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Abstract BackgroundPrioritizing wild relative diversity for improving crop adaptation to emerging drought-prone environments is challenging. Here, we combine the genome-wide environmental scans (GWES) in wheat diploid ancestorAegilops tauschii(Ae. tauschii) with allele testing in the genetic backgrounds of adapted cultivars to identify diversity for improving wheat adaptation to water-limiting conditions. ResultsWe evaluate the adaptive allele effects inAe. tauschii-wheat introgression lines phenotyped for multiple traits under irrigated and water-limiting conditions using both unmanned aerial system-based imaging and conventional approaches. The GWES show that climatic gradients alone explain more than half of genomic variation inAe. tauschii, with many alleles associated with climatic factors inAe. tauschiibeing linked with improved performance of introgression lines under water-limiting conditions. We find that the most significant GWES signals associated with temperature annual range in the wild relative are linked with reduced canopy temperature in introgression lines and increased yield. ConclusionsOur results suggest that introgression of climate-adaptive alleles fromAe. tauschiihas the potential to improve wheat performance under water-limiting conditions, and that variants controlling physiological processes responsible for maintaining leaf temperature are likely among the targets of adaptive selection in a wild relative. Adaptive variation uncovered by GWES in wild relatives has the potential to improve climate resilience of crop varieties. 

Abstract Key message The first cytological characterization of the 2N v S segment in hexaploid wheat; complete de novo assembly and annotation of 2N v S segment; 2N v S frequency is increasing 2N v S and is associated with higher yield. Abstract The Aegilops ventricosa 2N v S translocation segment has been utilized in breeding disease-resistant wheat crops since the early 1990s. This segment is known to possess several important resistance genes against multiple wheat diseases including root knot nematode, stripe rust, leaf rust and stem rust. More recently, this segment has been associated with resistance to wheat blast, an emerging and devastating wheat disease in South America and Asia. To date, full characterization of the segment including its size, gene content and its association with grain yield is lacking. Here, we present a complete cytological and physical characterization of this agronomically important translocation in bread wheat. We de novo assembled the 2N v S segment in two wheat varieties, ‘Jagger’ and ‘CDC Stanley,’ and delineated the segment to be approximately 33 Mb. A total of 535 high-confidence genes were annotated within the 2N v S region, with > 10% belonging to the nucleotide-binding leucine-rich repeat (NLR) gene families. Identification of groups of NLR genes that are potentially N genome-specific and expressed in specific tissues can fast-track testing of candidate genes playing roles in various disease resistances. We also show the increasing frequency of 2N v S among spring and winter wheat breeding programs over two and a half decades, and the positive impact of 2N v S on wheat grain yield based on historical datasets. The significance of the 2N v S segment in wheat breeding due to resistance to multiple diseases and a positive impact on yield highlights the importance of understanding and characterizing the wheat pan-genome for better insights into molecular breeding for wheat improvement.