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Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.)

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Twenty-seven QTLs were identified for rice seed vigor, in which 16 were novel QTLs. Fifteen elite parental combinations were designed for improving seed vigor in rice.

Abstract

Seed vigor is closely related to direct seeding in rice (Oryza sativa L.). Previous quantitative trait locus (QTL) studies for seed vigor were mainly derived from bi-parental segregating populations and no report from natural populations. In this study, association mapping for seed vigor was performed on a selected sample of 540 rice cultivars (419 from China and 121 from Vietnam). Population structure was estimated on the basis of 262 simple sequence repeat (SSR) markers. Seed vigor was evaluated by root length (RL), shoot length (SL) and shoot dry weight in 2011 and 2012. Abundant phenotypic and genetic diversities were found in the studied population. The population was divided into seven subpopulations, and the levels of linkage disequilibrium (LD) ranged from 10 to 80 cM. We identified 27 marker–trait associations involving 18 SSR markers for three traits. According to phenotypic effects for alleles of the detected QTLs, elite alleles were mined. These elite alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the elite alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design.

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Abbreviations

ANOVA:

Analysis of variance

FDR:

False discovery rate

GLM:

General linear model

H 2B :

Heritability in the broad sense

F IS :

F-statistics; individuals within subpopulations

F ST :

F-statistics; subpopulations within the total population

LD:

Linkage disequilibrium

MCMC:

Markov Chain Monte Carlo

PIC:

Polymorphic information content

PVE:

Proportion of phenotypic variance explained

QTL:

Quantitative trait locus

RL:

Root length

SDW:

Shoot dry weight

SL:

Shoot length

SSR:

Simple sequence repeat

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Acknowledgments

The authors are grateful to Dr. Linglong Liu (National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University) for critical review of the manuscript. Funding support was provided by a grant from the China national “863” program (2010AA101301), a grant from key program of Scientific Base Platform of Chinese Government (505005) and a grant from doctoral found of Educational Ministry (B0201100690).

Conflict of interest

No conflict of interest among authors and in the research work.

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Authors and Affiliations

  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

    Xiaojing Dang, Thu Giang Tran Thi, Guanshan Dong, Hui Wang, Wisdom Mawuli Edzesi & Delin Hong

  2. College of Agronomy, Hue University of Agriculture and Forestry, Hue University, 102 Phung Hung Street, Hue, Vietnam

    Thu Giang Tran Thi

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  1. Xiaojing Dang
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  2. Thu Giang Tran Thi
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Correspondence to Delin Hong.

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Dang, X., Thi, T.G.T., Dong, G. et al. Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.). Planta 239, 1309–1319 (2014). https://doi.org/10.1007/s00425-014-2060-z

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