A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs
A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs
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DOI：
10.1073/pnas.0905886106
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发表时间：
2009-10-27
影响因子：
11.1
通讯作者：
Close, Timothy J.
中科院分区：
文献类型：
--
作者：
Muchero, Wellington;Diop, Ndeye N.;Close, Timothy J.
共识遗传连锁图谱为分子标记辅助选择中的数量性状座位识别、图位克隆、遗传多样性评估、关联作图和应用育种提供了一个基因组框架。在基因组资源有限的“孤儿作物”中，如豌豆[Vigna unguulata(L.)(2n=2x=22)，在遗传图谱中使用转录本衍生的SNPs为自动化基因分型和基于共性分析的基因组结构估计提供了机会。在这里，我们报告了一种高通量EST衍生的豌豆SNP分析方法的建立和验证，它在建立共识图谱和确定参考基因组的共性方面的应用。从17个文库的183,118个EST序列中挖掘出约10,000个高置信度SNP，构建了Illumina 1,536-SNP GoldenGate基因分型阵列，并应用于来自6个作图群体的741个重组自交系。大约90%的SNPs在技术上是成功的，提供了1375个可靠的标记。其中928个标记被整合到一个长达680 cM、11个连锁群、平均标记距离为0.73 cM的遗传图谱中。将该遗传图谱与参考豆科植物大豆(Glyine Max)和紫花苜蓿(Medicago Truncatula)进行比较，发现了广泛的宏观同步性，分别涵盖了豌豆图谱的85%和82%。与较简单的二倍体豌豆相比，大豆基因组复制区域明显。与拟南芥的比较显示，广泛的基因组重排和一些保守的微结合。这些结果支持了豌豆和大豆之间的进化接近，并确定了豆科植物中基于同步性的功能基因组学研究的区域。
Consensus genetic linkage maps provide a genomic framework for quantitative trait loci identification, map-based cloning, assessment of genetic diversity, association mapping, and applied breeding in marker-assisted selection schemes. Among "orphan crops'' with limited genomic resources such as cowpea [Vigna unguiculata (L.) Walp.] (2n = 2x = 22), the use of transcript-derived SNPs in genetic maps provides opportunities for automated genotyping and estimation of genome structure based on synteny analysis. Here, we report the development and validation of a high-throughput EST-derived SNP assay for cowpea, its application in consensus map building, and determination of synteny to reference genomes. SNP mining from 183,118 ESTs sequenced from 17 cDNA libraries yielded approximate to 10,000 high-confidence SNPs from which an Illumina 1,536-SNP GoldenGate genotyping array was developed and applied to 741 recombinant inbred lines from six mapping populations. Approximately 90% of the SNPs were technically successful, providing 1,375 dependable markers. Of these, 928 were incorporated into a consensus genetic map spanning 680 cM with 11 linkage groups and an average marker distance of 0.73 cM. Comparison of this cowpea genetic map to reference legumes, soybean (Glycine max) and Medicago truncatula, revealed extensive macrosynteny encompassing 85 and 82%, respectively, of the cowpea map. Regions of soybean genome duplication were evident relative to the simpler diploid cowpea. Comparison with Arabidopsis revealed extensive genomic rearrangement with some conserved microsynteny. These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes.