Genetic analysis and fine mapping of the RK4 gene for round kernel in rice (Oryza sativa L.)
Li S., Zhang R., Chen J., Zou J., Liu T., Zhou G.:https://doi.org/10.17221/172/2016-CJGPBCitation:Li S., Zhang R., Chen J., Zou J., Liu T., Zhou G.: (2017): Genetic analysis and fine mapping of the RK4 gene for round kernel in rice (Oryza sativa L.). Czech J. Genet. Plant Breed., 53: 153-158.
Grain shape of rice is an important trait for both yield and quality. A rice rk4 (round kernel) mutant was obtained from the japonica variety Zhonghua 11 by radiation of 60Co-γ. The grain width of the mutant was increased and the length was decreased. Simultaneously, the 1000-grain weight was slightly reduced, therefore the grain shape of the mutant tended to be small and round. In this study, genetic analysis and gene mapping of the mutant gene were carried out using the F2 and F3 populations derived from the mutant and the indica variety Xianhui 8006. The results suggested that the round kernel was controlled by a single recessive allele (rk4) which was located on chromosome 5. The RK4 gene was further mapped between the molecular markers LSTS5-77 and LSTS5-60 with 0.57 and 0.096 cM, respectively. A BAC clone was found to span the RK4 locus, and the RK4 gene was placed in a 46 kb region that contains six annotated genes according to the available sequence annotation database. This result will help us to isolate the RK4 gene and reveal the molecular mechanism of the round kernel in rice.Keywords:
BSA; ESEM; kernel shape; SSR; STSReferences:
Alonso-Blanco C., Blankestijn-de Vries H., Hanhart C. J., Koornneef M. (1999): Natural allelic variation at seed size loci in relation to other life history traits of Arabidopsis thaliana. Proceedings of the National Academy of Sciences, 96, 4710-4717 https://doi.org/10.1073/pnas.96.8.4710Fan Chuchuan, Xing Yongzhong, Mao Hailiang, Lu Tingting, Han Bin, Xu Caiguo, Li Xianghua, Zhang Qifa (2006): GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theoretical and Applied Genetics, 112, 1164-1171 https://doi.org/10.1007/s00122-006-0218-1Feng Yue, Lu Qing, Zhai Rongrong, Zhang Mengchen, Xu Qun, Yang Yaolong, Wang Shan, Yuan Xiaoping, Yu Hanyong, Wang Yiping, Wei Xinghua (2016): Genome wide association mapping for grain shape traits in indica rice. Planta, 244, 819-830 https://doi.org/10.1007/s00425-016-2548-9Hu Jiang, Wang Yuexing, Fang Yunxia, Zeng Longjun, Xu Jie, Yu Haiping, Shi Zhenyuan, Pan Jiangjie, Zhang Dong, Kang Shujing, Zhu Li, Dong Guojun, Guo Longbiao, Zeng Dali, Zhang Guangheng, Xie Lihong, Xiong Guosheng, Li Jiayang, Qian Qian (2015): A Rare Allele of GS2 Enhances Grain Size and Grain Yield in Rice. Molecular Plant, 8, 1455-1465 https://doi.org/10.1016/j.molp.2015.07.002Huang Rongyu, Jiang Liangrong, Zheng Jingsheng, Wang Tiansheng, Wang Houcong, Huang Yumin, Hong Zonglie (2013): Genetic bases of rice grain shape: so many genes, so little known. Trends in Plant Science, 18, 218-226 https://doi.org/10.1016/j.tplants.2012.11.001Ishimaru Ken, Hirotsu Naoki, Madoka Yuka, Murakami Naomi, Hara Nao, Onodera Haruko, Kashiwagi Takayuki, Ujiie Kazuhiro, Shimizu Bun-ichi, Onishi Atsuko, Miyagawa Hisashi, Katoh Etsuko (2013): Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nature Genetics, 45, 707-711 https://doi.org/10.1038/ng.2612IWATA Nobuo, OMURA Takeshi (1975): Studies on the Trisomics in Rice Plants (Oryza sativa L.). : III. Relation between Trisomics and Genetic Linkage Groups. Ikushugaku zasshi, 25, 363-368 https://doi.org/10.1270/jsbbs1951.25.363IWATA Nobuo, OMURA Takeshi (1984): Studies on the trisomics in rice plants (Oryza sativa L.). VI. An accomplishment of a trisomic series in japonica rice plants.. The Japanese journal of genetics, 59, 199-204 https://doi.org/10.1266/jjg.59.199Lander Eric S., Green Philip, Abrahamson Jeff, Barlow Aaron, Daly Mark J., Lincoln Stephen E., Newburg Lee (1987): MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1, 174-181 https://doi.org/10.1016/0888-7543(87)90010-3Li Jiming, Thomson Michael, McCouch Susan R. (2004): Fine Mapping of a Grain-Weight Quantitative Trait Locus in the Pericentromeric Region of Rice Chromosome 3. Genetics, 168, 2187-2195 https://doi.org/10.1534/genetics.104.034165Li Yibo, Fan Chuchuan, Xing Yongzhong, Jiang Yunhe, Luo Lijun, Sun Liang, Shao Di, Xu Chunjue, Li Xianghua, Xiao Jinghua, He Yuqing, Zhang Qifa (2011): Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nature Genetics, 43, 1266-1269 https://doi.org/10.1038/ng.977Lincoln S.E., Daly M.J., Lander E.S. (1993): Constructing Linkage Maps with MAPMAKER/EXP Version 3.0: A Tutorial Reference Manual. 3rd Ed. Cambridge, Whitehead Institute for Biomedical.Liu L., Tong H., Xiao Y., Che R., Xu F., Hu B., Liang C., Chu J., Li J., Chu C. (2015a): Activation of Big Grain1 significantly improves grain size by regulating auxin transport in rice. Proceedings of the National Academy of Sciences of the United States of America, 112: 11102–11107.Liu S., Hua L., Dong S., Chen H., Zhu X., Jiang J., Zhang F., Li Y., Fang X., Chen F. (2015b): OsMAPK6, a mitogen-activated protein kinase, influences rice grain size and biomass production. Plant Journal, 84: 672–681.Luo M., Dennis E. S., Berger F., Peacock W. J., Chaudhury A. (2005): MINISEED3 (MINI3), a WRKY family gene, and HAIKU2 (IKU2), a leucine-rich repeat (LRR) KINASE gene, are regulators of seed size in Arabidopsis. Proceedings of the National Academy of Sciences, 102, 17531-17536 https://doi.org/10.1073/pnas.0508418102Mao H., Sun S., Yao J., Wang C., Yu S., Xu C., Li X., Zhang Q. (2010): Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proceedings of the National Academy of Sciences, 107, 19579-19584 https://doi.org/10.1073/pnas.1014419107Michelmore R. W., Paran I., Kesseli R. V. (1991): Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations.. Proceedings of the National Academy of Sciences, 88, 9828-9832 https://doi.org/10.1073/pnas.88.21.9828Murray M.G., Thompson W.F. (1980): Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research, 8, 4321-4326 https://doi.org/10.1093/nar/8.19.4321Nagata Kazufumi, Ando Tsuyu, Nonoue Yasunori, Mizubayashi Tatsumi, Kitazawa Noriyuki, Shomura Ayahiko, Matsubara Kazuki, Ono Nozomi, Mizobuchi Ritsuko, Shibaya Taeko, Ogiso-Tanaka Eri, Hori Kiyosumi, Yano Masahiro, Fukuoka Shuichi (2015): Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a <i>japonica</i> × <i>indica</i> cross. Breeding Science, 65, 308-318 https://doi.org/10.1270/jsbbs.65.308Sanchez A.C., Khush G.S. (1998): Inheritance and linkage relationships of twenty-one genes in rice, Oryza sativa L. SABRAO Journal of Breeding and Genetics, 30: 51–60.Shomura Ayahiko, Izawa Takeshi, Ebana Kaworu, Ebitani Takeshi, Kanegae Hiromi, Konishi Saeko, Yano Masahiro (2008): Deletion