Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula
Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula
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DOI：
10.1007/s11103-007-9282-4
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发表时间：
2008-05-01
影响因子：
5.1
通讯作者：
Echenique, Viviana
中科院分区：
文献类型：
--
作者：
Cervigni, Gerardo D. L.;Paniego, Norma;Echenique, Viviana
曲面草（施拉德）Nees是一种饲草，原产于非洲南部半干旱地区，主要通过假配子双孢子无融合繁殖。从4个cDNA文库中获得est序列，其中3个文库来自具有不同倍性水平和生殖方式的近等基因系的穗部，1个文库来自12日龄植物叶片。共聚集和组装了12295条高质量的est，得到8864个单基因，其中包括1490个contigs和7394个singletons，基因组覆盖率为22%。通过BLASTX分析，共有7029个（79.11%）unigenes与公共数据库中的序列进行了功能分类，而根据Gene Ontology的序列仅能分类37.80%。与谷物基因指数（GI）的序列比对显示50%的显著性命中。219例单例和35例contigs共检测到254个EST-SSRs。二基序和三基序的比例相似，分别为38.95%和40.16%。此外，从3 ~ 4个文库中生成的18个contigs中检测到190个snp和indel。本研究获得的ESTs和分子标记将为基因鉴定、遗传作图、品种鉴定、遗传多样性分析、表型作图和标记辅助选择等广泛应用提供宝贵资源。
Eragrostis curvula (Schrad.) Nees is a forage grass native to the semiarid regions of Southern Africa, which reproduces mainly by pseudogamous diplosporous apomixis. A collection of ESTs was generated from four cDNA libraries, three of them obtained from panicles of near-isogenic lines with different ploidy levels and reproductive modes, and one obtained from 12 days-old plant leaves. A total of 12,295 high-quality ESTs were clustered and assembled, rendering 8,864 unigenes, including 1,490 contigs and 7,394 singletons, with a genome coverage of 22%. A total of 7,029 (79.11%) unigenes were functionally categorized by BLASTX analysis against sequences deposited in public databases, but only 37.80% could be classified according to Gene Ontology. Sequence comparison against the cereals genes indexes (GI) revealed 50% significant hits. A total of 254 EST-SSRs were detected from 219 singletons and 35 from contigs. Di- and tri- motifs were similarly represented with percentages of 38.95 and 40.16%, respectively. In addition, 190 SNPs and Indels were detected in 18 contigs generated from 3 to 4 libraries. The ESTs and the molecular markers obtained in this study will provide valuable resources for a wide range of applications including gene identification, genetic mapping, cultivar identification, analysis of genetic diversity, phenotype mapping and marker assisted selection.