甘蓝SNP标记开发及主要品种的DNA指纹图谱构建

doi:10.3864/j.issn.0578-1752.2018.14.014

Abstract

Abstract: 【Objective】The main cabbage varieties in production were collected and DNA fingerprinting of cabbage varieties were constructed with SNP markers to provide reference for variety distinctness and authenticity identification. 【Method】SNP loci were obtained by aligning resequencing data of 50 cabbage inbred lines to the reference genome of cabbage (02-12). The SNP loci were screened with two criteria: (i) high polymorphism information content (PIC), (ii) evenly distribution on each chromosome. And then KASP primers were designed based on these loci. The KASP platform was used to genotype the fifty-nine cabbage varieties. According to the result of genotyping, core primers were selected with high PIC value, no loci missing and even distribution on each chromosome. These core primers were used to establish SNP fingerprinting of fifty-nine cabbage varieties. Fifteen varieties randomly selected from the fifty-nine main varieties and five new unreleased combinations were mixed together to construct an artificial population. The artificially mixed population was used to validate the core primers in the variety distinctness and authenticity identification. 【Result】Two million five hundred and forty thousand SNP loci were obtained by aligning the resequencing data of fifty cabbage inbred lines to the reference genome of cabbage. Five hundred SNP markers were selected with high PIC value, low missing rates and even distribution on each chromosome, with 55.6 loci per chromosome. 442 of them were successfully transformed into KASP markers, occupying 88.4% of all the 500 SNP markers. The genotyping results showed that twenty-five pairs of KASP primers were unsuccessfully genotyped in more than five materials and were removed from further analysis. The PIC values among the 417 primers ranged from 0.12 to 0.38. The average PIC value was 0.36, showing moderate polymorphism. The number of varieties with heterozygous marker ratio greater than 30% was 57, occupying 88.4% of all the main varieties. The heterozygous marker ratio of ‘Yusheng Zaoshu Niuxin’ was the highest, which reaches 67.8%. Finally, fifty core markers were selected to construct DNA fingerprinting of 59 main varieties. PIC values of 50 core makers ranged from 0.35 to 0.38, and the average PIC was 0.36. The result of cluster analysis of core SNP markers indicated that the genetic similarity coefficient of 59 varieties varied from 0.43 to 0.98. The core SNP markers were validated by artificially mixed population and the results showed that SNP fingerprinting constructed with core markers could be used to identify the variety distinctness and authenticity effectively. 【Conclusion】Two million five hundred and forty thousand SNP loci were obtained by aligning resequencing data of cabbage inbred lines. Fifty pairs of core makers were selected and used to establish DNA fingerprint database of 59 cabbage varieties, and the core SNP markers were validated by artificially mixed population.

Key words: cabbage, SNP marker, main varieties, fingerprinting

LI ZhiYuan, YU HaiLong, FANG ZhiYuan, YANG LiMei, LIU YuMei, ZHUANG Mu, Lü HongHao, ZHANG YangYong. Development of SNP Markers in Cabbage and Construction of DNA Fingerprinting of Main Varieties[J].Scientia Agricultura Sinica, 2018, 51(14): 2771-2787.

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