Whole‐genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines

Abstract

Summary Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat's wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that novel introgressed genes are rarely expressed and those that directly replace a wheat orthologue have a tendency towards downregulation, with no discernible compensation in the expression of homoeologous copies. This study explores the genomic impact of introgression breeding and provides a schematic that can be followed to characterize introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilization of introgression pre‐breeding material in wheat breeding programmes.

Analysis of a diverse wheat germplasm panel reveals a highly diverse introgression landscape and provides evidence for inter-homoeolog chromosomal recombination

“…Reciprocal translocations were also described in rice (Wicker et al 2015), synthetic allopolyploid wheat (Zhang et al 2020) and more recently in newly produced Am. muticum /hexaploid wheat introgression lines (Coombes et al 2023). In the case of Ritmo we propose that chromosome 1D is ‘regular’, whereas the distal end of chromosome arm 1AS was replaced by the first 41 Mb of chromosome 1D, which would therefore occur twice in the genome of Ritmo (Fig.…”

“…This bivalent behaviour is enforced by several genes among which the Ph1 locus is the most important (Rey et al 2017). It was suggested that inter-homoeologous recombination depends on the suppression of Ph1 (Coombes et al 2023). Our data suggest that despite this tight genetic control, inter-homoeolog recombination can occur in hexaploid wheat.…”

“…Genetic recombination between non-homologous chromosomes of wheat is suppressed mainly by the Ph1 locus (Griffiths et al 2006). Therefore, the Ph1 locus is either removed before introgression breeding, or the cross is made with a species not containing the Ph1 locus, such as Ambylopyrum muticum (King et al 2017(King et al , 2019Coombes et al 2023). After a successful cross, the resulting offspring is subsequently backcrossed while selecting the offspring for the trait of interest.…”

Exotic alleles contribute to heat tolerance in wheat under field conditions

“…tauschii reference accession AL8/78 26 and 5 additional accessions that represent 5 different clades 27 , 4 Secale cereale accessions 67 , Secale. vavilovii 67 , Thinopyrum ponticum 68 , and T. aestivum cultivars Weebil 68 , Norin61 68 and Pavon76 69 were mapped to RefSeq v1.0 52 , filtered and SNP called as described for the genotyping above and in 25 . Homozygous SNPs were retained if they had between 10 and 60 reads supporting the alternative allele and an allele frequency > = 0.8.…”

“…Paired-end whole-genome sequencing data for the Ae. tauschii reference accession AL8/78 26 69 were mapped to RefSeq v1.0 52 , filtered and SNP called as described for the genotyping above and in 25 . Homozygous SNPs were retained if they had between 10 and 60 reads supporting the alternative allele and an allele frequency > = 0.8.…”