Genome-wide Association Analysis of Rice Seed Dehydration Rate at Maturity Stage

doi:10.16819/j.1001-7216.2024.230305

Abstract

Abstract:

【Objective】The dehydration rate of grains directly influences the safe harvesting and rapid drying of seeds. Therefore, to ensure seed quality and reduce production costs, varieties with low grain moisture content and fast dehydration rates were selected for production. 【Method】A total of 165 rice core germplasms from 82 different countries and regions were used as experimental materials. Genome-wide association analysis (GWAS) was conducted by combining the phenotype and genotype of seed dehydration rates at the maturity stage. This aimed to explore key genes sensitive to dehydration and their regulatory roles in rice germplasm, laying a foundation for cultivating and developing fast dehydration varieties. 【Results】1) Descriptive statistical analysis of dehydration rate traits of the rice core germplasm population showed that these traits exhibited continuously skewed normal distributions over two years, with significant correlations between years for rapid dehydration rates. Rapid dehydration rates were positively correlated with slow dehydration rates across different subgroups. 2) GWAS analysis identified 170 SNPs and 36 QTLs associated with dehydration rates. LD analysis revealed six QTLs closely related to dehydration rates: qGDR2.3, qGDR4.1, qGDR4.2, qGDR6.1, qGDR6.4, and qGDR10.1. 【Conclusion】 The main candidate genes within these QTL intervals, including OsPIP1;1, OsTIFY9, OsbZIP48, OsATG8b, OsDREB1C, OsSCP46, are closely associated with water transport activity, signal transduction, transcriptional regulation, and antioxidant defense. It is speculated that they play roles in seed dehydration rates and can serve as optimal candidate genes.

Key words: rice seed, dehydration rate, QTL, genome-wide association analysis

摘要：

【目的】籽粒脱水速率直接影响种子的安全收获和快速干燥。选育成熟期籽粒含水量低、脱水速率快的品种，可保障种子质量，降低生产成本。【方法】采用来自82个不同国家和地区的165份水稻核心种质作为试验材料，将成熟期种子脱水速率表型与基因型相结合进行GWAS分析，挖掘调控种子脱水的关键基因，为培育和创制脱水快速品种奠定基础。【结果】1）对165份水稻核心种质群体脱水速率性状进行描述性统计分析，结果显示2年脱水速率性状均呈连续性偏正态分布，2年快速脱水的脱水速率性状在年际间具有显著相关性。不同亚群之间快速脱水与慢速脱水速率正相关。2）GWAS关联分析共获得与脱水速率显著关联的SNP 170个，QTL 36个。通过LD分析定位到6个与脱水速率密切相关的QTL，分别为qGDR2.3、qGDR4.1、qGDR4.2、qGDR6.1、qGDR6.4、qGDR10.1。【结论】这些QTL区间内主要候选基因OsPIP1;1、OsTIFY9、OsbZIP48、OsATG8b、OsDREB1C、OsSCP46与水分转运活性、信号转导、转录调控、抗氧化防御密切相关，推测它们与成熟期水稻种子脱水速率相关，可作为候选基因。

关键词: 水稻种子, 脱水速率, 数量性状基因座, 全基因组关联分析

LIU Zhongqi, ZHANG Haiqing, HE Jiwai, GUI Jinxin. Genome-wide Association Analysis of Rice Seed Dehydration Rate at Maturity Stage[J]. Chinese Journal OF Rice Science, 2024, 38(2): 150-159.

刘忠奇, 张海清, 贺记外, 桂金鑫. 成熟期水稻种子脱水速率全基因组关联分析[J]. 中国水稻科学, 2024, 38(2): 150-159.

