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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Wheat variety PBW343, released in India in 1995, became the most widely grown cultivar in the country by the year 2000 owing to its wide adaptability and yield potential. It initially succumbed to leaf rust, and resistance genes Lr24 and Lr28 were transferred to PBW343. After an unbroken reign of about 10 years, the virulence against gene Yr27 made PBW343 susceptible to stripe rust. Owing to its wide adaptability and yield potential, PBW343 became the prime target for marker-assisted introgression of stripe rust resistance genes. The leaf rust-resistant versions formed the base for pyramiding stripe rust resistance genes Yr5, Yr10, Yr15, Yr17, and Yr70, in different introgression programs. Advanced breeding lines with different gene combinations, PBW665, PBW683, PBW698, and PBW703 were tested in national trials but could not be released as varieties. The genes from alien segments, Aegilops ventricosa (Lr37/Yr17/Sr38) and Aegilops umbellulata (Lr76/Yr70), were later pyramided in PBW343. Modified marker-assisted backcross breeding was performed, and 81.57% of the genetic background was recovered in one of the selected derivative lines, PBW723. This line was evaluated in coordinated national trials and was released for cultivation under timely sown irrigated conditions in the North Western Plain Zone of India. PBW723 yields an average of 58.0 qtl/ha in Punjab with high potential yields. The genes incorporated are susceptible to stripe rust individually, but PBW723 with both genes showed enhanced resistance. Three years post-release, PBW723 occupies approximately 8–9% of the cultivated area in the Punjab state. A regular inflow of diverse resistant genes, their rapid mobilization to most productive backgrounds, and keeping a close eye on pathogen evolution is essential to protect the overall progress for productivity and resistance in wheat breeding, thus helping breeders to keep pace with pathogen evolution.

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Aegilops tauschii Coss., the D-genome donor of bread wheat, represents a rich source of resistance and productivity traits for wheat improvement. In this study, a direct hybridization approach using Ae. tauschii as the female in crosses with Triticum aestivum resulted in about 50 times more F 1 plants than the reciprocal cross. In a set of five Ae. tauschii · T. aestivum crosses, an average of 35% of the pollinated florets resulted in embryo formation. Following embryo rescue on artificial medium, an average of 6.8 F 1 plants could be obtained for every 100 florets pollinated. Colchicine treatment of the F 1 plants greatly enhanced backcross seed formation (14.9 backcross seeds compared to an average of 0.47 seeds per 100 florets for untreated tillers). The efficacy of this gene transfer system was demonstrated by improved cell membrane stability and chlorophyll retention in BC 1 F 4 lines derived from the crosses of three heat-tolerant accessions of Ae. tauschii with bread wheat cultivar ÔPBW 550Õ.

Heat stress is a major productivity lowering factor in wheat. Wild progenitor species offer a wide spectrum of adaptation traits and can serve as valuable donors of stress tolerance. In the present study, genetic variation in 129 accessions of Aegilops tauschii Coss., the D genome donor of wheat, was evaluated for two heat tolerance related traits viz., cell membrane stability (CMS) and TTC (2,3,5-Triphenyl tetrazolium chloride) based cell viability. Cell membrane stability in the Ae. tauschii accessions at vegetative stage ranged from 15.24 to 80.39%. Nineteen Ae. tauschii accessions were superior to the tolerant bread wheat control (C 273). At anthesis stage a similar spectrum of variation was observed with twenty three accessions showing higher cell membrane stability than C 273. The average CMS level of entire germplasm set at anthesis (47.61%) was lower than at vegetative stage (58.89%). Clear genotypic differences were also observed for TTC based cell viability test. Ae. tauschii accessions displayed a range from 18.73 to 84.39% with eight genotypes excelling over tolerant bread wheat. Correlation of CMS values recorded at two stages was significant but of low predictive value (r 2 = 0.137). Similarly significant but moderate correlation was obtained between CMS and TTC test (r 2 = 0.325). Consequently all the three parameters were used to derive a cell thermotolerance index which was in turn used to identify ten tolerant Ae. tauschii genotypes. The identified accessions were re-evaluated for 1 more year and the three parameters viz., CMS at vegetative (r 2 = 0.954) and anthesis stage (r 2 = 0.932) and TTC cell viability at vegetative stage (r 2 = 0.888) showed high correlation Strategy for use of identified accessions as donors is discussed.

Major paradigm shift in plant breeding since the availability of molecular marker technology is that mapping and characterizing the genetic loci that control a trait will lead to improved breeding. Often, one of the rationales for cloning of QTL is to develop the "perfect marker" for MAS, perhaps based on a functional polymorphism. In contrast, an advantage of genomic selection is precisely its black box approach to exploiting genotyping technology to expedite genetic progress. This is an advantage in our view because it does not rely on a "breeding by design" engineering approach to cultivar development requiring knowledge of biological function before the creation of phenotypes. Breeders can therefore use genomic selection without the large upfront cost of obtaining that knowledge. In addition, genomic selection can maintain the creative nature of phenotypic selection which couple's random mutation and recombination to sometimes arrive at solutions outside the engineer's scope. Currently, the lion's share of research on genomic selection has been performed in livestock breeding, where effective population size, extent of LD, breeding objectives, experimental design, and other characteristics of populations and breeding programs are quite different from those of crop species. Nevertheless, a great number of findings within this literature are very illuminating for genomic selection in crops and should be studied and built upon by crop geneticists and breeders. The application of powerful, relatively new statistical methods to the problem of high dimensional marker data for genomic selection has been nearly as important to the development of genomic selection as the creation of high-density marker platforms and greater computing power. The methods can be classified by what type of genetic architecture they try to capture.