基于QTL定位发现的OsWRI3调控水稻种子的落粒性

doi:10.3724/SP.J.1006.2025.42059

摘要/Abstract

摘要：

水稻是世界上重要的粮食作物, 落粒性与水稻的产量息息相关。培育适合现代机械化收获且落粒性适中的水稻品种是提高水稻产量的重要策略。然而水稻的落粒性是一个复杂的数量性状且受多方面的影响, 现有理论不能完全解释落粒的现象。因此, 为了挖掘控制水稻落粒的数量性状基因座(quantitative trait loci, QTL)与基因并完善水稻落粒基因的调控网络, 本研究以易落粒的父本YZX和难落粒的母本02428所构建的192个重组自交系(recombinant inbred lines, RIL)为试验材料进行QTL定位。采用直拉法和斜拉法对开花第30天的192份RIL群体材料进行了全面的分析, 以鉴定在不同环境条件下与水稻种子落粒相关的QTL。在不同环境不同方法下共发现19个与落粒相关的QTL。此外, 通过斜拉法鉴定出1个新的共定位QTL qBSH5.2。通过数据库分析、基因表达量分析、转录组与基因序列分析, 在qBSH5.2中挖掘到了OsWRI3。OsWRI3突变体与野生型(wild type, WT)相比, 表现为更难落粒。在扫描电镜下发现, 突变体相较于WT脱落表面更粗糙且存在弹簧状毛刺结构。同时, 我们发现OsWRI3在水稻穗部与离区的表达量与成熟度呈正相关。并且与WT相比突变体的离区中参与乙烯前体合成的基因下调表达下调。单倍型分析也表明了OsWRI3在调节水稻落粒方面发挥重要的作用, 并且我们挖掘了落粒性适中的优异单倍型组合以适应现代机械化收获。总之, 编码AP2转录因子的OsWRI3的发现不仅为完善与丰富水稻落粒基因调控网络提供了重要的线索, 也为培育适合机械化收获的水稻品种提供了新的遗传资源。

关键词: 水稻, 种子落粒性, QTL定位, AP2转录因子, 单倍型分析

Abstract:

Rice is a staple food crop worldwide, and seed shattering is a critical trait that directly affects yield. Developing rice varieties with moderate seed shattering that are suitable for mechanized harvesting is essential for improving yield. However, seed shattering is a complex quantitative trait influenced by multiple factors, and existing theories do not fully explain its underlying mechanisms. To identify quantitative trait loci (QTL) associated with seed shattering and refine the gene regulatory network governing this trait, we utilized a population of 192 recombinant inbred lines (RILs) derived from a cross between the male parent YZX, which exhibits high seed shattering, and the female parent 02428, which has low seed shattering. QTL mapping was conducted using seed shattering data collected at 30 days after flowering, assessed through both pulling and bending methods under different environmental conditions. A total of 19 QTL associated with seed shattering were identified across various environments and methods. Notably, a novel co-located QTL, qBSH5.2, was detected using the bending method. Further analysis, including database searches, gene expression profiling, RNA sequencing, and gene sequence analysis, identified OsWRI3 as a candidate gene within the qBSH5.2 locus. Functional validation showed that the OsWRI3 mutant exhibited significantly reduced seed shattering compared to the wild type (WT). Scanning electron microscopy revealed that the fracture surface of the mutant was rougher and contained spring-like burr structures, distinguishing it from the WT. Additionally, OsWRI3 expression in the rice panicle and abscission zone was positively correlated with maturity, and genes involved in ethylene precursor synthesis were downregulated in the abscission zone of the mutant compared to the WT. Haplotype analysis further confirmed the regulatory role of OsWRI3 in seed shattering, and we identified favorable haplotype combinations that confer moderate seed shattering, making them suitable for mechanized harvesting. In conclusion, the discovery of OsWRI3, an AP2 transcription factor, not only enhances our understanding of the genetic regulation of seed shattering but also provides valuable genetic resources for breeding rice varieties optimized for mechanized harvesting.

Key words: rice, seed shattering, QTL mapping, AP2 transcription factor, haplotype analysis

杨海洋, 吴林宣, 李博纹, 石翰峰, 袁禧龙, 刘金朝, 蔡海荣, 陈诗怡, 郭涛, 王慧. 基于QTL定位发现的OsWRI3调控水稻种子的落粒性[J]. 作物学报, 0, (): 0-.

