Development of a core set of KASP markers for assaying genetic diversity in Brassica rapa subsp. chinensis Makino

Single‐nucleotide polymorphisms (SNPs) are rapid, economical and reliable genotyping tools. Non‐heading Chinese cabbage (Brassica rapa L. subsp. chinensis Makino) is now an economically important vegetable crop worldwide. In this study, 1,167 SNPs were evaluated for 7polymorphism among 70 representa...

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Bibliographic Details
Published in:Plant breeding 2019-06, Vol.138 (3), p.309-324
Main Authors: Li, Peirong, Su, Tongbing, Wang, Huiping, Zhao, Xiuyun, Wang, Weihong, Yu, Yangjun, Zhang, Deshuang, Wen, Changlong, Yu, Shuancang, Zhang, Fenglan, Snowdon, Rod
Format: Article
Language:English
Subjects:
Brassica
Brassica oleracea
Brassica rapa
Breeding
Chinese cabbage
Cost analysis
Cultivars
Genetic diversity
Genotyping
Germplasm
Inbreeding
KASP assays
Markers
molecular markers
non‐heading Chinese cabbage
Principal components analysis
Single-nucleotide polymorphism
single‐nucleotide polymorphism (SNP)
Subgroups
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Summary:Single‐nucleotide polymorphisms (SNPs) are rapid, economical and reliable genotyping tools. Non‐heading Chinese cabbage (Brassica rapa L. subsp. chinensis Makino) is now an economically important vegetable crop worldwide. In this study, 1,167 SNPs were evaluated for 7polymorphism among 70 representative non‐heading Chinese cabbage inbred lines using a Kompetitive Allele Specific PCR (KASP) genotyping assay. On the basis of identified polymorphisms and the results of a principal component analysis, we selected 50 core SNPs that were balanced sufficiently to provide adequate information for genetic identification. The core SNPs were used for construction of a neighbour‐joining dendrogram that separated the 70 inbred lines into four main groups and several subgroups corresponding to Caixin, Heiyebaicai, Huangxinwu, Naibaicai, Taitsai, Pak‐choi, and Wutatsai. This categorization was superior to that achieved using a dataset of 479 polymorphic SNPs. To confirm the utility of the core SNP markers in genetic identification, we tested their stability and resolution using 162 commercial hybrid cultivars. The SNPs, which represent a cost‐effective, accurate marker set for germplasm analysis and cultivar identification, are suitable for molecular marker‐assisted breeding in non‐heading Chinese cabbage.
ISSN:0179-9541
1439-0523
DOI:10.1111/pbr.12686