Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection.
Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection.
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DOI：
10.1155/2017/9272363
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发表时间：
2017
影响因子：
2.9
通讯作者：
Khanh TD
中科院分区：
文献类型：
--
作者：
Trinh H;Nguyen KT;Nguyen LV;Pham HQ;Huong CT;Xuan TD;Anh H;Caccamo M;Ayling S;Diep NT;Nguyen C;Trung KH;Khanh TD
下一代测序技术为全植物基因组的研究提供了许多应用机会。本研究对5个具有代表性的水稻地方品种（包括3个籼稻和2个粳稻）进行了序列测定和生物信息学分析。与日本晴参考基因组相比，总共6.884亿个100 bp配对末端读段产生了大约30倍的覆盖率。其中，少数读数被映射到染色体和细胞器基因组。在籼稻和粳稻品系中已经发现了超过280万个单核苷酸多态性（SNPs）和插入缺失（InDels）位点，这些位点对基因的多个转录本具有潜在的影响。SNP沙漠，连续SNP低的区域，被发现在染色体1，4，和5的所有基因组的水稻检查。基于每100个酶对的SNPs分布，构建了地方品种之间的系统发育关系。这是揭示越南水稻基因组的几个显著特征的第一步，并为进一步在水稻育种计划中进行标记辅助选择（MAS）提供重要的信息资源。
Next generation sequencing technologies have provided numerous opportunities for application in the study of whole plant genomes. In this study, we present the sequencing and bioinformatic analyses of five typical rice landraces including three indica and two japonica with potential blast resistance. A total of 688.4 million 100 bp paired-end reads have yielded approximately 30-fold coverage to compare with the Nipponbare reference genome. Among them, a small number of reads were mapped to both chromosomes and organellar genomes. Over two million and eight hundred thousand single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) in indica and japonica lines have been determined, which potentially have significant impacts on multiple transcripts of genes. SNP deserts, contiguous SNP-low regions, were found on chromosomes 1, 4, and 5 of all genomes of rice examined. Based on the distribution of SNPs per 100 kilobase pairs, the phylogenetic relationships among the landraces have been constructed. This is the first step towards revealing several salient features of rice genomes in Vietnam and providing significant information resources to further marker-assisted selection (MAS) in rice breeding programs.