New Stably Expressed Loci Responsible for Panicle Angle Trait in Japonica Rice in Four Environments

doi:10.1016/S1672-6308(13)60119-5

Abstract

Abstract:

Panicle angle (PA) of 254 recombinant inbred lines derived from a cross between two japonica varieties Xiushui 79 and C Bao was investigated under four environments, and a genetic linkage map including 111 SSR markers was constructed. Genetic analysis was conducted by mixed major gene plus polygene inheritance models, and quantitative trait loci (QTLs) identification by the QTLNetwork 2.0 and the composite interval mapping approach of WinQTLCart 2.5 software. Results showed that the PA trait was controlled by two major genes plus polygenes, mainly by major genes. Eight QTLs for PA were detected by the QTLNetwork 2.0 software, and each locus explained 0.01% to 39.89% of the phenotypic variation. Twelve QTLs for PA were detected by the WinQTLCart 2.5 software, with each locus explaining 2.83% to 30.60% of the phenotypic variation. Two major QTLs (qPA9.2 and qPA9.5) distributed between RM3700 and RM3600 and between RM5652 and RM410, respectively, and a moderate QTL (qPA9.7) distributed between RM257 and OSR28, were both detected by the two methods in all of the four environments. The negative effect alleles of the three QTLs were from Xiushui 79. In addition, eight pairs of epistatic QTLs with minor effects were also detected. QTL × environment interactions were not significant for additive QTLs and epistatic QTL pairs.

Key words: japonica rice, panicle angle, growing environment, mixed inheritance model, quantitative trait locus

NIU Fu-an, LIU Jian, GUO Yuan, CHEN Lan, JIANG Jian-hua, HONG De-lin. New Stably Expressed Loci Responsible for Panicle Angle Trait in Japonica Rice in Four Environments[J]. RICE SCIENCE, DOI: 10.1016/S1672-6308(13)60119-5 .

