Lee Jonghoon, Izzah Nur Kholilatul, Jayakodi Murukarthick, Perumal Sampath, Joh Ho Jun, Lee Hyeon Ju, Lee Sang-Choon, Park Jee Young, Yang Ki-Woung, Nou Il-Sup, Seo Joodeok, Yoo Jaeheung, Suh Youngdeok, Ahn Kyounggu, Lee Ji Hyun, Choi Gyung Ja, Yu Yeisoo, Kim Heebal, Yang Tae-Jin
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
Indonesian Research Institute for Industrial and Beverage Crops (IRIIBC), Pakuwon, Sukabumi, Indonesia.
BMC Plant Biol. 2015 Feb 3;15:32. doi: 10.1186/s12870-015-0424-6.
Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference.
Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F2:3 progenies and identified one major QTL and three minor QTLs.
We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.
黑腐病是一种具有破坏性的细菌性病害，会导致甘蓝型油菜大幅减产并降低品质。为了检测黑腐病抗性的数量性状位点（QTL），我们对两个甘蓝亲本系进行了全基因组重测序，并以最近发表的甘蓝型油菜基因组序列为参考进行全基因组单核苷酸多态性（SNP）鉴定。
每个亲本系产生了约11.5 Gb的测序数据。参考基因组引导的图谱构建和SNP检测揭示了两个甘蓝系之间有674,521个SNP，平均每662.5 bp有一个SNP。在从候选SNP衍生的167个dCAPS标记中，117个（70.1%）被验证为真正的SNP，在亲本系之间表现出多态性。然后，我们通过添加103个标记（包括87个基于SNP的dCAPS标记）提高了先前遗传图谱的分辨率。新图谱由368个标记组成，覆盖1467.3 cM，相邻标记之间的平均间隔为3.88 cM。我们使用F2:3后代在三次独立接种试验中评估了作图群体的黑腐病抗性，并鉴定出一个主效QTL和三个微效QTL。
我们报告了全基因组重测序在大规模SNP鉴定和遗传图谱构建分子标记开发中的成功应用。此外，我们鉴定了新的黑腐病抗性QTL。高密度遗传图谱将促进甘蓝型油菜其他重要农艺性状的QTL分析和标记辅助育种。