Figures/Tables 5

References 29

[1]	刘忠奇, 贺记外, 张海清, 刘爱民. 植物种子脱水耐性的研究现状分析与展望[J]. 中国农学通报, 2020, 36(2): 36-41.
	Liu Z Q, He J W, Zhang H Q, Liu A M. Dehydration tolerance of plant seeds: Current research situation and prospects[J]. Chinese Agricultural Science Bulletin, 2020, 36(2): 36-41. (in Chinese with English abstract)
[2]	Zhou G F, Hao D R, Xue L, Chen G Q, Lu H H, Zhang Z L, Shi M L, Mao Y X. Genome-wide association study of kernel moisture content at harvest stage in maize[J]. Breeding Science, 2018, 68(5): 622-628.
[3]	Jia T J, Wang L F, Li J J, Ma J, Cao Y Y, Lübbersted T, Li H Y. Integrating a genome-wide association study with transcriptomic analysis to detect genes controlling grain drying rate in maize (Zea mays L)[J]. Theoretical and Applied Genetics, 2020, 133(2): 623-634.
[4]	刘显君, 王振华, 王霞, 李庭锋, 张林. 玉米籽粒生理成熟后自然脱水速率QTL的初步定位[J]. 作物学报, 2010, 36(1): 47-52.
	Liu X J, Wang Z H, Wang X, Li T F, Zhang L. Primary mapping of QTL for dehydration rate of maize kernel after physiological maturing[J]. Acta Agronomica Sinica, 2010, 36(1): 47-52. (in Chinese with English abstract)
[5]	Sala R G, Andrade F H, Camadro E L, Cerono J C. Quantitative trait loci for grain moisture at harvest and field grain drying rate in maize (Zea mays L.)[J]. Theoretical and Applied Genetics, 2006, 112: 462-471.
[6]	Li Y L, Dong Y B, Yang M L, Wang Q L, Shi Q, Zhou Q, Deng F, Ma Z Y, Qiao D H, Xu H. QTL detection for grain water relations and genetic correlations with grain matter accumulation at four stages after pollination in maize[J]. Journal of Plant Biochemistry and Physiology, 2014, 2(1): 1-9.
[7]	Capelle V, Remoué C, Moreau L, Reyss A, MahéahssMassonneau A, Falque M, Charcosset A, Thévenot C, Rogowsky P, Coursol S, Prioul J L. QTLs and candidate genes for desiccation and abscisic acid content in maize kernels[J]. BMC Plant Biology, 2010, 10(1): 1-22.
[8]	孙乐秀. 玉米自交系机械化收获相关性状及其SNP标记关联分析[D]. 泰安: 山东农业大学, 2015.
	Sun L X. Traits related to mechanical harvesting and their association analysis with SNP markers in maize inbred lines[D]. Tai’an: Shandong Agricultural University, 2015. (in Chinese with English abstract)
[9]	Li W Q, Yu Y H, Wang L X, Luo Y, Peng Y, Xu Y C, Liu X G, Wu S S, Jian L M, Xu J T, Xiao Y J, Yan J B. The genetic architecture of the dynamic changes in grain moisture in maize[J]. Plant Biotechnology Journal, 2021, 19: 1195-1205.
[10]	朱冬梅, 胡文静, 别同德, 陆成彬, 赵仁慧, 高德荣. 利用四交RIL群体定位小麦籽粒脱水速率 QTL[J]. 麦类作物学报, 2020, 40(1): 49-54.
	Zhu D M, Hu W J, Bie T D, Lu C B, Zhao R H, Gao D R. QTL mapping for kernel dehydration rate after physiological maturity using in four way RIL populations of wheat[J]. Journal of Triticeae Crop, 2020, 40(1): 49-54. (in Chinese with English abstract)
[11]	于澎湃. 高粱耐密性研究及籽粒脱水速率的QTL定位[D]. 天津: 天津农学院, 2019.
	Yu P P. Studies on sorghum density tolerance and QTL mapping of grain dehydration rate[D]. Tianjin:Tianjin Agricultural University, 2019. (in Chinese with English abstract)
[12]	袁静, 任育军, 赵洁. 水稻胚胎发育过程相关基因的鉴定[J]. 分子细胞生物学报, 2008, 41(3): 238-244.
	Yuan J, Ren Y J, Zhao J. Identification of genes associated with early and late embryo development in rice[J]. Journal of Molecular Cell Biology, 2008, 41(3): 238-244. (in Chinese with English abstract)
[13]	张娟, 牛百晓, 鄂志国, 陈忱. 水稻胚乳发育遗传调控的研究进展[J]. 中国水稻科学, 2021, 35(4): 326-341.
	Zhang J, Niu B X, E Z G, Chen C. Towards understanding the genetic regulations of endosperm development in rice[J]. Chinese Journal of Rice Science, 2021, 35(4): 326-341. (in Chinese with English abstract)
[14]	Samarah N H, Mullen R E, Alqudah A M. An index to quantify seed moisture loss rate in relationship with seed desiccation tolerance in common vetch[J]. Seed Science and Technology, 2009, 37: 413-422.
[15]	Zhao K Y, Tung C W, Eizenga G C, Wright M H, Ali M L, Price A H, Norton G J, Islam M R, Reynolds A, Mezey J, McClung A M, Bustamante C D, McCouch S R. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa[J]. Nature Communications, 2011, 2: 467-477.
[16]	林晋军, 姚威, 彭沙莎, 刘文韬, 陈文凤, 刘雄伦, 刘金灵. 水稻抽穗期性状QTL的全基因组关联定位分析[J]. 湖南农业大学学报, 2021, 47(3): 283-290.
	Lin J J, Yao W, Peng S S, Liu W T, Chen W F, Liu X L, Liu J L. Genome-wide association dissection of QTLs for heading date traits in rice[J]. Journal of Hunan Agricultural University, 2021, 47(3): 283-290. (in Chinese with English abstract)
[17]	Liu C W, Tatsuya F, Tadashi M, Gena P, Frascaria D, Kaneko T, Katsuhara M, Zhong S H, Sun X L, Zhu Y M, Iwasaki I, Kitagawa Y L. Aquaporin OsPIP1;1 promotes rice salt resistance and seed germination[J]. Plant Physiology and Biochemistry, 2013, 63: 151-158.
[18]	Dubouzet J G, Sakuma Y, Ito Y, Kasuga M, Dubouzet E G, Miura S, Seki M, Shinozak K, Shinozaki Y. OsDREB genes in rice, encode transcription activators that function in drought, high-salt and cold responsive gene expression[J]. The Plant Journal, 2003, 33(4): 751-763.
[19]	Li Z Y, Tang L Q, Qiu J H, Zhang W, Wang Y F, Tong X H, Wei X J, Hou Y X, Zhang J. Serine carboxypeptidase 46 regulates grain filling and seed germination in rice[J]. PLoS One, 2016, 11(7): 1-18.
[20]	Ji Q, Zhang L S, Wang Y F, Wang J. Genome-wide analysis of basic leucine zipper transcription factor families in Arabidopsis thaliana, Oryza sativa and Populus trichocarpa[J]. Journal of Shanghai University, 2009, 13(2): 174-182.
[21]	Ye H, Du H, Tang N, Li X, Xiong L. Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice[J]. Plant Molecular Biology, 2009, 71(3): 291-305.
[22]	Izumi M, Hidema J, Wada S, Kondo E, Makino A, Ishida H. Establishment of monitoring methods for autophagy in rice reveals autophagic recycling of chloroplasts and root plastids during energy limitation[J]. Plant Physiology, 2015, 167(4): 1307-1320.
[23]	渠建洲. 玉米籽粒含水率和脱水速率的基因挖掘与分析[D]. 杨凌: 西北农林科技大学, 2021.
	Qu J Z. Gene mining and analysis of maize kernel moisture content and dehydration rate[D]. Yangling: Northwest A＆F University, 2021. (in Chinese with English abstract)
[24]	Si J K, Arifa A. Tissue and cell-specific localization of rice aquaporins and their water transport activities[J]. Plant and Cell Physiology, 2008, 49(1): 30-39.
[25]	张凤启, 王邑双, 丁勇, 张君, 赵霞, 赵发欣, 唐保军. 玉米籽粒脱水速率研究进展[J]. 农学学报, 2018, 8(11): 4-11.
	Zhang F Q, Wang Y S, Ding Y, Zhang J, Zhao X, Zhao F X, Tang B J. Corn kernel dehydration rate: Research progress[J]. Journal of Agriculture, 2018, 8(11): 4-11. (in Chinese with English abstract)
[26]	Peng B, Kong H L, Li Y B, Wang L Q, Zhong M, Sun L, Gao G J, Zhang Q L, Luo L J, Wang G W, Xie W B, Chen J X, Yao W, Peng Y, Lei L, Lian X M, Xiao J H, Xu C G, Li X H, He Y Q. OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice[J]. Nature Communications, 2014, 5: 5847. (in Chinese with English abstract)
[27]	彭波, 孙艳芳, 庞瑞华, 周棋赢, 袁红雨, 宋世枝. 植物氨基酸转运蛋白的研究进展[J]. 热带作物学报, 2016, 37(6): 1238-1243.
	Peng B, Sun Y F, Pang R H, Zhou Q Y, Yuan H Y, Song S Z. Research progress of amino acid transporters in plants[J]. Chinese Journal of Tropical Crops, 2016, 37(6): 1238-1243. (in Chinese with English abstract)
[28]	叶玲飞, 罗光宇, 向建华, 刘爱玲, 陈信波. 丝氨酸羧肽酶及其类蛋白的研究进展[J]. 植物生理学报, 2013, 49(2): 122-126.
	Ye L F, Luo G Y, Xiang J H, Liu A L, Chen X B. Research progress of serine carboxypeptidases and serine carboxypeptidase like proteins[J]. Plant Physiology Journal, 2013, 49(2): 122-126. (in Chinese with English abstract)
[29]	叶玲飞. 水稻OsSCP基因的耐逆相关功能研究[D]. 长沙: 湖南农业大学, 2013.
	Ye L F. Studies on the stress resistance functions of OsSCP gene[D]. Changsha: Hunan Agricultural University, 2013. (in Chinese with English abstract)

