Authors
Juan Xiang, Zhuoling Zhong, Chengming Zhang, Min He, Kun Cai, Lanping Gu, Li Xu, Shilin Su, Yi Zou, Jie Li, Kehao Cui, Huimin Qiu, Bengang Xian, Shaohong Fu, Ling Chen, Xiaowei Liu
Published in
PloS one. Volume 21. Issue 8. Pages e0343756. Epub Aug 14, 2026.
Abstract
Cowpea (Vigna unguiculata (L.) Walp.) is a globally important legume crop. However, the scarcity of efficient molecular markers has hindered molecular breeding efforts and the protection of plant breeders' rights. In this study, we employed double-digest restriction-site associated DNA sequencing (ddRAD-seq) to characterize the genetic diversity of 19 cowpea accessions. A total of 791,621 SNPs were identified, of which 13,469 high-quality SNPs were retained after filtering. Population structure and phylogenetic analyses revealed that these accessions clustered into three distinct groups. To facilitate cost-effective and rapid genotyping, we developed a panel of KASP (Kompetitive Allele-Specific PCR) markers. Through rigorous screening for polymorphism and stability, we identified six core KASP markers located in exonic regions. These six markers alone were sufficient to discriminate all 19 accessions. Based on these core markers, we constructed a unique DNA fingerprinting profile and assigned specific QR codes for each accession. This study demonstrates that selecting core KASP markers from ddRAD-seq data is a powerful strategy for germplasm identification. The developed fingerprinting system provides a robust, low-cost tool for seed purity testing, variety authentication, and marker-assisted selection in cowpea breeding programs.
PMID:
42599890
Bibliographic data and abstract were imported from PubMed on 15 Aug 2026.
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