Chinese Journal OF Rice Science >
QTL Analysis for Grain Weight and Shape and Validation of qTGW1.2/qGL1.2
#These authors contributed equally to this work
Received date: 2020-12-08
Revised date: 2021-01-26
Online published: 2021-07-10
【Objective】 Grain weight and shape have an important impact on the yield and quality of rice. The purpose is to further reveal the genetic mechanism of grain weight and shape in rice by primary mapping of QTLs for grain weight and shape and validating of the newly identified qTGW1.2/qGL1.2 on the long arm of chromosome 1. 【Method】 An F2:3 population consisting of 277 individuals and a recombinant inbred line (RIL) population with 211 individuals were derived from the cross between the large-grain male parent FM9, and the small-grain female parent EFT. The 1000-grain weight (TGW), grain length (GL) and grain width (GW) were measured. QTL mapping was performed by the inclusive composite interval mapping. As for the qTGW1.2/qGL1.2 region, two residual heterozygotes were screened and self-fertilized to produce segregated populations for QTL validation. 【Results】 A total of 35 QTLs for TGW, GL and GW were detected by QTL primary mapping. Among them, 11 QTLs were detected in both populations, 18 QTLs were detected only in the F2:3 population, and six QTLs only in the RIL population. The effects of the newly identified qTGW1.2/qGL1.2 on TGW and GL were validated by using the segregated populations derived from the two residual heterozygotes. Additionally, significant variations in the length of glume cells were observed, and qPCR results demonstrated that the expression levels of genes related to cell cycle, auxin metabolism and grain shape were up- or down-regulated significantly. 【Conclusion】 The primary mapping of 35 QTLs and the validating of qTGW1.2/qGL1.2 will contribute to a deep insight into the genetic basis underlying grain weight and shape of rice, and also lay a foundation for gene cloning and marker assisted selection.
Key words： rice; grain weight; grain shape; QTL; residual heterozygote
Chengxing DU, Huali ZHANG, Dongqing DAI, Mingyue WU, Minmin LIANG, Junyu CHEN, Liangyong MA . QTL Analysis for Grain Weight and Shape and Validation of qTGW1.2/qGL1.2 [J]. Chinese Journal OF Rice Science, 2021 , 35(4) : 359 -372 . DOI: 10.16819/j.1001-7216.2021.201205
| [1] | Wang A H, Hou Q Q, Si L Z, Huang X H, Luo J H, Lu D F, Zhu J J, Shangguan Y Y, Miao J S, Xie Y F, Wang Y C, Zhao Q, Feng Q, Zhou C C, Li Y, Fan D L, Lu Y Q, Tian Q L, Wang Z X, Han B.The PLATZ transcription factor GL6 affects grain length and number in rice[J]. Plant Physiology, 2019, 180(4): 2077-2090. |
| [2] | 罗玉坤, 朱智伟, 陈能, 段彬伍, 章林平. 中国主要稻米的粒型及其品质特性[J]. 中国水稻科学, 2004(2): 49-53. |
| [2] | Luo Y K, Zhu Z W, Chen N, Duan B W, Zhang L P.Grain types and related quality characteristics of rice in China[J]. Chinese Journal of Rice Science, 2004(2): 49-53. (in Chinese with English abstract) |
| [3] | 杨联松, 白一松, 张培江, 许传万, 胡兴明, 王伍梅, 佘德红, 陈桂芝. 谷粒形状与稻米品质相关性研究[J]. 杂交水稻, 2001(4): 51-53, 57. |
| [3] | Yang L S, Bai Y S, Zhang P J, Xu C W, Hu X M, Wang W M.Studies on the correlation between grain shape and grain quality in rice[J]. Hybrid Rice, 2001(4): 51-53, 57. (in Chinese with English abstract) |
