing countries relying on wheat based diets. Varieties with genetically enhanced levels of grain micronutrient concentrations can provide a cost-effective and sustainable option to resource poor wheat consumers. To determine the effects of commonly deployed dwarfing genes on wheat grain Zn, Fe, Mn and Mg concentrations, nine bread wheat (Triticum aestivum) and six durum wheat (T. turgidum) isoline pairs differing for Rht1 (= Rht-B1b) and one bread wheat pair for Rht2 (= Rht-D1b) dwarfing genes were evaluated for three crop seasons at N.E. Borlaug Research Station, Cd. Obregon, Sonora, Mexico. Presence of dwarfing genes have significantly reduced grain Zn concentration by 3.9 ppm (range 1.9-10.0 ppm), and Fe by 3.2 ppm (range 1.0-14.4 ppm). On the average, about 94 ppm Mg and 6 ppm Mn reductions occurred in semidwarf varieties compared to tall varieties. The thousand kernel weight (TKW) of semidwarf isolines was 2.6 g (range 0.7-5.6 g) lower than the tall counterparts whereas the plant height decreased by 25 cm (range 16-37 cm). Reductions for all traits in semidwarfs were genotype dependent and the magnitude of height reductions did not correlate with reductions in micronutrient concentrations in wheat grain. We conclude that increased grain yield potential of semidwarf wheat varieties is associated with reduced grain micronutrient concentrations; however, the magnitude of reductions in micronutrients varied depending on genetic background and their associated pleiotropic effect on yield components.

QTL Mapping of Grain Zn and Fe Concentrations in Two Hexaploid Wheat RIL Populations with Ample Transgressive Segregation.

More than 50% of undernourished children live in Asia and more than 25% live in Africa. Coupled with an inadequate food supply, mineral deficiencies are widespread in these populations; particularly zinc (Zn) and iron (Fe) deficiencies that lead to retarded growth, adverse effects on both the immune system and an individual's cognitive abilities. Biofortification is one solution aimed at reducing the incidence of these deficiencies. To efficiently breed a biofortified wheat variety, it is important to generate knowledge of the genomic regions associated with grain Zn (GZn) and Fe (GFe) concentration. This allows for the introgression of favorable alleles into elite germplasm. In this study we evaluated two bi-parental populations of 188 recombinant inbred lines (RILs) displaying a significant range of transgressive segregation for GZn and GFe during three crop cycles in CIMMYT, Mexico. Parents of the RILs were derived from Triticum spelta L. and synthetic hexaploid wheat crosses. QTL analysis identified a number of significant QTL with a region denominated as QGZn.cimmyt-7B_1P2 on chromosome 7B explaining the largest (32.7%) proportion of phenotypic variance (PVE) for GZn and leading to an average additive effect of -1.3. The QTL with the largest average additive effect for GFe (-0.161) was found on chromosome 4A (QGFe.cimmyt-4A_P2), with 21.14% of the PVE. The region QGZn.cimmyt-7B_1P2 co-localized closest to the region QGZn.cimmyt-7B_1P1 in a consensus map built from the linkage maps of both populations. Pleiotropic or tightly linked QTL were also found on chromosome 3B, however of minor effects and PVE between 4.3 and 10.9%. Further efforts are required to utilize the QTL information in marker assisted backcrossing schemes for wheat biofortification. A strategy to follow is to intercross the transgressive individuals from both populations and then utilize them as sources in biofortification breeding pipelines.