YANG Hai-Yang, WU Lin-Xuan, LI Bo-Wen, SHI Han-Feng, YUAN Xi-Long, LIU Jin-Zhao, CAI Hai-Rong, CHEN Shi-Yi, GUO Tao, WANG Hui. OsWRI3, identified based on QTL mapping, regulates seed shattering in rice[J]. Acta Agronomica Sinica, 0, (): 0-.

参考文献

[1] Li C B, Zhou A L, Sang T. Rice domestication by reducing shattering. Science, 2006, 311: 1936–1939.

[2] Doebley J. Unfallen grains: how ancient farmers turned weeds into crops. Science, 2006, 312: 1318–1319.

[3] Fuller D Q, Qin L, Zheng Y F, Zhao Z J, Chen X G, Hosoya L A, Sun G P. The domestication process and domestication rate in rice: spikelet bases from the Lower Yangtze. Science, 2009, 323: 1607–1610.

[4] Patterson S E. Cutting loose. abscission and dehiscence in Arabidopsis. Plant Physiol, 2001, 126: 494–500.

[5] Jin I D. On the formation and development of abscission layer in rice plants, Oryza sativa L. Jpn J Crop Sci, 1986, 55: 451–457.

[6] Estornell L H, Agustí J, Merelo P, Talón M, Tadeo F R. Elucidating mechanisms underlying organ abscission. Plant Sci, 2013, 199/200: 48–60.

[7] Balanzà V, Roig-Villanova I, Di Marzo M, Masiero S, Colombo L. Seed abscission and fruit dehiscence required for seed dispersal rely on similar genetic networks. Development, 2016, 143: 3372–3381.

[8] Lewis M W, Leslie M E, Liljegren S J. Plant separation: 50 ways to leave your mother. Curr Opin Plant Biol, 2006, 9: 59–65.

[9] Thurber C S, Hepler P K, Caicedo A L. Timing is everything: early degradation of abscission layer is associated with increased seed shattering in U.S. weedy rice. BMC Plant Biol, 2011, 11: 14.

[10] Lang H, He Y T, Li F C, Ma D R, Sun J. Integrative hormone and transcriptome analysis underline the role of abscisic acid in seed shattering of weedy rice. Plant Growth Regul, 2021, 94: 261–273.

[11] Ogawa M, Kay P, Wilson S, Swain S M. ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE1 (ADPG1), ADPG2, and QUARTET2 are Polygalacturonases required for cell separation during reproductive development in Arabidopsis. Plant Cell, 2009, 21: 216–233.

[12] Taylor J E, Whitelaw C A. Signals in abscission. New Phytol, 2001, 151: 323–340.

[13] Zhao X H, Xie W G, Zhang J C, Zhang Z Y, Wang Y R. Histological characteristics, cell wall hydrolytic enzymes activity and candidate genes expression associated with seed shattering of Elymus sibiricus accessions. Front Plant Sci, 2017, 8: 606.

[14] Aneja M, Gianfagna T, Ng E. The roles of abscisic acid and ethylene in the abscission and senescence of cocoa flowers. Plant Growth Regul, 1999, 27: 149–155.

[15] 朱子超, 王楚桃, 何永歆, 蒋刚, 欧阳杰, 黄乾龙, 李贤勇. 水稻落粒性的遗传分析和基因定位. 杂交水稻, 2014, 29(1): 62–66.

Zhu Z C, Wang C T, He Y X, Jiang G, Ou-Yang J, Huang Q L, Li X Y. Genetic analysis and molecular mapping of seed shattering in rice. Hybrid Rice, 2014, 29(1): 62–66 (in Chinese with English abstract).

[16] 李仕贵, 马玉清, 何平, 黎汉云, 陈英, 周开达, 朱立煌. 水稻籼粳杂交落粒性的遗传分析和基因定位. 西南农业学报, 1999, 12(增刊2): 77–80.

Li S G, Ma Y Q, He P, Li H Y, Chen Y, Zhou K D, Zhu L H. Genetic analysis and mapping the shattering habit in rice (Oryza Sativa L.). Southwest China J Agric Sci, 1999, 12(S2): 77–80 (in Chinese with English abstract).

[17] 宋颖娉, 宋立明. 水稻落粒性的分子生物学研究进展. 江苏农业科学, 2015, 43(7): 88–90.

Song Y P, Song L M. Advances in molecular biological research on rice seed shattering. Jiangsu Agric Sci, 2015, 43(7): 88–90 (in Chinese).