| [4] | Huang R Y, Jiang L R, Zheng J S, Wang T S, Wang H C, Huang Y M, Hong Z L.Genetic bases of rice grain shape: So many genes, so little known[J]. Trends in Plant Science, 2013, 18(4): 218-226. |
| [5] | Xing Y Z, Zhang Q F.Genetic and molecular bases of rice yield[J]. Annual Review of Plant Biology, 2010, 61(1): 421-442. |
| [6] | Chan A N, Wang L L, Zhu Y J, Fan Y Y, Zhuang J Y, Zhuang Z H. Identification through fine mapping and verification using CRISPR/Cas9-targeted mutagenesis for a minor QTL controlling grain weight in rice[J]. Theoretical and Applied Genetics, 2021, 134: 327-337. . |
| [7] | Li N, Xu R, Duan P, Li Y H.Control of grain size in rice[J]. Plant Reproduction, 2018, 31: 237-251. |
| [8] | 康艺维, 陈玉宇, 张迎信. 水稻粒型基因克隆研究进展及育种应用展望[J]. 中国水稻学, 2020, 34(6): 479-490. |
| [8] | Kang Y W, Chen Y Y, Zhang Y X.Research progress and breeding prospects of grain size associated genes in rice[J]. Chinese Journal of Rice Science, 2020, 34(6): 479-490. (in Chinese with English abstract) |
| [9] | Yamamoto T, Yonemaru J, Yano M.Towards the understanding of complex traits in rice: Substantially or superficially[J]. DNA Research, 2009, 16: 141-154. |
| [10] | Takai T, Ikka T, Kondo K, Nonoue Y, Ono N, Arai-Sanoh Y, Yoshinaga S, Nakano H, Yano M, Kondo M, Yamamoto T.Genetic mechanisms underlying yield potential in the rice high-yielding cultivar Takanari, based on reciprocal chromosome segment substitution lines[J]. BMC Plant Biology, 2014, 14(1): 295. |
| [11] | Nagata K, Ando T, Nonoue Y, Mizubayashi T, Kitazawa N, Shomura A, Matsubara K, Ono N, Mizobuchi R, Shabaya T, Ogisotanaka E, Hori K, Yano M, Fukuoka S.Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica ×indica cross[J]. Breeding Science, 2015, 65(4): 308-318. |
| [12] | 王琳琳, 陈玉宇, 郭梁, 张宏伟, 樊叶杨, 庄杰云. 水稻第1染色体qTGW1.2区域粒重组分性状QTL的剖析[J]. 中国水稻科学, 2015, 29(3): 232-240. |
| [12] | Wang L L, Chen Y Y, Guo L, Zhang H W, Fan Y Y, Zhuang J Y.Dissection of quantitative trait loci for grain weight and its component traits in the qTGW1.2 region on chromosome 1 of rice[J]. Chinese Journal of Rice Science, 2015, 29(3): 232-240. (in Chinese with English abstract) |
| [13] | 朱安东, 孙志超, 朱玉君, 张荟, 牛小军, 樊叶杨, 张振华, 庄杰云. 应用剩余杂合体衍生群体定位水稻粒重粒形QTL[J]. 中国水稻科学, 2019, 33(2): 144-151. |
| [13] | Zhu A D, Sun Z C, Zhu Y J, Zhang H, N X J, Fan Y Y, Zhang Z H, Zhuang J Y. Identification of QTL for grain weight and grain shape using populations derived from residual heterozygous lines of indica rice[J]. Chinese Journal of Rice Science, 2019, 33(2): 144-151. (in Chinese with English abstract) |
| [14] | Ye H, Foley M E, Gu X Y.New seed dormancy loci detected from weedy rice-derived advanced populations with major QTL alleles removed from the background[J]. Plant Science, 2010, 179(6): 612-619. |
| [15] | Bai X, Wu B, Xing Y.Yield-related QTLs and their applications in rice genetic improvement[J]. Journal of Integrative Plant Biology, 2012, 54: 300-311. |
| [16] | Wang Z, Chen J Y, Zhu Y J, Fan Y Y, Zhuang J Y.Validation of qGS10, a quantitative trait locus for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.)[J]. Journal of Integrative Agriculture, 2017, 16(1): 16-26. |
