Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes

BMC Plant Biology

Research Article

Vinh Nang Do¹  Nhung Thi Phuong Phung¹  Nhung Kim Ta²  Chung Duc Mai³  Pierre Mournet⁴  Julien Frouin⁴  Gaëtan Droc⁴  Brigitte Courtois⁴  Stefan Jouannic⁵  Pascal Gantet⁶  Loan Thi Lê⁷ 

[1] Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, Hanoi, Vietnam;Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, Hanoi, Vietnam;IRD, UMR-DIADE, LMI RICE, Hanoi, Vietnam;Université Montpellier 2, UMR DIADE, 34095, Montpellier, France;Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, Hanoi, Vietnam;University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam;Cirad, UMR-AGAP, 34398, Montpellier, France;IRD, UMR-DIADE, LMI RICE, Hanoi, Vietnam;IRD, UMR-DIADE, LMI RICE, Hanoi, Vietnam;Université Montpellier 2, UMR DIADE, 34095, Montpellier, France;University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam;Plant Resource Center, Hanoi, Vietnam;

关键词: DArT markers;    SNP;    Genetic diversity;    Linkage disequilibrium;    Rice;    Vietnam;   

DOI  :  10.1186/s12870-014-0371-7

 received in 2014-07-21, accepted in 2014-12-08,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundThe development of genome-wide association studies (GWAS) in crops has made it possible to mine interesting alleles hidden in gene bank resources. However, only a small fraction of the rice genetic diversity of any given country has been exploited in the studies with worldwide sampling conducted to date. This study presents the development of a panel of rice varieties from Vietnam for GWAS purposes.ResultsThe panel, initially composed of 270 accessions, was characterized for simple agronomic traits (maturity class, grain shape and endosperm type) commonly used to classify rice varieties. We first genotyped the panel using Diversity Array Technology (DArT) markers. We analyzed the panel structure, identified two subpanels corresponding to the indica and japonica sub-species and selected 182 non-redundant accessions. However, the number of usable DArT markers (241 for an initial library of 6444 clones) was too small for GWAS purposes. Therefore, we characterized the panel of 182 accessions with 25,971 markers using genotyping by sequencing. The same indica and japonica subpanels were identified. The indica subpanel was further divided into six populations (I1 to I6) using a model-based approach. The japonica subpanel, which was more highly differentiated, was divided into 4 populations (J1 to J4), including a temperate type (J2). Passport data and phenotypic traits were used to characterize these populations. Some populations were exclusively composed of glutinous types (I3 and J2). Some of the upland rice varieties appeared to belong to indica populations, which is uncommon in this region of the world. Linkage disequilibrium decayed faster in the indica subpanel (r2 below 0.2 at 101 kb) than in the japonica subpanel (r2 below 0.2 at 425 kb), likely because of the strongest differentiation of the japonica subpanel. A matrix adapted for GWAS was built by eliminating the markers with a minor allele frequency below 5% and imputing the missing data. This matrix contained 21,814 markers. A GWAS was conducted on time to flowering to prove the utility of this panel.ConclusionsThis publicly available panel constitutes an important resource giving access to original allelic diversity. It will be used for GWAS on root and panicle traits.

【 授权许可】

Unknown   
© Phung et al.; licensee BioMed Central. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.