Target Population of Environments for Wheat Breeding in India: Definition, Prediction and Genetic Gains.

In this study, we defined the target population of environments (TPE) for wheat breeding in India, the largest wheat producer in South Asia, and estimated the correlated response to the selection and prediction ability of five selection environments (SEs) in Mexico. We also estimated grain yield (GY) gains in each TPE. Our analysis used meteorological, soil, and GY data from the international Elite Spring Wheat Yield Trials (ESWYT) distributed by the International Maize and Wheat Improvement Center (CIMMYT) from 2001 to 2016. We identified three TPEs: TPE 1, the optimally irrigated Northwestern Plain Zone; TPE 2, the optimally irrigated, heat-stressed North Eastern Plains Zone; and TPE 3, the drought-stressed Central-Peninsular Zone. The correlated response to selection ranged from 0.4 to 0.9 within each TPE. The highest prediction accuracies for GY per TPE were derived using models that included genotype-by-environment interaction and/or meteorological information and their interaction with the lines. The highest prediction accuracies for TPEs 1, 2, and 3 were 0.37, 0.46, and 0.51, respectively, and the respective GY gains were 118, 46, and 123 kg/ha/year. These results can help fine-tune the breeding of elite wheat germplasm with stable yields to reduce farmers' risk from year-to-year environmental variation in India's wheat lands, which cover 30 million ha, account for 100 million tons of grain or more each year, and provide food and livelihoods for hundreds of millions of farmers and consumers in South Asia.

Haplotype-Based, Genome-Wide Association Study Reveals Stable Genomic Regions for Grain Yield in CIMMYT Spring Bread Wheat.

We untangled key regions of the genetic architecture of grain yield (GY) in CIMMYT spring bread wheat by conducting a haplotype-based, genome-wide association study (GWAS), together with an investigation of epistatic interactions using seven large sets of elite yield trials (EYTs) consisting of a total of 6,461 advanced breeding lines. These lines were phenotyped under irrigated and stress environments in seven growing seasons (2011-2018) and genotyped with genotyping-by-sequencing markers. Genome-wide 519 haplotype blocks were constructed, using a linkage disequilibrium-based approach covering 14,036 Mb in the wheat genome. Haplotype-based GWAS identified 7, 4, 10, and 15 stable (significant in three or more EYTs) associations in irrigated (I), mild drought (MD), severe drought (SD), and heat stress (HS) testing environments, respectively. Considering all EYTs and the four testing environments together, 30 stable associations were deciphered with seven hotspots identified on chromosomes 1A, 1B, 2B, 4A, 5B, 6B, and 7B, where multiple haplotype blocks were associated with GY. Epistatic interactions contributed significantly to the genetic architecture of GY, explaining variation of 3.5-21.1%, 3.7-14.7%, 3.5-20.6%, and 4.4- 23.1% in I, MD, SD, and HS environments, respectively. Our results revealed the intricate genetic architecture of GY, controlled by both main and epistatic effects. The importance of these results for practical applications in the CIMMYT breeding program is discussed.

Grain yield genetic gains and changes in physiological related traits for CIMMYT's High Rainfall Wheat Screening Nursery tested across international environments.

The effects of climate change together with the projected future demand represents a huge challenge for wheat production systems worldwide. Wheat breeding can contribute to global food security through the creation of genotypes exhibiting stress tolerance and higher yield potential. The objectives of our study were to (i) estimate the annual grain yield (GY) genetic gain of High Rainfall Wheat Yield Trials (HRWYT) grown from 2007 (15th HRWYT) to 2016 (24th HRWYT) across international environments, and (ii) determine the changes in physiological traits associated with GY genetic improvement. The GY genetic gains were estimated as genetic progress per se (GYP) and in terms of local checks (GYLC). In total, 239 international locations were classified into two groups: high- and low-rainfall environments based on climate variables and trial management practices. In the high-rainfall environment, the annual genetic gains for GYP and GYLC were 3.8 and 1.17 % (160 and 65.1 kg ha-1 yr-1), respectively. In the low-rainfall environment, the genetic gains were 0.93 and 0.73 % (40 and 33.1 kg ha-1 yr-1), for GYP and GYLC respectively. The GY of the lines included in each nursery showed a significant phenotypic correlation between high- and low-rainfall environments in all the examined years and several of the five best performing lines were common in both environments. The GY progress was mainly associated with increased grain weight (R2 = 0.35 p < 0.001), days to maturity (R2 = 0.20, p < 0.001) and grain filling period (R2 = 0.06, p < 0.05). These results indicate continuous GY genetic progress and yield stability in the HRWYT germplasm developed and distributed by CIMMYT.

Genetic dissection of zinc, iron, copper, manganese and phosphorus in wheat (Triticum aestivum L.) grain and rachis at two developmental stages.

