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

Hien Trinh,Can Thu Huong,Tran Dang Xuan,Khuat Huu Trung,Lam Van Nguyen,Nguyen Thuy Diep,Mario Caccamo,Huy Quang Pham,La Hoang Anh,Tran Dang Khanh,Cuong Nguyen,Khoa Truong Nguyen,Sarah Ayling

doi:10.1155/2017/9272363

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.

Highlights

Whole-genome sequencing (WGS) has revealed genetic information and genome structure and facilitated the identification of gene function of different plant species including some major crops such as rice, wheat, tomato, and soybean [1,2,3,4,5]
The whole genomes of three Vietnamese indica and two japonica rice landraces were resequenced and produced 688.4 million 100 bp paired-end reads in total
We have sequenced five Vietnamese rice genomes consisting of three indica and two japonica landraces

Summary

Introduction

Whole-genome sequencing (WGS) has revealed genetic information and genome structure and facilitated the identification of gene function of different plant species including some major crops such as rice, wheat, tomato, and soybean [1,2,3,4,5]. Combining NGS with bioinformatics is a powerful approach to detect DNA polymorphisms for quantitative trait loci (QTLs) analyses, marker-assisted selection, genome-wide association studies (GWAS), and linkage disequilibrium analysis in plants [8,9,10,11]. Rice (Oryza sativa L.) is a staple crop and provides daily food for over half of the world’s population. It contains two major groups, indica and japonica, which diverged more than one million years ago [13]. In 2002, the first draft sequence of the indica genome was established by shotgun sequencing and homologous genes were predicted by comparison

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