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豇豆（Vigna unguiculata L. Walp.）基因SSR标记开发的从头转录组分析

De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development.

作者信息

Chen Honglin, Wang Lixia, Liu Xiaoyan, Hu Liangliang, Wang Suhua, Cheng Xuzhen

机构信息

The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

出版信息

BMC Genet. 2017 Jul 11;18(1):65. doi: 10.1186/s12863-017-0531-5.

DOI:10.1186/s12863-017-0531-5
PMID:28693419
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5504845/
Abstract

BACKGROUND

Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding of cowpea. The objectives of this study were to analyse the cowpea transcriptome and develop genic molecular markers for future genetic studies of this genus.

RESULTS

Approximately 54 million high-quality cDNA sequence reads were obtained from cowpea based on Illumina paired-end sequencing technology and were de novo assembled to generate 47,899 unigenes with an N50 length of 1534 bp. Sequence similarity analysis revealed 36,289 unigenes (75.8%) with significant similarity to known proteins in the non-redundant (Nr) protein database, 23,471 unigenes (49.0%) with BLAST hits in the Swiss-Prot database, and 20,654 unigenes (43.1%) with high similarity in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Further analysis identified 5560 simple sequence repeats (SSRs) as potential genic molecular markers. Validating a random set of 500 SSR markers yielded 54 polymorphic markers among 32 cowpea accessions.

CONCLUSIONS

This transcriptomic analysis of cowpea provided a valuable set of genomic data for characterizing genes with important agronomic traits in Vigna unguiculata and a new set of genic SSR markers for further genetic studies and breeding in cowpea and related Vigna species.

摘要

背景

豇豆[Vigna unguiculata (L.) Walp.]是热带和半干旱地区最重要的豆类作物之一。然而，可用于豇豆遗传研究和育种的基因组信息相对较少。本研究的目的是分析豇豆转录组并开发基因分子标记，以供该属未来的遗传研究使用。

结果

基于Illumina双末端测序技术从豇豆中获得了约5400万个高质量的cDNA序列读数，并进行了从头组装，生成了47899个单基因，N50长度为1534 bp。序列相似性分析显示，36289个单基因（75.8%）与非冗余（Nr）蛋白质数据库中的已知蛋白质具有显著相似性，23471个单基因（49.0%）在Swiss-Prot数据库中有BLAST匹配，20654个单基因（43.1%）在京都基因与基因组百科全书（KEGG）数据库中具有高度相似性。进一步分析确定了5560个简单序列重复（SSR）作为潜在的基因分子标记。对一组随机的500个SSR标记进行验证，在32份豇豆种质中产生了54个多态性标记。

结论

豇豆的转录组分析为鉴定豇豆中具有重要农艺性状的基因提供了有价值的基因组数据集，并为豇豆及相关豇豆属物种的进一步遗传研究和育种提供了一组新的基因SSR标记。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8a5a/5504845/fd6bbfa702b7/12863_2017_531_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8a5a/5504845/a1e3c06e6970/12863_2017_531_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8a5a/5504845/cb02601cdf44/12863_2017_531_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8a5a/5504845/d109dea18b11/12863_2017_531_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8a5a/5504845/fd6bbfa702b7/12863_2017_531_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8a5a/5504845/a1e3c06e6970/12863_2017_531_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8a5a/5504845/cb02601cdf44/12863_2017_531_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8a5a/5504845/d109dea18b11/12863_2017_531_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8a5a/5504845/fd6bbfa702b7/12863_2017_531_Fig4_HTML.jpg

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