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Designing a mini-core collection effectively representing 3004 diverse rice accessions

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Title Designing a mini-core collection effectively representing 3004 diverse rice accessions
 
Creator Kumar, Angad
Kumar, Shivendra
Singh, Kajol B.M.
Prasad, Manoj
Thakur, Jitendra K.
 
Subject rice
mini-core
SNPs
GWAS
3KRG
agronomic trait
 
Description Accepted date: April 21, 2020
Genetic diversity provides the foundation for plant breeding and genetic research. Over 3000 rice genomes
were recently sequenced as part of the 3K Rice Genome (3KRG) Project. We added four additional Indian
rice accessions to create a panel of 3004 accessions. However, such a large collection of germplasm is
difficult to preserve and evaluate. The construction of core and mini-core collections is an efficient method
for the management of genetic resources. In this study, we developed a mini-core comprising 520 accessions that captured most of the SNPs and represented all of the phenotypes and geographic regions from
the original panel. The mini-core was validated using different statistical analyses and contained representatives from all major rice groups, including japonica, indica, aus/boro, and aromatic/basmati. Genomewide association analyses of the mini-core panel efficiently reproduced the marker–trait associations identified in the original panel. Haplotype analysis validated the utility of the mini-core panel. In the current era
with many ongoing large-scale sequencing projects, such a strategy for mini-core design should be useful
in many crops. The rice mini-core collection developed in this study would be valuable for agronomic trait
evaluation and useful for rice improvement via marker-assisted molecular breeding.
This study was financially supported by the grants BT/AB/NIPGR/SEED
BIOLOGY/2012 and BT/BI/04/069/2006 for the establishment of Distributed Information Sub-Centre from the Department of Biotechnology, Government of India.Author Contributions
A.K. performed all the analyses and contributed to the writing; S.K.
contributed to the analyses and wrote the initial draft with contributions
from all the authors; K.B.M.S. and M.P. provided technical assistance;
J.K.T. conceived and supervised the project, complemented the writing,
and secured funding for the project. A.K. acknowledges the University Grant Commission, Government of India and NIPGR for the Research Fellowships. S.K. acknowledges a National Postdoctoral Fellowship from the Science and Engineering
Research Board, Department of Science and Technology, Government
of India and a Short-Term Research Fellowship from NIPGR. K.B.M.S. acknowledges the Council of Scientific and Industrial Research, Government of India for the Junior Research Fellowship. The authors are grateful
to the DBT-eLibrary Consortium for providing access to literature. No conflict of interest declared.
 
Date 2020-06-26T06:19:01Z
2020-06-26T06:19:01Z
2020
 
Type Article
 
Identifier Plant Communications, 1: 100049
2590-3462
https://doi.org/10.1016/j.xplc.2020.100049
https://www.sciencedirect.com/science/article/pii/S2590346220300328
http://223.31.159.10:8080/jspui/handle/123456789/1071
 
Language en_US
 
Format application/pdf
 
Publisher Elsevier B.V.