Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.)

Han, Guohao; Liu, Shiyu; Jin, Yuli; Jia, Mengshu; Ma, Pengtao; Lv, Hong; Wang, Jing; An, Diaoguo

doi:10.1186/s12864-020-6624-y

Cited by 28 publications

(19 citation statements)

References 66 publications

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“…The Kompetitive allele-specific PCR (KASP) platform has been demonstrated to be a flexible, efficient and cost-effective system for genotyping of introgression lines using wild relative genome-specific SNPs (Bansal et al 2020;Grewal et al 2020b;Han et al 2020). However, hexaploid wheat's polyploid genome makes it complicated to develop codominant interspecific SNPs.…”

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

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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%

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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show abstract

“…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). The Kompetitive allele-specific polymerase chain reaction (KASP) platform has been demonstrated to be a flexible, efficient, and cost-effective system for genotyping of introgression lines using wild relative genome-specific SNPs (Bansal et al, 2020;Grewal et al, 2020b;Han et al, 2020). However, hexaploid wheat's polyploid genome makes it complicated to develop co-dominant interspecific SNPs.…”

Section: Core Ideasmentioning

confidence: 99%

“…The Kompetitive allele‐specific polymerase chain reaction (KASP) platform has been demonstrated to be a flexible, efficient, and cost‐effective system for genotyping of introgression lines using wild relative genome‐specific SNPs (Bansal et al., 2020; Grewal et al., 2020b; Han et al., 2020). However, hexaploid wheat's polyploid genome makes it complicated to develop co‐dominant interspecific SNPs.…”

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.

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“…SNPs have become the preferred markers for numerous genetics and genomics applications (Li et al 2019 ). In particular, the revolutionary advances in genome sequencing (Ryu et al 2018 ; Han et al 2020 ) have made the SNP-based genotyping technology an effective method for large-scale genotyping, genetic diversity analyses, and genetic map construction in many plant species (Li et al 2019 ). Kompetitive allele-specific PCR (KASP) is a novel and extensively used genotyping technology that enables bi-allelic scoring of SNPs (Han et al 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis and genetic diversity of Allium victorialis germplasms from the Changbai Mountains

Feng

Wang²,

Chen

et al. 2021

Mitochondrial DNA Part B

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The Changbai Mountains comprise one of the main distribution areas of A. victorialis in China, and this species is endangered owing to habitat changes and overexploitation. However, A. victorialis germplasms have not been systematically collected and studied. The aims of this study were to obtain some detailed genetic information, analyze the genetic diversity, and further promote the protection of A. victorialis germplasms from the Changbai Mountains. Transcriptomic analysis was performed with six A. victorialis samples collected from the Changbai Mountains. At least 146,759 genes for each sample were obtained after performing de novo assembly of the RNA-seq data, and at least 92% of these genes were found to have only one mRNA isoform. These sequences and their functional annotations provided a large-scale genetic resource of this species. Phylogenetic analysis showed that A. victorialis was genetically distant from some related species, e.g. Allium sativum , Allium fistulosum , and Allium cepa , but genetically close to Allium tuberosum . The two A. victorialis var. listera samples were phylogenetically separated from the other four samples, and these two samples should be regarded as Allium listera . In addition, two KASP markers for discriminating the Dongfeng samples from the other four A . victorialis samples were successfully developed. This study lays the foundation for future studies on the genetic diversity and evolution of Allium species, as well as for the conservation of A. victorialis germplasms from the Changbai Mountains and other populations of this species.

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Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.)

Cited by 28 publications

References 66 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

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

Transcriptome analysis and genetic diversity of Allium victorialis germplasms from the Changbai Mountains

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