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Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection.


ABSTRACT: 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.

SUBMITTER: Trinh H 

PROVIDER: S-EPMC5318636 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection.

Trinh Hien H   Nguyen Khoa Truong KT   Nguyen Lam Van LV   Pham Huy Quang HQ   Huong Can Thu CT   Xuan Tran Dang TD   Anh La Hoang H   Caccamo Mario M   Ayling Sarah S   Diep Nguyen Thuy NT   Nguyen Cuong C   Trung Khuat Huu KH   Khanh Tran Dang TD  

International journal of genomics 20170207


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 <i>indica</i> and two <i>japonica</i> 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 m  ...[more]

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