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.

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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.

The mode of inheritance and allelic relationships among genes conferring resistance to Karnal bunt were studied in seven bread-wheat

Karnal bunt caused by Tilletia indica Mitra [syn. Neovossia indica (Mitra) Mundkur] is a significant biosecurity concern for wheat-exporting countries that are free of the disease. It is a seed-, soil-and air-borne disease with no effective chemical control measures. The current study used data from multi-year field experiments of two bi-parental populations and a genome-wide association (GWA) mapping panel to unravel the genetic basis for resistance in common wheat. Broad-sense heritability for Karnal bunt resistance in the populations varied from 0.52 in the WH542×HD29 population, to 0.61 in the WH542×W485 cross and 0.71 in a GWAS panel. Quantitative trait locus (QTL) analysis with seven years of phenotypic data identified a major locus on chromosome 3B (R 2 = 27.8%) and a minor locus on chromosome 1A (R 2 = 12.2%), in the WH542×HD29 population, with both parents contributing the high-value alleles. A major locus (R 2 = 27.8%) and seven minor loci (R 2 = 4.4–15.8%) were detected in the WH542×W485 population. GWA mapping validated QTL regions in the bi-parent populations, but also identified novel loci not previously associated with Karnal bunt resistance. Meta-QTL analysis aligned the results from this study with those reported in wheat over the last two decades. Two major clusters were detected, the first on chromosome 4B, which clustered with Qkb.ksu-4B , QKb.cimmyt-4BL , Qkb.cim-4BL , and the second on chromosome 3B, which clustered with Qkb.cnl-3B , QKb.cimmyt-3BS and Qkb.cim-3BS1 . The results provide definitive chromosomal assignments for QTL/genes controlling Karnal bunt resistance in common wheat, and will be useful in pre-emptive breeding against the pathogen in wheat-producing areas that are free of the disease.

Karnal bunt (Tilletia indica Mitra) infestation of wheat (Triticum aestivum L.) kernels reduces grain quality. Deployment of genetic resistance would be preferable to chemical applications for control of the disease. Inoculation studies were carried out in a wheat mapping population with the aim of locating genes for resistance. Recombinant inbred (RI) lines from a cross between a resistant synthetic wheat (Triticum turgidum 'Altar 84' x T. tauschii) and the susceptible common wheat cultivar 'Opata 85' were inoculated with Karnal bunt sporidial suspension and evaluated for symptom development in the field for three seasons and in the greenhouse. Based on restriction fragment length polymorphism (RFLP) analyses, regions on chromosome arms 3BS and SAL carrying marker alleles from the Altar durum parent were consistently associated with reduced kernel disease. Main marker effects accounted for up to 32% of disease variation in the field but only 15% in the greenhouse, where the level of disease was higher, suggesting an environmental component of resistance. The tagging of these Karnal bunt partial-resistance genes in tetraploid and hexaploid backgrounds may facilitate the accumulation of resistance via marker-assisted transfer to susceptible durum and common wheat cultivars. This practice should reduce laborious disease screening requirements. R^R NAL or partial bunt (KB) was first identified in 1931 in wheat fields near Karnal, India. Susceptible wheat cultivars are attacked via floral infection by seed-, air-, or soil-borne sporidia, resulting in partial replacement of kernels with masses of teliospores. These impart a foul odor to the grain and reduce its fitness for consumption. The principal wheat-growing areas affected by KB include northwestern India, Pakistan, and northwestern Mexico. The disease appeared in the Yaqui Valley of Mexico in the early 1970s and recently has caused problems in the U.S. states of Arizona and California (Anonymous, 1996).

Synthetic hexaploids (SH) developed at the International Maize and Wheat Improvement Center (CIM-MYT), involving four Triticum turgidum and nine T. tauschii parents, were evaluated for resistance to Karnal bunt (KB) (Tilletia indica Mitra) during three crop seasons over three years at Ciudad Obregon, Sonora, Mexico. Ten tillers of each SH at boot stage, taken at random, were injected with a suspension of sporidia in water (10,000 spores/ml of water). At maturity the inoculated spikes were threshed individually and evaluated for the percentage KB-infected grains. Based on the mean KB score of each entry for three seasons, 49 % of the SH were immune (0 % infection) to KB. Highly resistant expressions characterized the SH which appeared to be influenced by the resistance of their T. turgidum and/or T. tauschii parents. The overall mean infection of the SH wheats was 0.24 % compared to 56.14 % in the susceptible bread wheat check cultivat 'WL711'. Transfer of KB resistance genes from SH wheats into bread wheat is currently underway at CIMMYT.