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

Authors: COOMBES, BENEDICT - Earlham Institute; Fellers, John; GREWAL, SURBHI - University Of Nottingham; RUDHOLME-PILCHER, RACHEL - Earlham Institute; HUBBART-EDWARDS, STELLA - University Of Nottingham; YANG, CAI-YUN - University Of Nottingham; JOYNSON, RYAN - Earlham Institute; KING, IAN - University Of Nottingham; KING, JULIE - University Of Nottingham; HALL, ANTHONY - Earlham Institute

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/15/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary: Wheat is an important source of carbohydrate nutrition in the world. As the human population is growing, the need for increased crop production is becoming paramount. Geneticists are looking to wheat wild relatives to find new genes to help improve yield and nutritional quality. Many wild relatives can be crossed to wheat, but it is difficult and deleterious traits can be associated with the wild relative's introduced chromosome fragments. Until recently, these fragments could only be characterized by chromosome staining and microscopy and were sometimes difficult to see. In this work, we used high throughput genome sequencing to find the chromosome fragments and determine the sizes introgressed into wheat. Wheat wild relative Amblyopyrum muticum was crossed into bread wheat and 17 of the lines were evaluated. The genome of Am. muticum was sequenced and used to show that many more Am. muticum fragments were present in wheat lines than what could be seen by staining. RNA sequencing showed that the Am. muticum genes were expressing lower or were shut off in comparison to wheat. This project showed the utility of using next generation sequencing in determining the amount of wild relative DNA transferred to wheat and how those genes are regulated in the plant. The approach has low costs and can be integrated into a plant breeding program.

Technical Abstract: 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 is an important component of overcoming this low variation. Synthetically derived introgression lines provide the raw material for the incorporation of alien variation into breeding programmes but a lack of genomic resolution and understanding of genomic impact limits their optimal utilisation. Whole genome sequencing data from 17 hexaploid wheat/Ambylopyrum muticum introgression lines and their parent lines has enabled the first high resolution genomic analysis of wheat introgression lines. We have uncovered new segments and precisely pinpointed the size and position of introgressed segments, including segment overlaps that explain differential resistance phenotypes previously reported between lines. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of novel Am. muticum genes that are candidates for resistance within these segments. 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 introgressed genes tend to be downregulated or silenced when compared to the wheat orthologue they replace. This shifts the expression balance of triads towards suppression of the introgressed region, with little overall compensation in the expression of the remaining homoeologous copies. A high-resolution genomic analysis of a set of wheat introgression lines has uncovered new segments, defined introgression boundaries to a high-resolution and identified novel candidate genes for rust resistances. Large-scale structural disruption and analysis of gene expression provides important contributions to untangling the genomic impact of introgression breeding. Our outlined approach will provide an affordable way for breeders to better characterise introgression lines and more effectively deploy wild relative variation.