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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 Additive gene action is assumed to underly quantitative traits, but the eventual poor performance of elite wheat lines as parents suggests that epistasis could be the underlying genetic architecture. Sign epistasis is characterized by alleles having either a beneficial or detrimental effect depending on the genetic background, which can result in elite lines that fail as parents in certain parental combinations. Hence, the objective of this study were to test the existence of sign epistasis and examine its consequences to wheat breeding. The presence of sign epistasis is expected to distort the allele frequency distribution between two interacting genes compared to neutral sites, creating strong linkage disequilibrium (LD). To test this hypothesis, analysis of interchromosomal LD in breeding families was performed and detected 19 regions in strong disequilibrium, whose allele frequency distribution matched the sign epistasis prediction and falsified the competing hypothesis of additive selection. To validate these candidate interactions while avoiding the biases of a circular analysis and the confounding effects of genetic drift, two independent sets of populations were analyzed. Genetic drift was attributed to creating the sign epistasis patterns observed in eleven interactions, but there was not sufficient evidence to reject the sign epistasis hypothesis in eight interactions. Sign epistasis may explain the poor performance of elite lines as parents, as crossing lines with complementary allelic combination re-establishes epistatic variance in the offspring. Reduction in the effective population size in certain crosses may also occur when unfavorable sign epistatic combinations are deleterious. The potential existence of di-genic and higher order epistatic interactions in elite germplasm can tremendously impact breeding strategies as managing epistasis becomes imperative for success. 

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. 

Abstract Rye ( Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye’s incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye–wheat introgressions.