The value of exotic wheat genetic resources for accelerating grain yield gains is largely unproven and unrealized. We used next-generation sequencing, together with multi-environment phenotyping, to study the contribution of exotic genomes to 984 three-way-cross-derived (exotic/elite1//elite2) pre-breeding lines (PBLs). Genomic characterization of these lines with haplotype map-based and SNP marker approaches revealed exotic specific imprints of 16.1 to 25.1%, which compares to theoretical expectation of 25%. A rare and favorable haplotype (GT) with 0.4% frequency in gene bank identified on chromosome 6D minimized grain yield (GY) loss under heat stress without GY penalty under irrigated conditions. More specifically, the ‘T’ allele of the haplotype GT originated in Aegilops tauschii and was absent in all elite lines used in study. In silico analysis of the SNP showed hits with a candidate gene coding for isoflavone reductase IRL-like protein in Ae. tauschii. Rare haplotypes were also identified on chromosomes 1A, 6A and 2B effective against abiotic/biotic stresses. Results demonstrate positive contributions of exotic germplasm to PBLs derived from crosses of exotics with CIMMYT’s best elite lines. This is a major impact-oriented pre-breeding effort at CIMMYT, resulting in large-scale development of PBLs for deployment in breeding programs addressing food security under climate change scenarios.

Climate change and slow yield gains pose a major threat to global wheat production. Underutilized genetic resources including landraces and wild relatives are key elements for developing high-yielding and climate-resilient wheat varieties. Landraces introduced into Mexico from Europe, also known as Creole wheats, are adapted to a wide range of climatic regimes and represent a unique genetic resource. Eight thousand four hundred and sixteen wheat landraces representing all dimensions of Mexico were characterized through genotyping-by-sequencing technology. Results revealed sub-groups adapted to specific environments of Mexico. Broadly, accessions from north and south of Mexico showed considerable genetic differentiation. However, a large percentage of landrace accessions were genetically very close, although belonged to different regions most likely due to the recent (nearly five centuries before) introduction of wheat in Mexico. Some of the groups adapted to extreme environments and accumulated high number of rare alleles. Core reference sets were assembled simultaneously using multiple variables, capturing 89% of the rare alleles present in the complete set. Genetic information about Mexican wheat landraces and core reference set can be effectively utilized in next generation wheat varietal improvement.

Aegilops tauschii, the D-genome progenitor of Triticum aestivum, encompasses huge diversity for various traits of potential economic importance such as yield, biotic and abiotic stress tolerance, quality and nutrition. In the present study, variation for grain size in Ae. tauschii germplasm was studied and its genetic basis dissected using genome-wide association study (GWAS). Grain length, width, and weight evaluated in 177 Ae. tauschii accessions over 3 years showed near normal distribution with 1.74-, 1.75-, and 2.82-fold variation, respectively. These lines were genetically characterized using genotyping-by-sequencing (GBS) protocol that produced 11,489 single nucleotide polymorphic (SNP) markers. Genetic diversity analysis revealed the presence of two distinct subgroups (designated as lineage 1 and 2) in Ae. tauschii. Based on GBS markers, the genetic similarity was calculated between the accessions and GWAS was conducted using 114 non-redundant accessions and 5,249 SNP markers. A total of 17 SNPs associated with grain size traits distributed over all the seven chromosomes were revealed with 6D, 5D, and 2D harboring most significant marker–trait associations. Some of the chromosomal regions such as 6D_66.4–71.1 cM, 1D_143.5–156.7 cM, and 2D_89.9–92.5 cM had associations with multiple traits. Candidate genes associated with cell division and differentiation were identified for some of the associated SNP markers. Further efforts to validate these loci will help to understand their role in determining grain size and allelic diversity in current germplasm and its effect on grain size upon transfer to bread wheat background.

Stripe rust, caused by Puccinia striiformis West. f.sp. tritici, is one of the most damaging diseases of wheat worldwide. Forty genes for stripe rust resistance have been catalogued so far, but the majority of them are not effective against emerging pathotypes. Triticum monococcum and T. boeoticum have excellent levels of resistance to rusts, but so far, no stripe rust resistance gene has been identified or transferred from these species. A set of 121 RILs generated from a cross involving T. monococcum (acc. pau14087) and T. boeoticum (acc. pau5088) was screened for 3 years against a mixture of pathotypes under field conditions. The parental accessions were susceptible to all the prevalent pathotypes at the seedling stage, but resistant at the adult plant stage. Genetic analysis of the RIL population revealed the presence of two genes for stripe rust resistance, with one gene each being contributed by each of the parental lines. A linkage map with 169 SSR and RFLP loci generated from a set of 93 RILs was used for mapping these resistance genes. Based on phenotypic data for 3 years and the pooled data, two QTLs, one each in T. monococcum acc. pau14087 and T. boeoticum acc. pau5088, were detected for resistance in the RIL population. The QTL in T. monococcum mapped on chromosome 2A in a 3.6 cM interval between Xwmc407 and Xwmc170, whereas the QTL from T. boeoticum mapped on 5A in 8.9 cM interval between Xbarc151 and Xcfd12 and these were designated as QYrtm.pau-2A and QYrtb.pau-5A, respectively. Based on field data for 3 years, their R2 values were 14 and 24%, respectively. T. monococcum acc. pau14087 and three resistant RILs were crossed to hexaploid wheat cvs WL711 and PBW343, using T. durum as a bridging species with the objective of transferring these genes into hexaploid wheat. The B genome of T. durum suppressed resistance in the F1 plants, but with subsequent backcrossing one resistance gene could be transferred from one of the RILs to the hexaploid wheat background. This gene was derived from T. boeoticum acc. pau5088 as indicated by co-introgression of T. boeoticum sequences linked to stripe rust resistance QTL, QYrtb.pau-5A. Homozygous resistant progenies with 40-42 chromosomes have been identified.