| [17] | Zhang H W, Fan Y Y, Zhu Y J, Chen J Y, Yu S B, Zhuang J Y.Dissection of the qTGW1.1 region into two tightly-linked minor QTLs having stable effects for grain weight in rice[J]. BMC Genetics, 2016, 17: 98. |
| [18] | 王建康. 数量性状基因的完备区间作图方法[J]. 作物学报, 2009, 35(2): 239-245. |
| [18] | Wang J K.Inclusive composite interval mapping of quantitative trait genes[J]. Acta Agronomica Sinica, 2009, 35(2): 239-245. (in Chinese with English abstract) |
| [19] | McCouch S R, CGSNL (Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative). Gene nomenclature system for rice[J]. Rice, 2008, 1(1): 72-84. |
| [20] | Ruan B P, Shang L S, Zhang B, Hu J, Wang Y X, LIN H, Zhang A P, Liu C L, P Y L, Zhu L, Ren D Y, Shen L, Dong G J, Zhang G H, Zeng D L, Guo L B, Qian Q, Gao Z Y. Natural variation in the promoter of TGW2 determines grain width and weight in rice[J]. New Phytologist, 2020, 227(2): 629-640. |
| [21] | 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[J]. Nature Genetics, 2007, 39: 623-630. |
| [22] | 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 putative transmembrane protein[J]. Theoretical and Applied Genetics, 2006, 112: 1164-1171. |
| [23] | Mao H L, Sun S Y, Yao J L, Wang C R, Yu S B, Xu C G, Li X H, Zhang Q F.Linking differential domain functions of the GS3 protein to natural variation of grain size in rice[J]. Proceedings of the National Academy of the Sciences of the United States of America, 2010, 107: 19579-19584. |
| [24] | Dong N Q, Sun Y W, Guo T, Shi C L, Zhang Y M, Kan Y, Xiang Y H, Zhang H, Yang Y B, Li Y C, Zhao H Y, Yu H X, Lu Z Q, Wang Y, Ye W W, Shan J X, Lin H X.UDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic fux redirection in rice[J]. Nature Communications, 2020, 11: 2629. |
| [25] | Li Y B, Fan CC, Xing Y Z, Jiang Y H, Luo L J, Sun L, Shao D, Xu C J, Li X H, Xiao J H, He Y Q, Zhang Q F. Natural variation in GS5 plays an important role in regulating grain size and yield in rice[J]. Nature Genetics, 2011, 43(12): 1266-1269. |
| [26] | Xu C J, Liu Y, Li Y B, Xu X B, Xu C J, Li X H, Xiao J H, Zhang Q F.Differential expression of GS5 regulates grain size in rice[J]. Journal of Experimental Botany, 2015, 66(9): 2611-2623. |
| [27] | Duan P G, Xu J S, Zeng D L, Zhang B L, Geng M F, Zhang G Z, Huang K, Huang L J, Xu R, Ge S, Qian Q, Li Y H.Natural variation in the promoter of GSE5 contributes to grain size diversity in rice[J]. Molecular Plant, 2017, 10: 685-694. |
| [28] | Liu J, Chen J, Zheng X, Wu F, Lin Q, Heng Y, Cheng Z, Zhou K, Lin Q, Zhang X, Guo X, Wang J, Wang H, Wan J.GW5 acts in the brassinosteroid signaling pathway to regulate grain width and weight in rice[J]. Nature Plants, 2017, 3: 17043. |
| [29] | Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M.Deletion in a gene associated with grain size increased yields during rice domestication[J]. Nature Genetics, 2008, 40: 1023-1028. |
| [30] | Wan X Y, Weng J F, Zhai H Q, Wang J K, Lei C L, Liu X L, Guo T, Jiang L, Su N, Wan J M.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[J]. Genetics, 2008, 179: 2239-2252. |
