Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel

Frontiers in Plant Science
Caijin ChenAdam H Price

Abstract

Salinity is a major abiotic stress which inhibits rice production in coastal, arid and semi-aid areas in many countries, such as India and Bangladesh. Identification of salt tolerant cultivars, quantitative trait loci (QTLs) and genes is essential for breeding salt tolerant rice. The aus subpopulation of rice is considered to have originated predominantly from Bangladesh and India and have rich genetic diversity with wide variation in abiotic stress resistance. The objective of this study was to identify QTLs, and subsequently candidate genes using cultivars from the aus subpopulation and compare the results of two different seedling stage screening methods. Salt tolerance at the rice seedling stage was evaluated on 204 rice accessions from the Bengal and Assam Aus Panel (BAAP) grown in both hydroponics and soil under control and salt stress conditions. Ten salt related traits of stress symptoms, plant growth and the content of sodium and potassium were measured. Three cultivars, BRRI dhan 47, Goria, and T 1 showed more salt tolerance than the tolerant check Pokkali in both systems. Genome-wide association mapping was conducted on salt indices traits with 2 million SNPs using an efficient mixed model (EMMA) controlling populati...Continue Reading

References

Aug 6, 2000·The Plant Journal : for Cell and Molecular Biology·Y SaijoK Izui
Feb 14, 2002·Plant, Cell & Environment·R. Munns
Dec 1, 1996·Plant Physiology·FJM. MaathuisN. A. Walker
Sep 27, 2003·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·H X LinD Y Chao
Jan 18, 2005·Genetics·Amanda J GarrisSusan McCouch
May 3, 2005·Annual Review of Plant Biology·Nicolas BouchéHillel Fromm
Sep 13, 2005·Nature Genetics·Zhong-Hai RenHong-Xuan Lin
Mar 3, 2006·Journal of Experimental Botany·Rana MunnsAndré Läuchli
Jun 21, 2008·The New Phytologist·Timothy J Flowers, Timothy D Colmer
Nov 18, 2008·Annals of Botany·Nelson J M SaiboMaria Margarida Oliveira
Dec 17, 2009·The Biochemical Journal·Thomas A DeFalcoWayne A Snedden
Dec 30, 2009·Molecular Genetics and Genomics : MGG·Yujie FangLizhong Xiong
Oct 26, 2010·Nature Genetics·Xuehui HuangBin Han
Dec 27, 2011·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Lei TianChuanqing Sun
Apr 21, 2012·Briefings in Bioinformatics·Helga ThorvaldsdóttirJill P Mesirov
Nov 3, 2012·Plant Biotechnology Journal·Sónia NegrãoM Margarida Oliveira
May 1, 1990·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·A R YeoT J Flowers
May 1, 1987·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·J C Glaszmann
Apr 30, 2014·The Plant Journal : for Cell and Molecular Biology·Zhong Jie DingShao Jian Zheng
Oct 3, 2014·Nucleic Acids Research·Hu ZhaoWeibo Xie
Jan 30, 2015·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Vinod KumarTrilochan Mohapatra
Apr 25, 2017·Plant, Cell & Environment·Juan PatishtanFrans J M Maathuis
May 4, 2018·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
Oct 20, 2018·Frontiers in Plant Science·Yanru CuiYongli Zhou
Nov 22, 2019·Frontiers in Plant Science·Mohammad Umer Sharif ShohanZeba I Seraj

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Citations

May 5, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Caijin ChenGareth J Norton

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Methods Mentioned

BETA
genotyping
salt treatment
salt stress
Atomic Emission Spectroscopy
salt
PCA

Software Mentioned

EMMAX
factoextra
fastSTRUCTURE
Minitab
PLINK
RiceVarMap
R
LDheatmap
CLUMP
PIQUE ( Parallel Identification of EMMAX7

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