Genome-wide introgression from a bread wheat × Lophopyrum elongatum amphiploid into wheat

Xu, Jiale; Wang, Le; Deal, Karin R.; Zhu, Tingting; Ramasamy, Ramesh; Luo, Ming‐Cheng; Malvick, Julia; You, Frank M.; McGuire, Patrick E.; Dvořák, Jan

doi:10.1007/s00122-020-03544-w

Cited by 7 publications

(7 citation statements)

References 60 publications

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“…The wild relatives of wheat, however, have a vast resource of untapped genetic variation that could be used to enrich and diversify the wheat genome. Recent studies have demonstrated the dramatic improvement in wheat-wild relative introgressions achieved through homoeologous recombination and genomics-based marker technologies (Qi et al 2007;Tiwari et al 2014;King et al 2017;Grewal et al 2018b;Cseh et al 2019b;Xu et al 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Even though these genotyping arrays can be ultrahigh-throughput and efficient, these SNPs cannot distinguish between homozygous and heterozygous individuals which limits their widespread use in crop breeding. Recently, whole genome and transcriptome sequencing have been used to develop genome-specific SNPs for Lophopyrum elongatum and tools such as high-resolution melting (HRM) markers and the Sequenom MassARRAY SNP genotyping platform, utilising these SNPs, were deployed for detecting L. elongatum introgressions in a wheat background (Lou et al 2017;Xu et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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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: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

View full text Add to dashboard Cite

show abstract

“…Work with the AgCS amphiploid and previously produced aneuploids derived from it suggested that the short arm of wheatgrass chromosome 4E from L. elongatum contributed to the postsexual cycle regrowth that characterizes perenniality in the caespitose wheatgrasses (Lammer et al, 2004). More recent work with AgCS, these aneuploids, and nine introgression lines derived from a wheat‐ L. elongatum introgression population (Xu et al, 2020), implicated a gene (designated Pscr1 ) mapped into a short, 31‐ to 36‐Mb distal region in chromosome arm 4ES (Abbasi et al, 2020). However, the full regulation of caespitose perenniality is complex, this same study also implicates regions on other wheatgrass chromosomes besides 4E that increase postsexual cycle regrowth.…”

Section: Discussionmentioning

confidence: 99%

Perennial growth and salinity tolerance in wheat × wheatgrass amphiploids varying in the ratio of wheat to wheatgrass genomes

et al. 2020

Self Cite

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“…The wild relatives of wheat, however, have a vast resource of untapped genetic variation that could be used to enrich and diversify the wheat genome. Recent studies have demonstrated the dramatic improvement in wheat–wild relative introgressions achieved through homoeologous recombination and genomics‐based marker technologies (Qi et al., 2007; Tiwari et al., 2014; King et al., 2017; Grewal et al., 2018b; Cseh et al., 2019b; Xu et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Even though these genotyping arrays can be ultra‐high‐throughput and efficient, these SNPs cannot distinguish between homozygous and heterozygous individuals which limits their widespread use in crop breeding. Recently, whole genome and transcriptome sequencing have been used to develop genome‐specific SNPs for Lophopyrum elongatum (Host) Á. Löve and tools such as high‐resolution melting markers and the Sequenom MassARRAY SNP genotyping platform, utilizing these SNPs, were deployed for detecting L. elongatum introgressions in a wheat background (Lou et al., 2017; Xu et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines

et al. 2022

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Many wild‐relative species are being used in prebreeding programs to increase the genetic diversity of wheat (Triticum aestivum L.). Genotyping tools such as single nucleotide polymorphism (SNP)‐based arrays and molecular markers have been widely used to characterize wheat–wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP‐based Kompetitive allele‐specific polymerase chain reaction (KASP) markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome‐ and polymerase chain reaction (PCR)‐amplicon‐based sequencing of the wild species. But chromosome‐specific KASP 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 (Boiss.) Eig and development of a de novo SNP discovery pipeline that generated ∼38,000 SNPs in unique 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 diagnostic for Am. muticum in a wheat background. 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.

show abstract

Genome-wide introgression from a bread wheat × Lophopyrum elongatum amphiploid into wheat

Cited by 7 publications

References 60 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

Perennial growth and salinity tolerance in wheat × wheatgrass amphiploids varying in the ratio of wheat to wheatgrass genomes

Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines

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