The development of high-yielding wheat genotypes containing micronutrient-dense grains are the main priorities of biofortification programs. At the International Maize and Wheat Improvement Center, breeders have successfully crossed high zinc progenitors including synthetic hexaploid wheat, T. dicoccum, T. spelta and landraces to generate high-zinc varieties. In this study, we report a genome-wide association using a wheat diversity panel to dissect the genetics controlling zinc, iron, copper, manganese and phosphorus concentrations in the grain and rachis during grain development and at physiological maturity. Significant marker-trait associations (MTAs) were identified for each nutrient using multi-locus mixed model methodologies. For mature grain, markers that showed significant pleiotropic effects were found on chromosomes 1A, 3B and 5B, of which those on chromosome 5B at ∼95.5 cM were consistent over two growing seasons. Co-located MTAs were identified for the nutrient concentrations in developing grain, rachis and mature grain on multiple chromosomes. The identified genomic regions included putative candidate genes involved in metal uptake and transport and storage protein processing. These findings add to our understanding of the genetics of the five important nutrients in wheat grain and provide information on genetic markers for selecting high micronutrient genotypes.

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.

QTL mapping for micronutrients concentration and yield component traits in a hexaploid wheat mapping population.

Bread wheat is a major staple cereal provides more than 20% of dietary energy and protein supply to global population. However, with increasing population growth, the problem of nutritional deficiencies is increasingly affecting the health of resource people with predominantly cereal-based diet. Therefore, the development of wheat genotypes with micronutrient-dense grains along with high-yield potential is one of the major priorities of wheat biofortification program at CIMMYT. We conducted a QTL mapping study using a recombinant inbred line (RIL) population derived from a cross between a Chinese parental line with highGZnC and a Mexican commercial bread wheat cultivar Roelfs F2007 to identify QTLs that could potentially be integrated in mineral nutrient concentrations and agronomic-related traits breeding. We evaluated 200 RIL lines for mineral nutrient concentrations and agronomic-related traits over two years. A total of 60 QTLs were detected, of which 10 QTLs for GZnC, 9 for GFeC, 5 for GPC and 36 for agronomic-related traits. Moreover, a total of 55 promising candidate genes were identified from the list of associated markers for GFeC and GZnC using the recently annotated wheat genome sequence. We identified the promising genomic regions with high mineral nutrient concentrations and acceptable yield potential, which are good resource for further use in wheat biofortification breeding programs.

Genetic dissection of grain zinc concentration in spring wheat for mainstreaming biofortification in CIMMYT wheat breeding.

Wheat is an important staple that acts as a primary source of dietary energy, protein, and essential micronutrients such as iron (Fe) and zinc (Zn) for the world's population. Approximately two billion people suffer from micronutrient deficiency, thus breeders have crossed high Zn progenitors such as synthetic hexaploid wheat, T. dicoccum, T. spelta, and landraces to generate wheat varieties with competitive yield and enhanced grain Zn that are being adopted by farmers in South Asia. Here we report a genome-wide association study (GWAS) using the wheat Illumina iSelect 90 K Infinitum SNP array to characterize grain Zn concentrations in 330 bread wheat lines. Grain Zn phenotype of this HarvestPlus Association Mapping (HPAM) panel was evaluated across a range of environments in India and Mexico. GWAS analysis revealed 39 marker-trait associations for grain Zn. Two larger effect QTL regions were found on chromosomes 2 and 7. Candidate genes (among them zinc finger motif of transcription-factors and metal-ion binding genes) were associated with the QTL. The linked markers and associated candidate genes identified in this study are being validated in new biparental mapping populations for marker-assisted breeding.

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.

Variability in iron, zinc and phytic acid content in a worldwide collection of commercial durum wheat cultivars and the effect of reduced irrigation on these traits.

Diets very rich in cereals have been associated with micronutrient malnutrition, and the biofortification of them, has been proposed as one of the best approaches to alleviate the problem. Durum wheat is one of the main sources of calories and protein in many developing countries. In this study, 46 durum varieties grown under full and reduced irrigation, were analyzed for micronutrients and phytate content to determine the potential bioavailability of the micronutrients. The variation was 25.7-40.5mg/kg for iron and of 24.8-48.8mg/kg for zinc. For phytate determination (0.462-0.952 %), a modified methodology was validated in order to reduce testing costs while speeding up testing time. Variation was detected for phytate:iron and zinc molar ratios (12.1-29.6 and 16.9-23.6, respectively). The results could be useful to generate varieties with appropriate levels of phytate and micronutrients, which can lead to the development of varieties rich in micronutrients to overcome malnutrition.

Genetic Yield Gains In CIMMYT's International Elite Spring Wheat Yield Trials By Modeling The Genotype × Environment Interaction.

