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Acta Agron Sin ›› 2009, Vol. 35 ›› Issue (2): 255-261.doi: 10.3724/SP.J.1006.2009.00255


QTL Mapping and Interaction Analysis for 1000-Grain Weight and Percentage of Grains with Chalkiness in Rice

ZHOU Li-Jun1,JIANG Ling1,LIU Xi1,CHEN Hong1,CHEN Liang-Ming1,LIU Shi-Jia1,WAN Jian-Min1,2,*   

  1. 1State Key Laboratory of Crop Genetics and Germplasm enhancement/Jiangsu Plant Gene  Engineering Research Center, Nanjing Agricultural University, Nanjing 210095,China;2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081,China
  • Received:2008-07-31 Revised:2008-10-08 Online:2009-02-12 Published:2008-12-10
  • Contact: WAN Jian-Min


There is a close correlation between 1000-grian weight (TGW, an important yield factor) and percentage of grains with chalkiness (PGWC, an important rice quality index). In this study, a backcross inbred lines (BIL) population derived from a cross between Koshihikari (japonica) and Kasalath (indica) was used to detect correlations and among interactions QTL, epistatic and environment on TGW and PGWC. Correlation analysis showed that there was a significantly positive correlation between TGW and PGWC in the BIL population and the correlation coefficients were 0.42 and 0.35 (P<0.001) in 2005 and 2006, respectively. A total of eleven QTLs and eight epistatic interactions for TGW were detected in 2005 and 2006; of them, five QTLs were repeatedly detected in the two years, and five QTLs and seven epistatic interactions had significantly QE interaction. A total of six QTLs and nine epistatic interactions for PGWC were detected in 2005 and 2006; of them, three QTLs and four epistatic interactions had markedly QE interaction. Three main-effect QTLs simultaneously controlling TGW and PGWC were detected, and their alleles increasing TGW and PGWC were from the same parent; one epistatic interaction had similar effects on TGW and PGWC. Some main-effect QTLs, controlling TGW but not PGWC, such as qTGW-3c, qTGW-4a,and qTGW-6b, could be used for breeding. The strategy was discussed in using QTL mapping results for the marker-assisted selection breeding of TGW and PGWC.

Key words: Rice, 1000-grain weight (TGW), Percentage of grains with chalkiness(PGWC), QTL, epistatic interaction, QTLXenvironment interaction(QE)

