The role of gene flow and chromosomal instability in shaping the bread wheat genome

Przewieslik-Allen, Alexandra M.; Wilkinson, Paul; Burridge, Amanda J.; Winfield, Mark; Dai, Xiaoyang; Beaumont, Mark A.; King, Julie; Yang, Caiyun; Griffiths, Simon; Wingen, Luzie U.; Horsnell, Richard; Bentley, Alison R.; Shewry, Peter R.; Barker, G. L.; Edwards, Keith J.

doi:10.1038/s41477-020-00845-2

Cited by 44 publications

(41 citation statements)

References 33 publications

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“…2b. This is expected given that gene density on wheat chromosomes decreases towards centromeric regions (Appels et al 2018;Brinton et al 2020;Walkowiak et al 2020;Przewieslik-Allen et al 2021).…”

Section: Snp Discoverymentioning

confidence: 87%

A novel approach to develop wheat chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in doubled haploid introgression lines

Grewal

Coombes

Joynson

et al. 2021

Preprint

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Many wild relative species are being used in pre-breeding programmes to increase the genetic diversity of wheat. Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterise wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based KASP markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and PCR-amplicon-based sequencing of the wild species. But chromosome-specific KASPs assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum and development of a SNP discovery pipeline that generated ~38,000 SNPs in single-copy wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as functional. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.

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Section: Snp Discoverymentioning

confidence: 87%

A novel approach to develop wheat chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in doubled haploid introgression lines

Grewal

Coombes

Joynson

et al. 2021

Preprint

Self Cite

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“…The release of high-throughput sequencing data enables genome-wide identification and analysis of NLR proteins [13,14] as well species-wide inventories of these proteins [8,15]. Release of the wheat reference genome (IWGSC RefSeq v1.0) [16] and mass resequencing data [17][18][19][20] have allowed us to identify the genome-wide repertoire of NLRs in wheat, determine their diversity in wheat relatives, and recover the diverse NLR gene pool through breeding and improvement of disease resistance in wheat.…”

Section: Introductionmentioning

confidence: 99%

Dynamic Diversity of NLR Genes in Triticum and Mining of Promising NLR Alleles for Disease Resistance

Cheng

2021

CIMB

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Bread wheat is an essential crop with the second-highest global production after maize. Currently, wheat diseases are a serious threat to wheat production. Therefore, efficient breeding for disease resistance is extremely urgent in modern wheat. Here, we identified 2012 NLR genes from hexaploid wheat, and Ks values of paired syntenic NLRs showed a significant peak at 3.1–6.3 MYA, which exactly coincided with the first hybridization event between A and B genome lineages at ~5.5 MYA. We provided a landscape of dynamic diversity of NLRs from Triticum and Aegilops and found that NLR genes have higher diversity in wild progenitors and relatives. Further, most NLRs had opposite diversity patterns between genic and 2 Kb-promoter regions, which might respectively link sub/neofunctionalization and loss of duplicated NLR genes. Additionally, we identified an alien introgression of chromosome 4A in tetraploid emmer wheat, which was similar to that in hexaploid wheat. Transcriptome data from four experiments of wheat disease resistance helped to profile the expression pattern of NLR genes and identified promising NLRs involved in broad-spectrum disease resistance. Our study provided insights into the diversity evolution of NLR genes and identified beneficial NLRs to deploy into modern wheat in future wheat disease-resistance breeding.

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“…To accelerate wheat improvement through breeding, haplotype mapping is frequently used for investigating genetic pedigrees and to identify blocks of linked alleles that are likely to be inherited together in genetic diversity panels as well as to identify genomic regions that contain novel sequence segments derived from other wheat genotypes and / or acquired through wider introgression breeding (Przewieslik‐Allen et al ., 2021 ). Here, we analysed the homozygous SNPs in the promoters and 5′UTRs of 908 gene homoeologues (contributing to different traits) across the 95 Triticum sp.…”

Section: Resultsmentioning

confidence: 99%

Exploring the diversity of promoter and 5′UTR sequences in ancestral, historic and modern wheat

Hammond-Kosack

King

Kanyuka

et al. 2021

Plant Biotechnology Journal

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A data set of promoter and 5′UTR sequences of homoeo‐alleles of 459 wheat genes that contribute to agriculturally important traits in 95 ancestral and commercial wheat cultivars is presented here. The high‐stringency myBaits technology used made individual capture of homoeo‐allele promoters possible, which is reported here for the first time. Promoters of most genes are remarkably conserved across the 83 hexaploid cultivars used with <7 haplotypes per promoter and 21% being identical to the reference Chinese Spring. InDels and many high‐confidence SNPs are located within predicted plant transcription factor binding sites, potentially changing gene expression. Most haplotypes found in the Watkins landraces and a few haplotypes found in Triticum monococcum, germplasms hitherto not thought to have been used in modern wheat breeding, are already found in many commercial hexaploid wheats. The full data set which is useful for genomic and gene function studies and wheat breeding is available at https://rrescloud.rothamsted.ac.uk/index.php/s/DMCFDu5iAGTl50u/authenticate.

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The role of gene flow and chromosomal instability in shaping the bread wheat genome

Cited by 44 publications

References 33 publications

A novel approach to develop wheat chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in doubled haploid introgression lines

A novel approach to develop wheat chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in doubled haploid introgression lines

Dynamic Diversity of NLR Genes in Triticum and Mining of Promising NLR Alleles for Disease Resistance

Exploring the diversity of promoter and 5′UTR sequences in ancestral, historic and modern wheat

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