Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage.
Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage.
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DOI：
10.1186/s12870-015-0424-6
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发表时间：
2015-02-03
影响因子：
5.3
通讯作者：
Yang TJ
中科院分区：
文献类型：
--
作者：
Lee J;Izzah NK;Jayakodi M;Perumal S;Joh HJ;Lee HJ;Lee SC;Park JY;Yang KW;Nou IS;Seo J;Yoo J;Suh Y;Ahn K;Lee JH;Choi GJ;Yu Y;Kim H;Yang TJ
黑腐病是甘蓝的一种毁灭性细菌性病害，严重影响甘蓝的产量和品质。为了检测甘蓝抗黑腐病的数量性状位点（QTL），我们对两个甘蓝亲本进行了全基因组重测序，并利用最近发表的B进行了全基因组SNP鉴定。甘蓝基因组序列作为参考。从每个亲本系产生约11.5Gb的测序数据。参考基因组引导的定位和SNP调用揭示了两个甘蓝品系之间的674，521个SNP，平均每662.5 bp一个SNP。在来自候选SNP的167个dCAPS标记中，117个（70.1%）被验证为显示亲本系之间多态性的真实SNP。然后，我们通过添加103个标记（包括87个基于SNP的dCAPS标记）来提高先前遗传图谱的分辨率。新图谱由368个标记组成，覆盖范围为1467.3cM，标记间距平均为3.88cM。利用F2：3后代进行了3次独立接种试验，对作图群体的黑腐病抗性进行了评价，确定了1个主效QTL和3个次效QTL。我们报告了成功利用全基因组重测序进行大规模SNP鉴定和开发用于遗传图谱构建的分子标记。此外，我们确定了新的QTL的黑腐病抗性。该高密度遗传图谱的构建将促进B其它重要农艺性状的QTL分析和分子标记辅助育种。甘蓝。本文的在线版本（doi：10.1186/s12870-015-0424-6）包含补充材料，可供授权用户使用。
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. The online version of this article (doi:10.1186/s12870-015-0424-6) contains supplementary material, which is available to authorized users.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
5.4
作者：
Luis Iniguez-Luy, Federico;Lukens, Lewis;Osborn, Thomas C.
通讯作者：
Osborn, Thomas C.
DOI：
10.3329/ijns.v1i1.8591
发表时间：
2011-01-01
期刊：
International Journal of Natural Sciences
影响因子：
--
作者：
Doullah, M. A. U.;Mohsin, G. M.;Okazaki, K.
通讯作者：
Okazaki, K.
影响因子：
1.8
作者：
Jensen, BD;Massomo, SMS;Andersen, SB
通讯作者：
Andersen, SB
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
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