[1]You A Q, Lu X G, Jin H J, Ren X, Liu K, Yang G C, Yang H Y, Zhu L L, He G C. Identification of quantitative trait loci across recombinant inbred lines and testcross populations for traits of agronomic importance in rice. Genetics, 2006, 172: 1287-1300
[2]Mei H W, Li Z K, Shu Q Y, Guo L B, Wang Y P, Yu X Q, Ying C S, Luo L J. Gene actions of QTL affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations. Theor Appl Genet, 2005, 110: 649-659
[3]Yang S-H(杨仕华), Cheng B-Y(程本义), Shen W-F(沈伟峰), Liao X-Y(廖西元). Progress and strategy of the improvement of indica rice varieties in the Yangtze Valley of China. Chin J Rice Sci (中国水稻科学), 2004, 18(2): 89-93 (in Chinese with English abstract)
[4]Min J(闵捷), Zhu Z-W(朱智伟), Xu L(许立), Mou R-X(牟仁祥). Studies on grain quality and high quality rate of japonica hybrid rice in China. Hybrid Rice (杂交水稻), 2007, 22(1): 67-70 (in Chinese with English abstract)
[5]Cheng F M, Zhong L J, Wang F, Zhang G P. Differences in cooking and eating properties between chalky and translucent parts in rice grains. Food Chem, 2005, 90: 39-46
[6]Del Rosario A R, Briones V P, Vidal A J, Juliano B O. Composi-tion and endosperm structure of developing and mature rice ker-nel. Cereal Chem, 1968, 45: 225-235
[7]Yamakawa H, Hirose T, Kuroda M, Yamaguchi T. Comprehen-sive expression profiling of rice grain filling-related genes under high temperature using DNA microarray. Plant Physiol, 2007, 144: 258-277
[8]Tan Y F, Xing Y Z, Li J X, Yu S B, Xu C G, Zhang Q F. Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid. Theor Appl Genet, 2000, 101: 823-829
[9]Kang H G, Park S H, Matsuoka M, An G H. White-core en-dosperm floury endosperm-4 in rice is generated by knockout mutations in the C4-type pyruvate orthophosphate dikinase gene (OsPPDKB). Plant J, 2005, 42: 901-911
[10]Fujita N, Yoshida M, Kondo T, Saito K, Utsumi Y, Tokunaga T, Nishi A, Satoh H, Park J H, Jane J L, Miyao A, Hirochika H, Nakamura Y. Characterization of SSIIIa-deficient mutants of rice: The function of SSIIIa and pleiotropic effects by SSIIIa defi-ciency in the rice endosperm. Plant Physiol, 2007, 144: 2009-2023
[11]Song X J, Huang W, Shi M, Zhu M Z, Lin H X. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet, 2007, 39: 623-630
[12]Rice Genome Resource Center (RGRC). Koshihikari/Kasalath Backcross Inbred Lines (BIL) 182 lines.2004.3.20, available at http://www.rgrc.dna.affrc.go.jp/ineKKBIL 182.htm1. 2002
[13]NSPRC (National Standard of People Republic of China). GB/T 17891-1999, High Quality Paddy. Beijing: Standards Press of China, 1999
[14]Wang D L, Zhu J, Li Z K, Paterson A H. Mapping QTL with epistatic effects and QTL environment interactions by mixed lin-ear model approaches. Theor Appl Genet, 1999, 99: 1255-1264
[15]Xing Y Z, Tan Y F, Hua J P, Sun X L, Xu C G, Zhang Q F. Characterization of the main effects, epistatic effects and their environmental interactions of QTL on the genetic basis of yield traits in rice. Theor Appl Genet, 2002, 105: 248-257
[16]Wan X Y, Wan J M, Weng J F, Jiang L, Bi J C, Wang C M, Zhai H Q. Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments. Theor Appl Genet, 2005, 110: 1334-1346
[17]Li Z F, Wan J M, Xia J F, Zhai H Q. Mapping quantitative trait loci underlying appearance quality of rice grains. Acta Genet Sin, 2003, 30: 251-259
[18]Zhuang J Y, Fan Y Y, Rao Z M, Wu J L, Xia Y W, Zheng K L. Analysis on additive effects and additive-by-additive epistatic ef-fects of QTLs for yield traits in a recombinant inbred line popula-tion of rice. Theor Appl Genet, 2002, 105: 1137-1145
[19]Gao Y M, Zhu J. Mapping QTLs with digenic epistasis under multiple environments and predicting heterosis based on QTL effects. Theor Appl Genet, 2007, 115: 325-333
[20]Septiningsih E M, Prasetiyono J, Lubis E, Tai T H, Tjubaryat T, Moeljopawiro S, McCouch S R. Identification of quantitative trait loci for yield and yield components in an advanced back-cross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet, 2003, 107: 1419-1432
[21]Hittalmani S, Huang N, Venuprasad B C R, Shashidhar H E, Zhuang J Y, Zheng K L, Liu G F, Wang G C, Sidhu J S, Srivan-taneeyakul S, Singh V P, Bagali P G, Prasanna H C, McLaren G, Khush G S. Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia. Theor Appl Genet, 2003, 107: 679-690
[22]Brondani C, Range P H N, Brondani R P V, Ferreira M E. QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa L.) using microsa-tellite markers. Theor Appl Genet, 2002, 104: 1192-1203
[23]Fan C C, Xing Y Z, Mao H L, Lu T T, Han B, Xu C G, Li X H, Zhang Q F. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a puta-tive transmembrane protein. Theor Appl Genet, 2006, 112: 1164-1171
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