| [31] | Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, Zhang X, Cheng Z, Guo X, Wang J, Jiang L, Zhai H, Wan J.Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight[J]. Cell Research, 2008, 18: 1199-1209. |
| [32] | Yan C J, Zhou J H, Yan S, Chen F, Yeboah M, Tang S Z, Liang G H, Gu M H.Identification and characterization of a major QTL responsible for erect panicle trait in japonica rice (Oryza sativa L.)[J]. Theoretical and Applied Genetics, 2007, 115(8): 1093-1100. |
| [33] | Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X.Natural variation at the DEP1 locus enhances grain yield in rice[J]. Nature Genetics, 2009, 41(4): 494-497. |
| [34] | Fumio T S, Yasushi K, Hiroshi K, Haruko O, Akemi T, Naho H, Akio M, Hirohiko H, Hidemi K, Masahiro Y, Seiichi T.A loss-of-function mutation of rice DENSE PANICLE 1 causes semi-dwarfness and slightly increased number of spikelets[J]. Breeding Science, 2011, 61(1): 17-25. |
| [35] | Sun H, Qian Q, Wu K, Luo J, Wang S, Zhang C, Ma Y, Liu Q, Huang X, Yuan Q, Han R, Zhao M, Dong G, Guo L, Zhu X, Gou Z, Wang W, Wu Y, Lin H, Fu X.Heterotrimeric G proteins regulate nitrogen-use efficiency in rice[J]. Nature Genetics, 2014, 46(4): 652-656. |
| [36] | Li M, Li X, Zhou Z, Wu P, Fang M, Pan X, Lin Q, Luo W, Wu G, Li H.Reassessment of the four yield-related genes Gn1a, DEP1, GS3, and IPA1 in rice using a CRISPR/Cas9 system[J]. Frontiers in Plant Science, 2016, 7: 377. |
| [37] | Liu Q, Han R, Wu K, Zhang J, Ye Y, Wang S, Chen J, Pan Y, Li Q, Xu X, Zhou J, Tao D, Wu Y, Fu X.G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice[J]. Nature Communications, 2018, 9: 852. |
| [38] | Sun S, Wang L, Mao H, Shao L, Li X, Xiao J, Ouyang Y, Zhang Q.A G-protein pathway determines grain size in rice[J]. Nature Communications, 2018, 9: 851. |
| [39] | Li N, Li Y H. Signaling pathways of seed size control in plants[J]. Current Opinion in Plant Biology, 2016, 33: 23-32. |
| [40] | Yu S. B, Li J. X, Xu C. G, Tan Y. F, Gao Y. J, Li X. H, Zhang Q F, Maroof S. Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid[J]. Proceedings of the National Academy of the Sciences of the United States of America, 1997, 94: 9226-9231. |
| [41] | Zeng Y X, Ji Z J, Wen Z H, Liang Y, Yang C D.Combination of eight alleles at four quantitative trait loci determines grain length in rice[J]. PLoS ONE, 2016, 11: 3. |
| [42] | Odonkor S, Choi S, Chakraborty D, Martinez-Bello L, Wang X, Bahri B A, Tenaillon M I, Panaud O, Devos K M.QTL mapping combined with comparative analyses identified candidate genes for reduced shattering in Setaria italica[J]. Frontiers in Plant Science, 2018, 9: 918. |
| [43] | Li J X, Yu S B, Xu C G, Xu C G, Tan Y F, Gao Y J, Li X H, Zhang Q F.Analyzing quantitative trait loci for yield using a vegetatively replicated F2 population from a cross between the parents of an elite rice hybrid[J]. Theoretical and Applied Genetics, 2000, 101: 248-254. |
| [44] | 庄杰云, 樊叶杨, 吴建利, 夏英武, 郑康乐. 应用二种定位法比较不同世代水稻产量性状QTL的检测结果[J]. 遗传学报, 2001(5): 458-464. |
| [44] | Zhuang J Y, Fan Y Y, Wu J L, Xia Y W, Zheng K L.Comparison of the detection of QTL for yield traits in different generations of a rice cross using two mapping approaches[J]. Acta Genetica Sinica, 2001(5): 458-464. |