染色体Chromosome	位点 Locus	候选基因 Candidate gene	功能注释 Functional annotation
1	qGDR1.2	LOC_Os01g49710	谷胱甘肽S-转移酶 Glutathione S-transferase
2	qGDR2.2	LOC_Os02g36974	14-3-3蛋白 14-3-3 protein
2	qGDR2.3	LOC_Os02g44630	水通道蛋白 Aquaporin protein	OsPIP1;1^[17]
4	qGDR4.1	LOC_Os04g32480	锌指蛋白 Zinc-finger protein	OsTIFY9^[21]
4	qGDR4.2	LOC_Os04g53240	自噬相关蛋白 Autophagy-related protein	OsATG8b^[22]
6	qGDR6.1	LOC_Os06g03670	脱水反应元件结合蛋白 Dehydration-responsive element-binding protein	OsDREB1C^[18]
6	qGDR6.2	LOC_Os06g12350	氨基酸转运蛋白 Amino acid transporter
6	qGDR6.4	LOC_Os06g39960	bZIP转录因子结构域含蛋白 bZIP transcription factor domain containing protein	OsbZIP48^[20]
7	qGDR7.3	LOC_Os07g37890	蛋白磷酸酶2C Protein phosphatase 2C
7	qGDR7.4	LOC_Os07g38580	锌指家族蛋白 Zinc finger family protein
7	qGDR7.6	LOC_Os07g47250	脂肪酶前体 Lipase precursor
8	qGDR8.2	LOC_Os08g06240	MYB家族转录因子 MYB family transcription factor
8	qGDR8.3	LOC_Os08g15149	硫氧还蛋白结构域蛋白9 Thioredoxin domain-containing protein 9
9	qGDR9.1	LOC_Os09g20990	海藻糖-6-磷酸合成酶 Trehalose-6-phosphate synthase
9	qGDR9.2	LOC_Os09g26170	MYB家族转录因子 MYB family transcription factor
10	qGDR10.1	LOC_Os10g01134	OsSCP46-推定丝氨酸羧肽酶同源物 OsSCP46-putative Serine Carboxypeptidase homologue	OsSCP46^[19]
10	qGDR10.3	LOC_Os10g25010	OsCML8-钙调素相关钙传感器蛋白 OsCML8-calmodulin-related calcium sensor protein
11	qGDR11.1	LOC_Os11g37000	热激蛋白DnaJ Heat shock protein DnaJ