in a gene associated with grain size increased yields during rice domestication. Nature Genetics, 40, 1023-1028 https://doi.org/10.1038/ng.169Song Xian-Jun, Huang Wei, Shi Min, Zhu Mei-Zhen, Lin Hong-Xuan (2007): A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nature Genetics, 39, 623-630 https://doi.org/10.1038/ng2014Tan Y. F., Xing Y. Z., Li J. X., Yu S. B., Xu C. G., Zhang Qifa (2000): Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid. TAG Theoretical and Applied Genetics, 101, 823-829 https://doi.org/10.1007/s001220051549Wan X., Weng J., Zhai H., Wang J., Lei C., Liu X., Guo T., Jiang L., Su N., Wan J. (2008): Quantitative Trait Loci (QTL) Analysis For Rice Grain Width and Fine Mapping of an Identified QTL Allele gw-5 in a Recombination Hotspot Region on Chromosome 5. Genetics, 179, 2239-2252 https://doi.org/10.1534/genetics.108.089862Wang Ertao, Wang Jianjun, Zhu Xudong, Hao Wei, Wang Linyou, Li Qun, Zhang Lixia, He Wei, Lu Baorong, Lin Hongxuan, Ma Hong, Zhang Guiquan, He Zuhua (2008): Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature Genetics, 40, 1370-1374 https://doi.org/10.1038/ng.220Wang Shaokui, Wu Kun, Yuan Qingbo, Liu Xueying, Liu Zhengbin, Lin Xiaoyan, Zeng Ruizhen, Zhu Haitao, Dong Guojun, Qian Qian, Zhang Guiquan, Fu Xiangdong (2012): Control of grain size, shape and quality by OsSPL16 in rice. Nature Genetics, 44, 950-954 https://doi.org/10.1038/ng.2327Wang S., Li S., Liu Q., Wu K., Zhang J., Wang S., Wang Y., Chen X., Zhang Y., Gao C., Wang F., Huang H., Fu X. (2015a): The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nature Genetics, 47: 949–954.Wang Y., Xiong G., Hu J., Jiang L., Yu H., Xu J., Fang Y., Zeng L., Xu E., Xu J., Ye W., Meng X., Liu R., Chen H., Jing Y., Wang Y., Zhu X., Li J., Qian Q. (2015b): Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nature Genetics, 47: 944–948.Weng Jianfeng, Gu Suhai, Wan Xiangyuan, Gao He, Guo Tao, Su Ning, Lei Cailin, Zhang Xin, Cheng Zhijun, Guo Xiuping, Wang Jiulin, Jiang Ling, Zhai Huqu, Wan Jianmin (2008): Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Research, 18, 1199-1209 https://doi.org/10.1038/cr.2008.307Y. Xing, Y. Tan, J. Hua, X. Sun, C. Xu, Q. Zhang (2002): Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. TAG Theoretical and Applied Genetics, 105, 248-257 https://doi.org/10.1007/s00122-002-0952-yYin Changbin, Li Huihui, Li Shanshan, Xu Lidong, Zhao Zhigang, Wang Jiankang (2015): Genetic dissection on rice grain shape by the two-dimensional image analysis in one japonica × indica population consisting of recombinant inbred lines. Theoretical and Applied Genetics, 128, 1969-1986 https://doi.org/10.1007/s00122-015-2560-7Yoon D.-B., Kang K.-H., Kim H.-J., Ju H.-G., Kwon S.-J., Suh J.-P., Jeong O.-Y., Ahn S.-N. (2006): Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo. Theoretical and Applied Genetics, 112, 1052-1062 https://doi.org/10.1007/s00122-006-0207-4Zhou Y., Miao J., Gu H., Peng X., Leburu M., Yuan F., Gu H., Gao Y., Tao Y., Zhu J., Gong Z., Yi C., Gu M., Yang Z., Liang G. (2015): Natural Variations in SLG7 Regulate Grain Shape in Rice. Genetics, 201, 1591-1599 https://doi.org/10.1534/genetics.115.181115Zuo Jianru, Li Jiayang (2014): Molecular Genetic Dissection of Quantitative Trait Loci Regulating Rice Grain Size. Annual Review of Genetics, 48, 99-118 https://doi.org/10.1146/annurev-genet-120213-092138