[18] Wu H, He Q, Wang Q. Advances in rice seed shattering. Int J Mol Sci, 2023, 24: 8889.

[19] Konishi S, Izawa T, Lin S Y, Ebana K, Fukuta Y, Sasaki T, Yano M. An SNP caused loss of seed shattering during rice domestication. Science, 2006, 312: 1392–1396.

[20] Qin Y, Kim S M, Zhao X H, Jia B Y, Lee H S, Kim K M, Eun M Y, Jin I D, Sohn J K. Identification for quantitative trait loci controlling grain shattering in rice. Genes Genom, 2010, 32: 173–180.

[21] 袁睿智, 黄泽键, 罗亮, 赵能, 陈媛, 梁燕青, 万瑶, 刘芳, 李容柏. 基于广西普通野生稻染色体片段代换系的落粒性QTL鉴定及相关主效QTL定位. 南方农业学报, 2020, 51: 1004–1012.

Yuan R Z, Huang Z J, Luo L, Zhao N, Chen Y, Liang Y Q, Wan Y, Liu F, Li R B. Identification of grain-shattering QTL and preliminary mapping of a related major QTL based on chromosome segment substitution lines (CSSLs) of Guangxi common wild rice (Oryza rufipogon Griff.). J South Agric, 2020, 51: 1004–1012 (in Chinese with English abstract).

[22] Chen Y, Shi H F, Yang G L, Liang X Y, Lin X L, Tan S P, Guo T, Wang H. OsCRLK2, a receptor-like kinase identified by QTL analysis, is involved in the regulation of rice quality. Rice, 2024, 17: 24.

[23] Lin Z W, Li X R, Shannon L M, Yeh C T, Wang M L, Bai G H, Peng Z, Li J R, Trick H N, Clemente T E, et al. Parallel domestication of the Shattering1 genes in cereals. Nat Genet, 2012, 44: 720–724.

[24] Lyu S W, Wu W G, Wang M H, Meyer R S, Ndjiondjop M N, Tan L B, Zhou H Y, Zhang J W, Fu Y C, Cai H W, et al. Genetic control of seed shattering during African rice domestication. Nat Plants, 2018, 4: 331–337.

[25] Lin Z W, Griffith M E, Li X R, Zhu Z F, Tan L B, Fu Y C, Zhang W X, Wang X K, Xie D X, Sun C Q. Origin of seed shattering in rice (Oryza sativa L.). Planta, 2007, 226: 11–20.

[26] Zhou Y, Lu D F, Li C Y, Luo J H, Zhu B F, Zhu J J, Shangguan Y Y, Wang Z X, Sang T, Zhou B, et al. Genetic control of seed shattering in rice by the APETALA2 transcription factor shattering abortion1. Plant Cell, 2012, 24: 1034–1048.

[27] Yoon J, Cho L H, Kim S L, Choi H, Koh H J, An G. The BEL1-type homeobox gene SH5 induces seed shattering by enhancing abscission‐zone development and inhibiting lignin biosynthesis. Plant J, 2014, 79: 717–728.

[28] Ji H, Kim S R, Kim Y H, Kim H, Eun M Y, Jin I D, Cha Y S, Yun D W, Ahn B O, Lee M C, et al. Inactivation of the CTD phosphatase-like gene OsCPL1 enhances the development of the abscission layer and seed shattering in rice. Plant J, 2010, 61: 96–106.

[29] Sun P Y, Zhang W H, Wang Y H, He Q, Shu F, Liu H, Wang J, Wang J M, Yuan L P, Deng H F. OsGRF4 controls grain shape, panicle length and seed shattering in rice. J Integr Plant Biol, 2016, 58: 836–847.

[30] Cao H S, Zhuo L, Su Y, Sun L X, Wang X M. Non-specific phospholipase C1 affects silicon distribution and mechanical strength in stem nodes of rice. Plant J, 2016, 86: 308–321.

[31] Wu W G, Liu X Y, Wang M H, Meyer R S, Luo X J, Ndjiondjop M N, Tan L B, Zhang J W, Wu J Z, Cai H W, et al. A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nat Plants, 2017, 3: 17064.

[32] Ishii T, Numaguchi K, Miura K, Yoshida K, Thanh P T, Htun T M, Yamasaki M, Komeda N, Matsumoto T, Terauchi R, et al. OsLG1 regulates a closed panicle trait in domesticated rice. Nat Genet, 2013, 45: 462–465.

