Summary One of the major challenges for plant scientists is increasing wheat ( Triticum aestivum ) yield potential ( YP ). A significant bottleneck for increasing YP is achieving increased biomass through optimization of radiation use efficiency ( RUE ) along the crop cycle. Exotic material such as landraces and synthetic wheat has been incorporated into breeding programmes in an attempt to alleviate this; however, their contribution to YP is still unclear. To understand the genetic basis of biomass accumulation and RUE , we applied genome‐wide association study ( GWAS ) to a panel of 150 elite spring wheat genotypes including many landrace and synthetically derived lines. The panel was evaluated for 31 traits over 2 years under optimal growing conditions and genotyped using the 35K wheat breeders array. Marker‐trait association identified 94 SNP s significantly associated with yield, agronomic and phenology‐related traits along with RUE and final biomass ( BM _ PM ) at various growth stages that explained 7%–17% of phenotypic variation. Common SNP markers were identified for grain yield, BM _ PM and RUE on chromosomes 5A and 7A. Additionally, landrace and synthetic derivative lines showed higher thousand grain weight ( TGW ), BM _ PM and RUE but lower grain number ( GM 2) and harvest index ( HI ). Our work demonstrates the use of exotic material as a valuable resource to increase YP . It also provides markers for use in marker‐assisted breeding to systematically increase BM _ PM , RUE and TGW and avoid the TGW / GM 2 and BM _ PM / HI trade‐off. Thus, achieving greater genetic gains in elite germplasm while also highlighting genomic regions and candidate genes for further study.

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.

Non-random gene organization in eukaryotes plays a significant role in genome evolution. Here, we investigate the origin of a biosynthetic gene cluster for production of defence compounds in oat—the avenacin cluster. We elucidate the structure and organisation of this 12-gene cluster, characterise the last two missing pathway steps, and reconstitute the entire pathway in tobacco by transient expression. We show that the cluster has formed de novo since the divergence of oats in a subtelomeric region of the genome that lacks homology with other grasses, and that gene order is approximately colinear with the biosynthetic pathway. We speculate that the positioning of the late pathway genes furthest away from the telomere may mitigate against a ‘self-poisoning’ scenario in which toxic intermediates accumulate as a result of telomeric gene deletions. Our investigations reveal a striking example of adaptive evolution underpinned by remarkable genome plasticity.

Background Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations. Results We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat ( Triticum aestivum ). We observe that high-frequency crossover sites are shared between populations and that closely related parents lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We identify quantitative trait loci for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis. Conclusions This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage drag utilizing widespread gene conversions. Electronic supplementary material The online version of this article (10.1186/s13059-019-1675-6) contains supplementary material, which is available to authorized users.