title: 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 threeindicaand twojaponicawith 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) inindicaandjaponicalines 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.
authors.affiliation: Laboratory of Bioinformatics, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam.
authors.forename: Hien
authors.initials: H
authors.lastname: Trinh
authors.affiliation: Department of Genetic Engineering, Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Km2 Pham Van Dong, Tuliem, Hanoi, Vietnam.
authors.forename: Khoa Truong
authors.initials: KT
authors.lastname: Nguyen
authors.affiliation: Laboratory of Bioinformatics, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam.
authors.forename: Lam Van
authors.initials: LV
authors.lastname: Nguyen
authors.affiliation: Laboratory of Bioinformatics, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam.
authors.forename: Huy Quang
authors.initials: HQ
authors.lastname: Pham
authors.affiliation: Graduate School for International Development and Cooperation, Hiroshima University, Hiroshima 739-8529, Japan.
authors.forename: Can Thu
authors.initials: CT
authors.lastname: Huong
authors.affiliation: Graduate School for International Development and Cooperation, Hiroshima University, Hiroshima 739-8529, Japan.
authors.forename: Tran Dang
authors.initials: TD
authors.lastname: Xuan
authors.affiliation: Graduate School for International Development and Cooperation, Hiroshima University, Hiroshima 739-8529, Japan.
authors.forename: La Hoang
authors.initials: H
authors.lastname: Anh
authors.affiliation: Genetics and Breeding, National Institute of Agricultural Botany, Cambridge, UK.
authors.forename: Mario
authors.initials: M
authors.lastname: Caccamo
authors.affiliation: Genetics and Breeding, National Institute of Agricultural Botany, Cambridge, UK.
authors.forename: Sarah
authors.initials: S
authors.lastname: Ayling
authors.affiliation: Department of Genetic Engineering, Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Km2 Pham Van Dong, Tuliem, Hanoi, Vietnam.
authors.forename: Nguyen Thuy
authors.initials: NT
authors.lastname: Diep
authors.affiliation: Laboratory of Bioinformatics, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam.
authors.forename: Cuong
authors.identifier: 0000-0002-1745-248X
authors.initials: C
authors.lastname: Nguyen
authors.affiliation: Department of Genetic Engineering, Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Km2 Pham Van Dong, Tuliem, Hanoi, Vietnam.
authors.forename: Khuat Huu
authors.initials: KH
authors.lastname: Trung
authors.affiliation: Department of Genetic Engineering, Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Km2 Pham Van Dong, Tuliem, Hanoi, Vietnam.
authors.forename: Tran Dang
authors.identifier: 0000-0003-4426-7121
authors.initials: TD
authors.lastname: Khanh