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Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection
Joint Authors
Xuan, Tran Dang
Trinh, Hien
Nguyen, Khoa Truong
Nguyen, Lam Van
Pham, Huy Quang
Huong, Can Thu
Anh, La Hoang
Caccamo, Mario
Ayling, Sarah
Diep, Nguyen Thuy
Nguyen, Cuong
Trung, Khuat Huu
Khanh, Tran Dang
Source
International Journal of Genomics
Issue
Vol. 2017, Issue 2017 (31 Dec. 2017), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2017-02-07
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Trinh, Hien& Nguyen, Khoa Truong& Nguyen, Lam Van& Pham, Huy Quang& Huong, Can Thu& Xuan, Tran Dang…[et al.]. 2017. Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection. International Journal of Genomics،Vol. 2017, no. 2017, pp.1-11.
https://search.emarefa.net/detail/BIM-1167273
Modern Language Association (MLA)
Trinh, Hien…[et al.]. Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection. International Journal of Genomics No. 2017 (2017), pp.1-11.
https://search.emarefa.net/detail/BIM-1167273
American Medical Association (AMA)
Trinh, Hien& Nguyen, Khoa Truong& Nguyen, Lam Van& Pham, Huy Quang& Huong, Can Thu& Xuan, Tran Dang…[et al.]. Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection. International Journal of Genomics. 2017. Vol. 2017, no. 2017, pp.1-11.
https://search.emarefa.net/detail/BIM-1167273
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1167273