References

Chen W F, Xu Z J, Zhang L B, Zhou H F, Yang S R. 1995. Effects of different panicle type on canopy properties light distribution and dry matter production of rice population. Acta Agron Sin, 21(1): 83–89. (in Chinese with English abstract)
Chen X G, Liu J B, Hong D L. 2006. 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, 32(2): 1143–1150. (in Chinese with English abstract)
Cheng B S, Wan Z B, Hong D L. 2007. Establishment of SSR fingerprint map and analysis of genetic similarity among 35 varieties in japonica rice (Oryza sativa L.). J Nanjing Agric Univ, 30(3): 1–8. (in Chinese with English abstract)
Churchill G A, Doerge R W. 1994. Empirical threshold values for quantitative trait mapping. Genetics, 138(3): 963–971.
Gai J Y, Zhang Y M , Wang J K. 2003. Genetic System of Quantitative Traits in Plants. Beijing: Science Press: 8–94, 224 –260, 351–369. (in Chinese)
Guo Y, Hong D L. 2010. Novel pleiotropic loci controlling panicle architecture across environments in japonica rice (Oryza sativa L.). J Genet Genom, 37(8): 533–544.
Hui D F, Jiang C J, Mo H D. 1997. Comparison among mapping methods for detecting QTLs and estimating their effects. Acta Agron Sin, 23(2): 129–136. (in Chinese with English abstract)
Kong F N, Wang J Y, Zou J C, Shi L X, Jin D M, Xu Z J, Wang B. 2007. Molecular tagging and mapping of the erect panicle gene in rice. Mol Breeding, 19: 297–304.
Liu J B, Hong D L. 2005. Genetic analysis on panicle angle and number of spikelets per panicle in japonica rice (Oryza sativa). Chin J Rice Sci, 19(3): 223–230. (in Chinese with English abstract)
McCouch S R. 2008. Gene nomenclature system for rice. Rice, 1: 72–84.
Piao R H, Jiang W Z, Ham T H, Choi M S, Qiao Y L, Chu S H, Park J H, Woo M O, Jin Z X, An G, Lee J, Koh H J. 2009. Map-based cloning of the ERECT PANICLE 3 gene in rice. Theor Appl Genet, 119(8): 1497–1506.
Su C F, Zhao T J, Gai J Y. 2010a. Simulation comparisons of effectiveness among QTL mapping procedures of different statistical genetic models. Acta Agron Sin, 36(7): 1100–1107. (in Chinese with English abstract)
Su C F, Lu W G, Zhao T J, Gai J Y. 2010b. Verification and fine-mapping of QTLs conferring days to flowering in soybean using residual heterozygous lines. Chin Sci Bull, 55(6): 499–508.
Tang S Z, Zhang H G, Liang G H, Yan C J, Liu Q Q, Gu M H. 2008. Reasons and countermeasures of slow development on three-line japonica hybrid rice. Hybrid Rice, 23(1): 1–5. (in Chinese with English abstract)
Wang B L, Dong Y H, Wang S. 1997. Studies on genetic activities of semidwarfism and erect-panicle in rice. Shenyang Agric Univ, 28(2): 83–87. (in Chinese with English abstract)
Wang D Y, Zhang X F, Li H, Xu C M, Qian Q, Liao X Y. 2007. Study of yield and morphological character development of late japonica rice in Zhejiang Province using derived varieties of Nongken 58. Sci Agric Sin, 40(12): 2903–2909. (in Chinese with English abstract)
Wang J Y, Xu Z J, Chen W F. 2009a. Mixed major-gene plus polygenes inheritance analysis for erect panicle type in japonica. Hubei Agric Sci, 48(1): 4–8. (in Chinese with English abstract)
Wang J Y, Nakazaki T, Chen S Q, Chen W F, Saito H, Tsukiyama T, Okumoto Y, Xu Z J, Tanisaka T. 2009b. Identification and characterization of the erect-pose panicle gene EP conferring high grain yield in rice (Oryza sativa L.). Theor Appl Genet, 119: 85–91.
Xu D Y, Du Y, Fang Z W, Pan Q M, Yang J C, Zhu Q S. 2006. Comparison on main agronomical and quality characters between japonica cultivars with different panicle types in Jiang-Huai area. Acta Agron Sin, 32(2): 379–384. (in Chinese with English abstract)
Xu Q, Yuan X P, Yu H Y, Wang Y P, Tang S X, Wei X H. 2011. Mapping QTLs for drought resistance at seedling stage in rice by using a doubled haploid population. Rice Sci, 18 (1): 23–28.
Xu Z J, Chen W F, Zhang L B, Yang S R. 1990. Comparative study on light distribution in rice canopies with different panicle types. Sci Agric Sin, 23(4): 10–16. (in Chinese with English abstract)
Xu Z J, Chen W F, Zhang L B, Zhang C L. 1995. The heredity of the erect panicle character and relations with other characters in rice. Shenyang Agric Univ, 26(1): 1–7. (in Chinese with English abstract)
Xu Z J, Chen W F, Zhang W Z, Liu L X, Zhou S Q, Zhang L B, Yang S R. 2000. The yield potentiality of rice and its development of plant type. Shenyang Agric Univ, 31(6): 534– 536. (in Chinese with English abstract)
Yan C J, Zhou J H, Yan S, Chen F, Yeboah M, Tang S Z, Liang G H, Gu M H. 2007. Identification and characterization of a major QTL responsible for erect panicle trait in japonica rice (Oryza sativa L.). Theor Appl Genet, 115(8): 1093–1100.
Yang J, Zhu J. 2005. Methods for predicting superior genotypes under multiple environments based on QTL effects. Theor Appl Genet, 110: 1268–1274.
Zhang W Z, Xu Z J, Zhang L B, Chen W F, Sun G L, Wu S Q. 2002. Genetic characteristics of erect panicle rice and overall evaluation. Liaoning Agric Sci, (5): 24–27. (in Chinese)
Zhou Y, Zhu J Y, Li Z Y, Yi C D, Liu J, Zhang H G, Tang S Z, Gu M H, Liang G H. 2009. Deletion in a quantitative trait gene qPE9-1 associated with panicle erectness improves plant architecture during rice domestication. Genetics, 183(1): 315– 324.
Zhu L H, Gu M H. 1979. The inheritance of rice grain shattering. Hereditas, 1(4): 17–19. (in Chinese with English abstract)

