QTL Analysis for Seven Quality Traits of RIL Population in Japonica Rice Based on Three Genetic Statistical Models

LIU Qiang-ming1, JIANG Jian-hua1, 2, NIU Fu-an1, HE Ying-jun1, HONG De-lin1

doi:10.1016/S1672-6308(13)60105-5

Rice Science >

2013 , Vol. 20 >Issue 1: 31 - 38

DOI: https://doi.org/10.1016/S1672-6308(13)60105-5

Research Paper

QTL Analysis for Seven Quality Traits of RIL Population in Japonica Rice Based on Three Genetic Statistical Models

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1State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; 2Institute of Crops, Anhui Academy of Agricultural Sciences, Hefei 230031, China

Online published: 2013-01-06

Supported by

This work was supported by the National High Technology Research and Development Program of China (Grant No. 2010AA101301); the Program of Introducing International Advanced Agricultural Science and Technology in China (Grant No. 2006-G8[4]-31-1) and the Program of Science-Technology Basis and Conditional Platform in China (Grant No. 505005).

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Abstract

QTL mapping for seven quality traits was conducted by using 254 recombinant inbred lines (RIL) derived from a japonica-japonica rice cross of Xiushui 79/C Bao. The seven traits investigated were grain length (GL), grain length to width ratio (LWR), chalk grain rate (CGR), chalkiness degree (CD), gelatinization temperature (GT), amylose content (AC) and gel consistency (GC) of head rice. Three mapping methods employed were composite interval mapping in QTLMapper 2.0 software based on mixed linear model (MCIM), inclusive composite interval mapping in QTL IciMapping 3.0 software based on stepwise regression linear model (ICIM) and multiple interval mapping with regression forward selection in Windows QTL Cartographer 2.5 based on multiple regression analysis (MIMR). Results showed that five QTLs with additive effect (A-QTLs) were detected by all the three methods simultaneously, two by two methods simultaneously, and 23 by only one method. Five A-QTLs were detected by MCIM, nine by ICIM and 28 by MIMR. The contribution rates of single A-QTL ranged from 0.89% to 38.07%. All the QTLs with epistatic effect (E-QTLs) detected by MIMR were not detected by the other two methods. Fourteen pairs of E-QTLs were detected by both MCIM and ICIM, and 142 pairs of E-QTLs were detected by only one method. Twenty-five pairs of E-QTLs were detected by MCIM, 141 pairs by ICIM and four pairs by MIMR. The contribution rates of single pair of E-QTL were from 2.60% to 23.78%. In the Xiu-Bao RIL population, epistatic effect played a major role in the variation of GL and CD, and additive effect was the dominant in the variation of LWR, while both epistatic effect and additive effect had equal importance in the variation of CGR, AC, GT and GC. QTLs detected by two or more methods simultaneously were highly reliable, and could be applied to improve the quality traits in japonica hybrid rice.

Key words： quantitative trait locus; quality trait; genetic statistical model; japonica rice

Cite this article

LIU Qiang-ming1, JIANG Jian-hua1, 2, NIU Fu-an1, HE Ying-jun1, HONG De-lin1 . QTL Analysis for Seven Quality Traits of RIL Population in Japonica Rice Based on Three Genetic Statistical Models[J]. Rice Science, 2013 , 20(1) : 31 -38 . DOI: 10.1016/S1672-6308(13)60105-5

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