High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L.
High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L.
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DOI：
10.1186/1471-2164-14-120
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发表时间：
2013-02-22
期刊：
影响因子：
4.4
通讯作者：
Pauquet J
中科院分区：
文献类型：
--
作者：
Delourme R;Falentin C;Fomeju BF;Boillot M;Lassalle G;André I;Duarte J;Gauthier V;Lucante N;Marty A;Pauchon M;Pichon JP;Ribière N;Trotoux G;Blanchard P;Rivière N;Martinant JP;Pauquet J
利用在不同遗传背景下具有多态性的SNP标记构建的高密度遗传图谱对于研究农艺性状的遗传以及基因组的组织和进化是非常有用的。同时对分离群体和品种收集物进行高密度SNP基因分型。获得该物种的高密度遗传图谱，并研究其连锁不平衡模式。通过对4个分离的双单倍体群体进行高通量SNP基因分型，构建了一张完整的油菜遗传图谱。在四个单独的图谱之间观察到非常高水平的共线性，并且大量标记（>59%）是两个以上图谱共有的。该图谱包括5764个SNP标记和1603个PCR标记。总遗传长度为2250 cM，整合图谱包含3.27个标记（2.56 SNP）/cM的密度。这些映射的SNP标记的基因分型油菜收藏品允许多态性水平和连锁不平衡（LD）进行研究，在不同的收藏品（冬季与春季，不同的种子质量类型）和沿着连锁群。总体而言，多态性水平较高，LD在春季比“00”冬油菜类型衰减得更快，但这被证明是有很大的差异沿着连锁群。我们的研究为进一步利用连锁或关联作图进行遗传研究、标记辅助育种以及甘蓝型油菜序列组装和基因组组织分析提供了宝贵的资源。
High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution. Simultaneous dense SNP genotyping of segregating populations and variety collections was applied to oilseed rape (Brassica napus L.) to obtain a high density genetic map for this species and to study the linkage disequilibrium pattern. We developed an integrated genetic map for oilseed rape by high throughput SNP genotyping of four segregating doubled haploid populations. A very high level of collinearity was observed between the four individual maps and a large number of markers (>59%) was common to more than two maps. The precise integrated map comprises 5764 SNP and 1603 PCR markers. With a total genetic length of 2250 cM, the integrated map contains a density of 3.27 markers (2.56 SNP) per cM. Genotyping of these mapped SNP markers in oilseed rape collections allowed polymorphism level and linkage disequilibrium (LD) to be studied across the different collections (winter vs spring, different seed quality types) and along the linkage groups. Overall, polymorphism level was higher and LD decayed faster in spring than in “00” winter oilseed rape types but this was shown to vary greatly along the linkage groups. Our study provides a valuable resource for further genetic studies using linkage or association mapping, for marker assisted breeding and for Brassica napus sequence assembly and genome organization analyses.
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影响因子：
2.9
作者：
Ching A;Caldwell KS;Jung M;Dolan M;Smith OS;Tingey S;Morgante M;Rafalski AJ
通讯作者：
Rafalski AJ
影响因子：
5.4
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Stich, Benjamin
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4.5
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影响因子：
3.1
作者：
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通讯作者：
Ganal, M. W.
影响因子：
2.6
作者：
Excoffier, Laurent;Laval, Guillaume;Schneider, Stefan
通讯作者：
Schneider, Stefan