[1]	Sundus ZAFAR, XU Jianlong. Recent Advances to Enhance Nutritional Quality of Rice [J]. Rice Science, 2023, 30(6): 4-.
[2]	Shilin Ding, Chaolei Liu, Lianguang Shang, Shenglong Yang, Anpeng Zhang, Hongzhen Jiang, Banpu Ruan, Guonan Fang, Biao Tian, Guoyou Ye, Longbiao Guo, Qian Qian, Zhenyu Gao. Identification of QTLs for Cadmium Tolerance During Seedling Stage and Validation of qCDSL1 in Rice [J]. Rice Science, 2021, 28(1): 81-88.
[3]	Hui Wang, Jiayu Zhang, Farkhanda Naz, Juan Li, Shuangfei Sun, Guanghua He, Ting Zhang, Yinghua Ling, Fangming Zhao. Identification of Rice QTLs for Important Agronomic Traits with Long-Kernel CSSL-Z741 and Three SSSLs [J]. Rice Science, 2020, 27(5): 414-422.
[4]	Hussain Kashif, Yingxing Zhang, Anley Workie, Riaz Aamir, Abbas Adil, Hasanuzzaman Rani Md., Hong Wang, Xihong Shen, Liyong Cao, Shihua Cheng. Association Mapping of Quantitative Trait Loci for Grain Size in Introgression Line Derived from Oryza rufipogon [J]. Rice Science, 2020, 27(3): 246-254.
[5]	Yuan Chen, Yuxiang Zeng, Zhijuan Ji, Yan Liang, Zhihua Wen, Changdeng Yang. Identification of Stable Quantitative Trait Loci for Sheath Blight Resistance Using Recombinant Inbred Line [J]. Rice Science, 2019, 26(5): 331-338.
[6]	Wenhui Wang, Linlin Wang, Yujun Zhu, Yeyang Fan, Jieyun Zhuang. Fine-Mapping of qTGW1.2a, a Quantitative Trait Locus for 1000-Grain Weight in Rice [J]. Rice Science, 2019, 26(4): 220-228.
[7]	Wenqiang Liu, Xiaowu Pan, Yongchao Li, Yonghong Duan, Jun Min, Sanxiong Liu, Licheng Liu, Xinnian Sheng, Xiaoxiang Li. Identification of QTLs and Validation of qCd-2 Associated with Grain Cadmium Concentrations in Rice [J]. Rice Science, 2019, 26(1): 42-49.
[8]	Okechukwu Anyaoha Christian, Fofana Mamadou, Gracen Vernon, Tongoona Pangirayi, Mande Semon. Introgression of Two Drought QTLs into FUNAABOR-2 Early Generation Backcross Progenies Under Drought Stress at Reproductive Stage [J]. Rice Science, 2019, 26(1): 32-41.
[9]	Zongxiang Chen, Zhiming Feng, Houxiang Kang, Jianhua Zhao, Tianxiao Chen, Qianqian Li, Hongbing Gong, Yafang Zhang, Xijun Chen, Xuebiao Pan, Wende Liu, Guoliang Wang, Shimin Zuo. Identification of New Resistance Loci Against Sheath Blight Disease in Rice Through Genome-Wide Association Study [J]. Rice Science, 2019, 26(1): 21-31.
[10]	P. M. Swamy B., Kaladhar K., Anuradha K., K. Batchu Anil, Longvah T., Sarla N.. QTL Analysis for Grain Iron and Zinc Concentrations in Two O. nivara Derived Backcross Populations [J]. Rice Science, 2018, 25(4): 197-207.
[11]	Yaobin Qin, Peng Cheng, Yichen Cheng, Yue Feng, Derun Huang, Tingxu Huang, Xianjun Song, Jiezheng Ying. QTL-Seq Identified a Major QTL for Grain Length and Weight in Rice Using Near Isogenic F₂ Population [J]. Rice Science, 2018, 25(3): 121-131.
[12]	Rekha Talukdar Preeti, Rathi Sunayana, Pathak Khanin, Kumar Chetia Sanjay, Nath Sarma Ramendra. Population Structure and Marker-Trait Association in Indigenous Aromatic Rice [J]. Rice Science, 2017, 24(3): 145-154.
[13]	Anupam Alpana, Imam Jahangir, Mohammad Quatadah Syed, Siddaiah Anantha, Prasad Das Shankar, Variar Mukund, Prasad Mandal Nimai. Genetic Diversity Analysis of Rice Germplasm in Tripura State of Northeast India Using Drought and Blast Linked Markers [J]. Rice Science, 2017, 24(1): 10-20.
[14]	Daniel Abacar Jose, Zhao-miao Lin, Xin-cheng Zhang, Cheng-qiang Ding, She Tang, Zheng-hui Liu, Shao-hua Wang, Yan-feng Ding. Variation in Yield and Physicochemical Quality Traits among Mutants of Japonica Rice Cultivar Wuyujing 3 [J]. Rice Science, 2016, 23(1): 33-41.
[15]	Chao Xiang, Jie Ren, Xiu-qin Zhao, Zai-song Ding, Jing Zhang, Chao Wang, Jun-wei Zhang, Augustino Joseph Charles, Qiang Zhang, Yun-long Pang, Yong-ming Gao, Ying-yao Shi. Genetic Dissection of Low Phosphorus Tolerance Related Traits Using Selected Introgression Lines in Rice [J]. Rice Science, 2015, 22(6): 264-274.