We calculated the annual genetic gains for grain yield (GY) of wheat (Triticum aestivum L.) achieved over 8 yr of international Elite Spring Wheat Yield Trials (ESWYT), from 2006-2007 (27th ESWYT) to 2014-2015 (34th ESWYT). In total, 426 locations were classified within three main megaenvironments (MEs): ME1 (optimally irrigated environments), ME4 (drought-stressed environments), and ME5 (heat-stressed environments). By fitting a factor analytical structure for modeling the genotype × environment (G × E) interaction, we measured GY gains relative to the widely grown cultivar Attila (GYA) and to the local checks (GYLC). Genetic gains for GYA and GYLC across locations were 1.67 and 0.53% (90.1 and 28.7 kg ha-1 yr-1), respectively. In ME1, genetic gains were 1.63 and 0.72% (102.7 and 46.65 kg ha-1 yr-1) for GYA and GYLC, respectively. In ME4, genetic gains were 2.7 and 0.41% (88 and 15.45 kg ha-1 yr-1) for GYA and GYLC, respectively. In ME5, genetic gains were 0.31 and 1.0% (11.28 and 36.6 kg ha-1 yr-1) for GYA and GYLC, respectively. The high GYA in ME1 and ME4 can be partially attributed to yellow rust races that affect Attila. When G × E interactions were not modeled, genetic gains were lower. Analyses showed that CIMMYT's location at Ciudad Obregon, Mexico, is highly correlated with locations in other countries in ME1. Lines that were top performers in more than one ME and more than one country were identified. CIMMYT's breeding program continues to deliver improved and widely adapted germplasm for target environments.

Harnessing Diversity in Wheat to Enhance Grain Yield, Climate Resilience, Disease and Insect Pest Resistance and Nutrition Through Conventional and Modern Breeding Approaches.

Current trends in population growth and consumption patterns continue to increase the demand for wheat, a key cereal for global food security. Further, multiple abiotic challenges due to climate change and evolving pathogen and pests pose a major concern for increasing wheat production globally. Triticeae species comprising of primary, secondary, and tertiary gene pools represent a rich source of genetic diversity in wheat. The conventional breeding strategies of direct hybridization, backcrossing and selection have successfully introgressed a number of desirable traits associated with grain yield, adaptation to abiotic stresses, disease resistance, and bio-fortification of wheat varieties. However, it is time consuming to incorporate genes conferring tolerance/resistance to multiple stresses in a single wheat variety by conventional approaches due to limitations in screening methods and the lower probabilities of combining desirable alleles. Efforts on developing innovative breeding strategies, novel tools and utilizing genetic diversity for new genes/alleles are essential to improve productivity, reduce vulnerability to diseases and pests and enhance nutritional quality. New technologies of high-throughput phenotyping, genome sequencing and genomic selection are promising approaches to maximize progeny screening and selection to accelerate the genetic gains in breeding more productive varieties. Use of cisgenic techniques to transfer beneficial alleles and their combinations within related species also offer great promise especially to achieve durable rust resistance.

Genomic prediction for grain zinc and iron concentrations in spring wheat.

KEY MESSAGE: Predictability estimated through cross-validation approach showed moderate to high level; hence, genomic selection approach holds great potential for biofortification breeding to enhance grain zinc and iron concentrations in wheat. Wheat (Triticum aestivum L.) is a major staple crop, providing 20 % of dietary energy and protein consumption worldwide. It is an important source of mineral micronutrients such as zinc (Zn) and iron (Fe) for resource poor consumers. Genomic selection (GS) approaches have great potential to accelerate development of Fe- and Zn-enriched wheat. Here, we present the results of large-scale genomic and phenotypic data from the HarvestPlus Association Mapping (HPAM) panel consisting of 330 diverse wheat lines to perform genomic predictions for grain Zn (GZnC) and Fe (GFeC) concentrations, thousand-kernel weight (TKW) and days to maturity (DTM) in wheat. The HPAM lines were phenotyped in three different locations in India and Mexico in two successive crop seasons (2011-12 and 2012-13) for GZnC, GFeC, TKW and DTM. The genomic prediction models revealed that the estimated prediction abilities ranged from 0.331 to 0.694 for Zn and from 0.324 to 0.734 for Fe according to different environments, whereas prediction abilities for TKW and DTM were as high as 0.76 and 0.64, respectively, suggesting that GS holds great potential in biofortification breeding to enhance grain Zn and Fe concentrations in bread wheat germplasm.

Zinc and iron concentration QTL mapped in a Triticum spelta × T. aestivum cross.

KEY MESSAGE: Ten QTL underlying the accumulation of Zn and Fe in the grain were mapped in a set of RILs bred from the cross Triticum spelta × T. aestivum . Five of these loci (two for Zn and three for Fe) were consistently detected across seven environments. The genetic basis of accumulation in the grain of Zn and Fe was investigated via QTL mapping in a recombinant inbred line (RIL) population bred from a cross between Triticum spelta and T. aestivum. The concentration of the two elements was measured from grain produced in three locations over two consecutive cropping seasons and from a greenhouse trial. The range in Zn and Fe concentration across the RILs was, respectively, 18.8-73.5 and 25.3-59.5 ppm, and the concentrations of the two elements were positively correlated with one another (rp =+0.79). Ten QTL (five each for Zn and Fe accumulation) were detected, mapping to seven different chromosomes. The chromosome 2B and 6A grain Zn QTL were consistently expressed across environments. The proportion of the phenotype explained (PVE) by QZn.bhu-2B was >16 %, and the locus was closely linked to the SNP marker 1101425|F|0, while QZn.bhu-6A (7.0 % PVE) was closely linked to DArT marker 3026160|F|0. Of the five Fe QTL detected, three, all mapping to chromosome 1A were detected in all seven environments. The PVE for QFe.bhu-3B was 26.0 %.