Insights on SNP types, detection methods and their utilization in Brassica species: Recent progress and future perspectives

• Published in: Journal of biotechnology 2020-12, Vol.324, p.11-20
• Main Authors: Yang, Su, Gill, Rafaqat Ali, Zaman, Qamar U., Ulhassan, Zaid, Zhou, Weijun
• Format: Article
• Language: English
• Subjects: Association genetics; Brassica species; Gene sequencing; QTL mapping; SNP
• ISSN: 0168-1656; 1873-4863
• DOI: 10.1016/j.jbiotec.2020.09.018

•SNP plays a critical role in the study of forward genetics.•Brassica genus contains important oil crops, vegetables and medicinal plants.•Release of reference genomes and progress in SNP detection methods speed up the research progress in Brassica species.•SNP-GWAS helps to find the gene targeting phenotypic traits related to disease resistance, plant architecture, flowering time and seed yield etc. The genus Brassica, family Brassicaceae (Cruciferae), comprises many important species of oil crops, vegetables and medicinal plants including B. rapa, B. oleracea, B. nigra, B. napus, B. juncea, B. carinata. Genomic researches in Brassica species is constrained by polyploidization, mainly due to its complicated genomic structure. However, rapid development of methods for detecting single nucleotide polymorphisms (SNP), such as next generation sequencing and SNP microarray, has accelerated release of reference Brassica species genomes as well as discovery of large numbers and genome-wide SNPs, thus intensifying forward genetics in this genus. In this review, we summarize biological characteristics, classification and various methods for detecting SNPs, focusing on high-throughput techniques. Moreover, we describe the pivotal roles of SNPs in genetic diversity, linkage map construction and QTL mapping, comparative genomics, linkage disequilibrium and genome-wide association studies. These insights are expected to deepen our understanding and guide further advancements in Brassica species research.