关键词: 芸薹属, 分子标记, 数据库, 在线批量引物设计, KASP

Abstract:

As a direct characterization of genetic polymorphisms at DNA level，molecular markers have important application value in vegetable genetic research. Aiming at the problems of complex operation and low efficiency of primer design in existing molecular marker analysis tools，in this study，VEGMarkerDB，a molecular marker database for Brassica vegetables，was developed based on SNP and InDel markers with integrated data storage and high-throughput primers design. The system adopts B/S architecture，builds back-end services based on Django framework，and combines MySQL database management system. Resequencing data and VCF variation files of cabbage（Brassica rapa），cabbage（B. oleracea），rapeseed（B. napus）and mustard（B. juncea）were integrated. The database provides mutation site retrieval services，which can be queried according to the location of chromosomes to realize the rapid location of molecular marker information. This system provides real-time feedback on candidate primer parameters（e.g.，Tm value，GC content，amplicon length）via an interactive visual interface，while automatically generating standardized experimental reports. Experimental validation using laboratory materials demonstrated a KASP primer design success rate exceeding 95%. The system’s technical innovations include：(1) Establishment of an integrated management platform for multispecies molecular marker resources in Brassica vegetables；(2) Implementation of web-based parallel primer design architecture；(3) Development of a closed-loop optimization mechanism integrating experimental validation with algorithmic refinement. As a modular technical platform accessible at VEGMarkerDB（vegmarker.top/），this system not only advances molecular breeding research in vegetable crops but also demonstrates extensibility to other agricultural systems through its adaptable framework.

Key words: Brassica, molecular marker, database, high-throughput on-line primer design, KASP