Construction of SSR Linkage Map and Analysis of QTLs for Rolled Leaf in Japonica Rice

doi:10.1016/S1672-6308(08)60101-8

Abstract

Abstract: Genetic analysis of rolled leaf is important to rice ideotype breeding. To detect loci controlling rolled leaf of japonica restorer lines, SSR marker genotypes and phenotypes of flag leaf rolling index (LRI) were investigated in Xiushui 79 (P1, a japonica rice variety), C Bao (P2, a japonica restorer line) and 254 recombinant inbred lines derived from the cross between P1 and P2 , and in two environments. A genetic map of this cross was constructed, QTLs for LRI were detected and their interactions with environments were analyzed. Among 818 pairs of SSR primers, 90 primers showed polymorphism between P1 and P2, and 12 markers showed highly significant correlation with LRI in both environments based on single marker regression analysis. The genetic map containing 74 information loci has a total distance of 744.6 cM, with an average of 10.1 cM between two adjacent loci. Three QTLs (qRL-1, qRL-7 and qRL-8-1) were detected with two softwares: WinQTLCart 2.5 and QTLNetwork2.0. qRL-8-1 was a new locus, accounting for 15.5% and 12.8% of phenotypic variations in the two environments, respectively. The phenotypic variation explained by additive effect was 6.6%. No interaction was found between qRL-8-1 genotype and environments.

Key words: japonica rice, restorer line, leaf rolling index, quantitative trait locus, genotype and environment interaction

GUO Yuan, CHENG Bao-shan, HONG De-lin. Construction of SSR Linkage Map and Analysis of QTLs for Rolled Leaf in Japonica Rice[J]. RICE SCIENCE, 2010, 17(1): 28-34 .

References

1 Chen Z X, Pan X B, Hu J. Relationship between rolled-leaf and ideal plant type of rice (Oryza sativa L.). Jiangsu Agric Res, 2001, 22(4): 88–91. (in Chinese with English abstract)
2 Lang Y Z, Zhang Z J, Gu X Y, Yang J C, Zhu Q S. Physiological and ecological effects of crimpy leaf character in rice (Oryza sativa L.): I. Leaf orientation, canopy structure and light distribution. Acta Agron Sin, 2004, 30(8): 739–744. (in Chinese with English abstract)
3 Yuan L P. Super high yield breeding of hybrid rice. Hybrid Rice, 1997, 12(6): 1–6. (in Chinese with English abstract)
4 GRAMENE. GRAMENE Database. [2008-12-31]. http://www. gramene.org/rice_mutant/; accession NOS.GR: 0060764 - GR: 0060769.
5 Li S G, Ma Y Q, He P, Li H Y, Chen Y, Zhou K D, Zhu L H. Genetic analysis and mapping the flag leaf roll in rice (Oryza sativa L.). J Sichuan Agric Univ, 1998, 16(4): 391–393. (in Chinese with English abstract)
6 Shao Y J, Chen Z X, Zhang Y F, Chen E H, Qi D C, Miao J, Pan X B. One major QTL mapping and physical map construction for rolled leaf in rice. Acta Genet Sin, 2005, 32(5): 501–506. (in Chinese with English abstract)
7 Shao Y J, Pan C H, Chen Z X, Zuo S M, Zhang Y F, Pan X B. Fine mapping of incomplete recessive gene for leaf rolling in rice (Oryza sativa L.). Chinese Sci Bull, 2005, 50(19): 2107– 2113.
8 Yan C J, Yan S, Zhang Z Q, Liang G H, Lu J F, Gu M H. Genetic analysis and mapping gene for a rice novel mutant (rl9(t)) with rolling leaf character. Chinese Sci Bull, 2006, 51(1): 63–69.
9 Yan S, Yan C J, Zeng H X, Yang Y C, Fang Y W, Tian C Y, Sun Y W, Cheng Z K, Gu M H. ROLLED LEAF 9, encoding a GARP protein, regulates the leaf abaxial cell fate in rice. Plant Mol Biol, 2008, 68(3): 239–250.
10 Luo Z K, Yang Z L, Zhong B Q, Lin Y F, Xie R, Zhao F M, Ling Y H, He G H. Genetic analysis and fine mapping of a dynamic rolled leaf gene, RL10(t), in rice (Oryza sativa L.). Genome, 2007, 50: 811–817.
11 Shi Z Y, Wang J, Wan X S, Shen G Z, Wang X Q, Zhang J L. Over-expression of rice OsAG07 gene induces upward curling of the leaf blade that enhanced erect-leaf habit. Planta, 2007, 226: 99–108.
12 Liu J B, Hong D L. Genetic analysis on panicle angle and number of spikelets per panicle in japonica rice (Oryza sativa L.). Chinese J Rice Sci, 2005, 19(3): 223–230. (in Chinese with English abstract)
13 Chen X G, Liu J B, Hong D L. Genetic analysis on panicle angle and number of spikelets per panicle by using six generations of three crosses derived from erect × curve panicles in japonica rice (Oryza sativa L.). Acta Agron Sin, 2006, 32(8): 1143–1150. (in Chinese with English abstract)
14 Guo Y, Wan Z B, Chen X G, Hong D L. Genetic analysis on number of primary and secondary branches per panicle in japonica rice (Oryza sativa L.). J Nanjing Agric Univ, 2008, 31(3): 8–12. (in Chinese with English abstract)
15 Temnykh S, Park W D, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho Y G, Ishii T, McCouch S R. Mapping and genome organization of microsatellite sequence in rice (Oryza sativa L.). Theor Appl Genet, 2000, 100: 697–712.
16 McCouch S R, Teytelman L, Xu Y L, Lobos K B, Clare K, Walton M, Fu B Y, Maghirang R, Li Z K, Xing Y Z, Zhang Q F, Kono I, Yano M, Fjellstrom R, Declerck G, Schneider D, Cartinhour S, Ware D, Stein L. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res, 2002, 9: 199–207.
17 Wang S C, Basten C J, Zeng Z B. Windows QTL Cartographer Version 2.5. [2006-09-15]. http://statgen.ncsu.edu/qtlcart/ WinQTLCart.htm.
18 Churchill G A, Doerge R W. Empirical threshold values for quantitative trait mapping. Genetics, 1994, 138: 963–971.
19 Mather K, Jinks J L. Biometrical Genetics. 3rd edn. London: Chapman and Hall, 1982: 71–81.
20 Yang J, Zhu J. Predicting superior genotypes in multiple environments based on QTL effects. Theor Appl Genet, 2005, 110: 1268–1274.
21 Wang D L, Zhu J, Li Z K, Paterson A H. Mapping QTLs with epistatic effects and QTL×environment interactions by mixed linear model approaches. Theor Appl Genet, 1999, 99: 1255– 1264.
22 McCouch S R, Cho Y G, Yano M, Paul E, Blinstrub M, Morishima H, Kinoshita T. Report on QTL nomenclature. Rice Genet Newsl, 1997, 14: 11–13.
23 Gao Y M, Zhu J. Advance on methodology of QTL mapping for plants. Hereditas(Beijing), 2000, 22(3): 175–179. (in Chinese with English abstract)Hui D F, Jiang C J, Mo H D. Comparison among mapping methods for detecting QTLs and estimating their effects. Acta Agron Sin, 1997, 23(2): 129–132. (in Chinese with English abstract)

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