[33] Jiang L Y, Ma X, Zhao S S, Tang Y Y, Liu F X, Gu P, Fu Y C, Zhu Z F, Cai H W, Sun C Q, et al. The APETALA2-like transcription factor SUPERNUMERARY BRACT controls rice seed shattering and seed size. Plant Cell, 2019, 31: 17–36.

[34] 王穆穆, 何艳芳, 郑永胜, 王晖, 王丽媛, 王东建, 张晗, 李汝玉. 水稻落粒基因SH8的精细定位与克隆. 作物学报, 2022, 48: 1948–1956.

Wang M M, He Y F, Zheng Y S, Wang H, Wang L Y, Wang D J, Zhang H, Li R Y. Fine mapping and cloning of a seed shattering gene SH8 in rice (Oryza sativa L.). Acta Agron Sin, 2022, 48: 1948–1956 (in Chinese with English abstract).

[35] Ning J, He W, Wu L H, Chang L Q, Hu M, Fu Y C, Liu F X, Sun H Y, Gu P, Ndjiondjop M N, et al. The MYB transcription factor Seed Shattering 11 controls seed shattering by repressing lignin synthesis in African rice. Plant Biotechnol J, 2023, 21: 931–942.

[36] Wu H, He Q, He B, He S Y, Zeng L J, Yang L B, Zhang H, Wei Z R, Hu X M, Hu J, et al. Gibberellin signaling regulates lignin biosynthesis to modulate rice seed shattering. Plant Cell, 2023, 35: 4383–4404.

[37] Lee G H, Kang I K, Kim K M. Mapping of novel QTL regulating grain shattering using doubled haploid population in rice (Oryza sativa L.). Int J Genomics, 2016, 2016: 2128010.

[38] Chen L K, Gao W W, Chen S P, Wang L P, Zou J Y, Liu Y Z, Wang H, Chen Z Q, Guo T. High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice. Rice, 2016, 9: 48.

[39] Meng L, Li H H, Zhang L Y, Wang J K. QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J, 2015, 3: 269–283.

[40] Wu L X, Yue J C, Wang J F, Lu W Y, Huang M, Guo T, Wang H. RNA-seq and genome-wide association studies reveal potential genes for rice seed shattering. Int J Mol Sci, 2022, 23: 14633.

[41] Ji H S, Chu S H, Jiang W Z, Cho Y I, Hahn J H, Eun M Y, McCouch S R, Koh H J. Characterization and mapping of a shattering mutant in rice that corresponds to a block of domestication genes. Genetics, 2006, 173: 995–1005.

[42] Ali M R, Hasan M K, Saha C K, Alam M M, Hossain M M, Kalita P K, Hansen A C. Role of mechanical rice harvesting in socio-economic development of Bangladesh. In: Mani S, eds. 2018 ASABE Annual International Meeting. St. Joseph: American Society of Agricultural and Biological Engineers, 2018. pp 1–8.

[43] Hasan K, Tanaka T S T, Alam M, Ali R, Kumer Saha C. Impact of modern rice harvesting practices over traditional ones. Rev Agric Sci, 2020, 8: 89–108.

[44] Fu J W, Ji C, Liu H P, Wang W K, Zhang G Z, Gao Y, Zhou Y, Abdeen M A. Research progress and prospect of mechanized harvesting technology in the first season of ratoon rice. Agriculture, 2022, 12: 620.

[45] Mano F, Aoyanagi T, Kozaki A. Atypical splicing accompanied by skipping conserved micro-exons produces unique WRINKLED1, an AP2 domain transcription factor in rice plants. Plants, 2019, 8: 207.

[46] Sargent J A, Osborne D J, Dunford S M. Cell separation and its hormonal control during fruit abscission in the Gramineae. J Exp Bot, 1984, 35: 1663–1674.

[47] 王权帅, 赵丹莹, 申琳, 生吉萍. 脱落调节物质对植物器官脱落的调控. 西北植物学报, 2009, 29: 2352–2359.

Wang Q S, Zhao D Y, Shen L, Sheng J P. Regulation of plant organs abscission by abscission regulating substances. Acta Bot Boreali-Occident Sin, 2009, 29: 2352–2359 (in Chinese with English abstract).

[48] Jackson M B, Hartley C B, Osborne D J. Timing abscission in PHASEOLUS VULGARIS L. by controlling ethylene production and sensitivity to ethylene. New Phytol, 1973, 72: 1251–1260.

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