成熟期水稻种子脱水速率全基因组关联分析

doi:10.16819/j.1001-7216.2024.230305

摘要/Abstract

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

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

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.

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.

图/表 5

图1 供试水稻材料脱水速率群体分布 A：快速脱水处理（2019年）；B：快速脱水处理（2020年）；C：慢速脱水处理（2019年）；D：慢速脱水处理（2020年）。其中，快速脱水条件为恒温45脱水℃，慢速脱水条件为恒温40脱水℃。

Fig. 1. Distribution of rice seed dehydration rates of tested rice material A, Rapid dehydration treatment(2019); B, Rapid dehydration treatment (2020); C, Slow dehydration treatment(2019); D, Slow dehydration treatment(2020). The fast dehydration condition is constant temperature 45 ± 2℃, the slow dehydration condition is constant temperature 40 ± 2℃.

图2 不同亚群水稻种质群体在2年不同脱水方式下脱水速率差异的箱形图 A：快速脱水处理(2019年)；B：快速脱水处理(2020年)；C：慢速脱水处理(2019年)；D：慢速脱水处理(2020年)。箱体上标有不同小写字母者表示不同亚群间差异达0.05显著水平(Duncan多重比较)。

Fig. 2. Box plots of dehydration rate of different sub-groups of rice under different dehydration conditions in two years A, Rapid dehydration treatment(2019); B, Rapid dehydration treatment(2020); C, Slow dehydration treatment(2019); D, Slow dehydration treatment(2020). Different lowercase letters indicate significant difference of 0.05 level among different subgroups (Duncan multiple comparison). ADMIX, Intermediate type; AROM, Aromatic rice; AUS, Aus rice; IND, indica rice; TEJ, Temperate japonica rice; TRJ, Tropical japonica rice.

图3 水稻成熟种子快速脱水与慢速脱水条件下脱水速率QTL位点的曼哈顿图与QQ图 A：2019年快速脱水条件下脱水速率QTL位点的曼哈顿图，图中红色实线以上区域代表在P<0.001水平上极显著，下同；B：2019年快速脱水条件下脱水速率QTL位点的QQ图；C和D：2020年快速脱水；E和F：2019年慢速脱水；G和H：2020年慢速脱水。

Fig. 3. Manhattan map and QQ map of QTLs for seed dehydration rate at maturity under different dehydration treatments A, Manhattan plot of QTLs for seed dehydration rate at maturity under the fast dehydration conditions in 2019. The areas above the red solid line represent significant difference at P < 0.001 level, and the same below; B, QQ map of QTLs for seed dehydration rate at maturity under the fast dehydration conditions in 2019; C and D, Under the fast dehydration conditions in 2020; E and F, Under the low dehydration conditions in 2019; G and H, Under the low dehydration conditions in 2020.

表1 预测水稻成熟期种子脱水速率相关候选基因及其功能注释

Table 1. Candidate genes and their functional annotations for predicting the rate of seed dehydration in maturity

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

图4 候选QTL区间内关联位点的LD分析 A: qGDR2.3(OsPIP1;1的LD分析); B: qGDR6.1(OsDREB1C的LD分析); C: qGDR10.1(OsSCP46的LD分析); D: qGDR6.4(OsbZIP48的LD分析); E: qGDR4.1(OsTIFY9的LD分析); F: qGDR4.2(OsATG8b的LD分析)。

Fig. 4. LD analysis of association loci within candidate QTL intervals

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