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 39 publications

(32 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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“…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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“…Neither EGA Blanco nor Millewa contained known alien translocated segments in their genomes determined by PCR analysis for species-specific repetitive sequences (data not shown), therefore, small scale translocations between genomes of EGA Blanco and Millewa with respect to the reference genome are likely to reflect intrachromosomal rearrangements during domestication of these Australian cultivars. Cytogenetic analysis [ 34 , 35 ] and high-density SNP arrays identified significant large and small translocations, deletions and inversions in different cultivars and breeding lines when compared with the reference genome sequence [ 32 , 35 ], and postulated that chromosome rearrangements and complex breeding histories provided lineage divergence for selective advantages in diverse environments. In contrast, the alignment of markers between genetic and physical maps for the region on 5BL did not detect large-scale chromosomal rearrangements between genomes of EGA Blanco, Millewa and the Chinese Spring reference sequence, indicating that some regions of genomes may harbour smaller structural variants or more conserved regions required for selective adaptation of modern varieties to broader environments.…”

Section: Discussionmentioning

confidence: 99%

“…Rearrangements included an assortment of PAV, INDEL and SNP. There is increasing evidence that intrachromosomal variation between wheat varieties are common and gene sequences in breeding lines may not be represented in Chinese Spring [ 31 , 32 , 35 , 38 ], highlighting the limitations of using a single reference sequence to obtain a complete functional gene complement across breeding lines and cultivars. Therefore, it is possible that additional gene candidates within the QTL on 1BS and 5BL other than those identified in this study were represented in EGA Blanco and Millewa but not in Chinese Spring.…”

Section: Discussionmentioning

confidence: 99%

Genes Associated with Foliar Resistance to Septoria Nodorum Blotch of Hexaploid Wheat (Triticum aestivum L.)

Walker

Francki

2021

IJMS

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The genetic control of host response to the fungal necrotrophic disease Septoria nodorum blotch (SNB) in bread wheat is complex, involving many minor genes. Quantitative trait loci (QTL) controlling SNB response were previously identified on chromosomes 1BS and 5BL. The aim of this study, therefore, was to align and compare the genetic map representing QTL interval on 1BS and 5BS with the reference sequence of wheat and identify resistance genes (R-genes) associated with SNB response. Alignment of QTL intervals identified significant genome rearrangements on 1BS between parents of the DH population EGA Blanco, Millewa and the reference sequence of Chinese Spring with subtle rearrangements on 5BL. Nevertheless, annotation of genomic intervals in the reference sequence were able to identify and map 13 and 12 R-genes on 1BS and 5BL, respectively. R-genes discriminated co-located QTL on 1BS into two distinct but linked loci. NRC1a and TFIID mapped in one QTL on 1BS whereas RGA and Snn1 mapped in the linked locus and all were associated with SNB resistance but in one environment only. Similarly, Tsn1 and WK35 were mapped in one QTL on 5BL with NETWORKED 1A and RGA genes mapped in the linked QTL interval. This study provided new insights on possible biochemical, cellular and molecular mechanisms responding to SNB infection in different environments and also addressed limitations of using the reference sequence to identify the full complement of functional R-genes in modern varieties.

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

Cited by 39 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

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

Genes Associated with Foliar Resistance to Septoria Nodorum Blotch of Hexaploid Wheat (Triticum aestivum L.)

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