Micronutrient malnutrition affects a very large proportion of the world's population. For combating micronutrient malnutrition, biofortification through genetic manipulation has been proposed as an alternative to traditional fortification for increasing the bioavailable nutrient content of food crops. Wheat, being a staple food for a large section of the world's population, is targeted for increasing the Fe and Zn content in the grains. The cultivated germplasm of wheat does not have sufficient variability for grain Fe and Zn content but the wild species of wheat do show wider variation for grain micronutrient density. The analysis of Aegilops kotschyi and A. tauschii for Fe and Zn content in the grains using an atomic absorption spectrophotometer (AAS) indicated that the S and D genome species accumulate significantly higher iron and zinc in the grains than the cultivated wheats. One of the CIMMYT synthetics also had significantly higher Fe and Zn in the grains as compared with the cultivated wheats. Aegilops kotschyi as a promising source for Fe and Zn, is reported for the first time. A systematic programme to identify and utilize the additional sources for high Fe and Zn has been initiated.

Karnal bunt (KB) of wheat, caused by the fungus Tilletia indica, is a challenge to the grain industry, owing not to direct yield loss but to quarantine regulations that may restrict international movement of affected grain. Several different sources of resistance to KB have been reported. Understanding the genetics of resistance will facilitate the introgression of resistance into new wheat cultivars. The objectives of this study were to identify quantitative trait loci (QTLs) associated with KB resistance and to identify DNA markers in two recombinant inbred line populations derived from crosses of the susceptible cultivar WH542 with resistant lines HD29 and W485. Populations were evaluated for resistance against the KB pathogen for 3 years at Punjab Agricultural University, Ludhiana, India. Two new QTLs (Qkb.ksu-5BL.1 and Qkb.ksu-6BS.1) with resistance alleles from HD29 were identified and mapped in the intervals Xgdm116-Xwmc235 on chromosome 5B (deletion bin 5BL9-0.76-0.79) and Xwmc105-Xgwm88 on chromosome 6B (C-6BS5-0.76). They explained up to 19 and 13% of phenotypic variance, respectively. Another QTL (Qkb.ksu-4BL.1) with a resistance allele from W485 mapped in the interval Xgwm6-Xwmc349 on chromosome 4B (4BL5-0.86-1.00) and explained up to 15% of phenotypic variance. Qkb.ksu-6BS.1 showed pairwise interactions with loci on chromosomes 3B and 6A. Markers suitable for marker-assisted selection are available for all three QTLs.

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A comprehensive germplasm evaluation study of wheat accessions conserved in the Indian National Genebank was conducted to identify sources of rust and spot blotch resistance. Genebank accessions comprising three species of wheat–Triticum aestivum, T. durum and T. dicoccum were screened sequentially at multiple disease hotspots, during the 2011–14 crop seasons, carrying only resistant accessions to the next step of evaluation. Wheat accessions which were found to be resistant in the field were then assayed for seedling resistance and profiled using molecular markers. In the primary evaluation, 19,460 accessions were screened at Wellington (Tamil Nadu), a hotspot for wheat rusts. We identified 4925 accessions to be resistant and these were further evaluated at Gurdaspur (Punjab), a hotspot for stripe rust and at Cooch Behar (West Bengal), a hotspot for spot blotch. The second round evaluation identified 498 accessions potentially resistant to multiple rusts and 868 accessions potentially resistant to spot blotch. Evaluation of rust resistant accessions for seedling resistance against seven virulent pathotypes of three rusts under artificial epiphytotic conditions identified 137 accessions potentially resistant to multiple rusts. Molecular analysis to identify different combinations of genetic loci imparting resistance to leaf rust, stem rust, stripe rust and spot blotch using linked molecular markers, identified 45 wheat accessions containing known resistance genes against all three rusts as well as a QTL for spot blotch resistance. The resistant germplasm accessions, particularly against stripe rust, identified in this study can be excellent potential candidates to be employed for breeding resistance into the background of high yielding wheat cultivars through conventional or molecular breeding approaches, and are expected to contribute toward food security at national and global levels.