Time-course association mapping of the grain-filling rate in rice (Oryza sativa L.)

PloS One
Erbao LiuDelin Hong

Abstract

Detecting quantity trait locus (QTLs) and elite alleles that are associated with grain-filling rate (GFR) in rice is essential for promoting the utilization of hybrid japonica rice and improving rice yield. Ninety-five varieties including 58 landraces and 37 elite varieties from the core germplasm collection were genotyped with 263 simple sequence repeat (SSR) markers. The GFR of the 95 varieties was evaluated at five stages, 7, 14, 21, 28 and 35 days after flowering (DAF) both in 2011 and 2012. We found abundant phenotypic and genetic diversity in the studied population. A population structure analysis identified seven subpopulations. A linkage disequilibrium (LD) analysis indicated that the levels of LD ranged from 60.3 cM to 84.8 cM and artificial selection had enhanced the LD. A time-course association analysis detected 31 marker-GFR associations involving 24 SSR markers located on chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 11 and 12 of rice at five stages. The elite alleles for high GFR at each stage were detected. Fifteen excellent parental combinations were predicted, and the best parental combination 'Nannongjing62401×Laolaihong' could theoretically increase 4.086 mg grain(-1) d(-1) at the five stages. Our results demonstrate ...Continue Reading

References

Jun 1, 1992·Plant Molecular Biology·R J Okagaki
Jan 1, 1983·Journal of Molecular Evolution·M NeiY Tateno
Sep 13, 1996·Science·N Risch, K Merikangas
Feb 1, 1996·Bioscience, Biotechnology, and Biochemistry·J W HuangJ C Su
May 26, 1999·Proceedings of the National Academy of Sciences of the United States of America·K G Cassman
Jun 12, 1999·American Journal of Human Genetics·J K Pritchard, N A Rosenberg
Mar 3, 2001·Current Opinion in Plant Biology·M Yano
Jun 21, 2001·Proceedings of the National Academy of Sciences of the United States of America·Y TakahashiM Yano
Sep 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·D L RemingtonE S Buckler
Oct 3, 2002·Annual Review of Genetics·B S Weir, W G Hill
Feb 25, 2003·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Susan R McCouchLincoln Stein
Feb 25, 2003·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Susan R McCouchLincoln Stein
Sep 25, 2003·Annual Review of Plant Biology·Sherry A Flint-GarciaEdward S Buckler
Nov 19, 2003·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·K FujinoM Yano
Jan 18, 2005·Genetics·Amanda J GarrisSusan McCouch
Feb 12, 2005·Bioinformatics·Kejun Liu, Spencer V Muse
Jun 29, 2005·Journal of Experimental Botany·Toshiyuki TakaiTakeshi Horie
Oct 12, 2005·Plant Molecular Biology·Gurdev S Khush
Feb 3, 2006·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Chuchuan FanQifa Zhang
Dec 1, 2006·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Michael J ThomsonSusan R McCouch
Jun 26, 2007·Bioinformatics·Peter J BradburyEdward S Buckler
Jun 27, 2007·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·L Q WangQifa Zhang
Sep 12, 2008·Molecular Ecology Notes·Daniel FalushJonathan K Pritchard
Dec 5, 2009·Journal of Experimental Botany·Jianchang Yang, Jianhua Zhang
Dec 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·Zhixi TianJiayang Li
Mar 12, 2010·Nature·Wayne C Koff
Apr 7, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Liang JinJinsong Bao
Jun 26, 2012·Nature Genetics·Shaokui WangXiangdong Fu
Jan 1, 1971·Annales de génétique et de sélection animale·W Hill
Dec 14, 2012·Proceedings of the National Academy of Sciences of the United States of America·Xiaojun ZhangHongsheng Zhang
Dec 1, 1982·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·S S VirmaniG S Khush
Nov 8, 2014·Proceedings of the National Academy of Sciences of the United States of America·He GaoJianmin Wan

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Citations

Dec 10, 2015·Frontiers in Plant Science·Krishna S V JagadishNese Sreenivasulu
Aug 14, 2015·Plant Biotechnology Journal·Yang Jae KangSuk-Ha Lee
Sep 2, 2016·Frontiers in Plant Science·Peng ZhangHanhua Tong

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Methods Mentioned

BETA
dissection
PCR

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STRUCTURE
PowerMarker
Excel
TASSEL
Arlequin

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