| [45] | 姜树坤, 张喜娟, 黄成, 邢亚南, 郑旭, 徐正进, 陈温福. 基于粳稻F2和F2:6群体的连锁图谱及剑叶性状QTL比较分析[J]. 中国水稻科学, 2010, 24(4): 372-378. |
| [45] | Jiang S K, Zhang X J, Huang C, Xing Y N, Zheng X, Xu Z J, Chen W F.Comparison of genetic linkage map and QTLs controlling flag leaf traits based on F2 and F2:6 populations derived from japonica rice[J]. Chinese Journal of Rice Science, 2010, 24(4): 372-378. (in Chinese with English abstract) |
| [46] | 郭小蛟, 张涛, 蒋开锋, 杨莉, 曹应江, 杨乾华, 游书梅, 万先齐, 罗婧, 李昭祥, 高磊, 郑家奎. 水稻籼粳交F8、F2群体穗长QTL比较分析[J]. 中国农业科学, 2013, 46(23): 4849-4857. |
| [46] | Guo X J, Zhang T, Jiang K F, Yang L, Cao Y J, Yang Q H, You S M, Wan X Q, Luo J, Li Z X, Gao L, Zheng J K.Comparison of panicle length QTL based on F2 and F8 populations derived from rice subspecies cross[J]. Scientia Agricultura Sinica, 2013, 46(23): 4849-4857. (in Chinese with English abstract) |
| [47] | Mackay T F C, Stone E A, Ayroles J F. The genetics of quantitative traits: Challenges and prospects[J]. Nature Reviews Genetics, 2009, 10: 565-577. |
| [48] | Kumar J, Gupta D S, Gupta S, Dubey S, Gupta P, Kumar S.Quantitative trait loci from identification to exploitation for crop improvement[J]. Plant Cell Reports, 2017, 36: 1187-1213. |
| [49] | 李盼盼, 朱玉君, 郭梁, 庄杰云, 樊叶杨. 利用剩余杂合体衍生的近等基因系精细定位水稻粒长微效QTL qGL1.1[J]. 中国水稻科学, 2020, 34(2): 125-134. |
| [49] | Li P P, Zhu Y J, Guo L, Zhuang J Y, Fan Y Y.Fine mapping of qGL1.1, a minor QTL for grain length, using near isogenic lines derived from residual heterozygotes in rice[J]. Chinese Journal of Rice Science, 2020, 34(2): 125-134. (in Chinese with English abstract) |
| [50] | Zhang B, Shang L G, Ruan B P, Zhang A P, Yang S L, Jiang H Z, Liu C L, Hong K, Lin H, Gao Z Y, Hu J, Zeng D L, Guo L B, Qian Q.Development of three sets of high-throughput genotyped rice chromosome segment substitution lines and QTL mapping for eleven traits[J]. Rice, 2019, 12: 33. |
| [51] | Ma F Y, Du J, Wang D C, Wang H, Zhao B B,. He G H, Yang Z L, Zhang T, Wu R H, Zhao F M.Identification of long-grain chromosome segment substitution line Z744 and QTL analysis for agronomic traits in rice[J]. Journal of Integrative Agriculture, 2020, 19(5): 1163-1169. |
| [52] | Wang L L, Chen Y Y, Guo L, Zhang H W, Fan Y Y, Zhuang J Y.Dissection of qTGW1.2 to three QTLs for grain weight and grain size in rice (Oryza sativa L.)[J]. Euphytica, 2015, 202: 119-127. |
| [53] | Wang W H, Wang L L, Zhu Y J, Fan Y Y, Zhuang J Y.Fine-mapping of qTGW1.2a, a quantitative trait locus for 1000-grain weight in rice[J]. Rice Science, 2019, 26(4): 220-228. |
| [54] | Dong Q, Zhang Z H, Wang L L, Zhu Y J, Fan Y Y, Mou T M, Ma L Y, Zhuang J Y.Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice[J]. Rice, 2018, 11: 44. |
| [55] | Yan S, Zou G H, Li S J, Wang H, Li·H Q, Zhai G W, Guo P, Song H M, Yan C H, Tao Y Z. Seed size is determined by the combinations of the genes controlling different seed characteristics in rice[J]. Theoretical and Applied Genetics, 2011 123: 1173-1181. |
| [56] | Lu L, Shao D, Qiu X J, Sun L, Yan W H, Zhou X C, Yang L, He Y Q, Yu S B, Xing W Z.Natural variation and artificial selection in four genes determine grain shape in rice[J]. New Phytologist, 2013, 200(4): 1269-1280. |
/
| 〈 |
|
〉 |