染色体Chromosome	位点 Locus	候选基因 Candidate gene	功能注释 Functional annotation
1	qGDR1.2	LOC_Os01g49710	谷胱甘肽S-转移酶 Glutathione S-transferase
2	qGDR2.2	LOC_Os02g36974	14-3-3蛋白 14-3-3 protein
2	qGDR2.3	LOC_Os02g44630	水通道蛋白 Aquaporin protein	OsPIP1;1^[17]
4	qGDR4.1	LOC_Os04g32480	锌指蛋白 Zinc-finger protein	OsTIFY9^[21]
4	qGDR4.2	LOC_Os04g53240	自噬相关蛋白 Autophagy-related protein	OsATG8b^[22]
6	qGDR6.1	LOC_Os06g03670	脱水反应元件结合蛋白 Dehydration-responsive element-binding protein	OsDREB1C^[18]
6	qGDR6.2	LOC_Os06g12350	氨基酸转运蛋白 Amino acid transporter
6	qGDR6.4	LOC_Os06g39960	bZIP转录因子结构域含蛋白 bZIP transcription factor domain containing protein	OsbZIP48^[20]
7	qGDR7.3	LOC_Os07g37890	蛋白磷酸酶2C Protein phosphatase 2C
7	qGDR7.4	LOC_Os07g38580	锌指家族蛋白 Zinc finger family protein
7	qGDR7.6	LOC_Os07g47250	脂肪酶前体 Lipase precursor
8	qGDR8.2	LOC_Os08g06240	MYB家族转录因子 MYB family transcription factor
8	qGDR8.3	LOC_Os08g15149	硫氧还蛋白结构域蛋白9 Thioredoxin domain-containing protein 9
9	qGDR9.1	LOC_Os09g20990	海藻糖-6-磷酸合成酶 Trehalose-6-phosphate synthase
9	qGDR9.2	LOC_Os09g26170	MYB家族转录因子 MYB family transcription factor
10	qGDR10.1	LOC_Os10g01134	OsSCP46-推定丝氨酸羧肽酶同源物 OsSCP46-putative Serine Carboxypeptidase homologue	OsSCP46^[19]
10	qGDR10.3	LOC_Os10g25010	OsCML8-钙调素相关钙传感器蛋白 OsCML8-calmodulin-related calcium sensor protein
11	qGDR11.1	LOC_Os11g37000	热激蛋白DnaJ Heat shock protein DnaJ