广西水稻地方品种核心种质芽期耐盐性全基因组关联分析

doi:10.3724/SP.J.1006.2022.12030

Abstract

Abstract:

Rice is a salt-sensitive crop, and salt stress can cause significant reduction in rice yield. China's total saline area is large and growing rapidly. Therefore, it is necessary to screen for the salt-tolerant rice germplasm and cultivate these varieties. In this study, we evaluated the relative salt damage rate of 419 core germplasm of Guangxi rice landraces at seed germination stage under 1.5% NaCl salt stress, and identified the salt-tolerant loci by whole-genome association analysis. The results showed that the average germination rate under salt stress was 57.67%, which was significantly 92.55% lower than that of control group, and the Shapiro-Wilk test (0.9301) found that the distribution did not conform to normal distribution. Based on 208,993 SNP markers, 419 core germplasm was divided into 6 subgroups. We used general linear model (GLM) and mixed linear model (MLM) analysis to identify 129 and 1 significantly associated SNPs, respectively, which were distributed on chromosomes 1, 2, 3, 4, 5, 6, 8, 9, and 12. Among the 14 regions that were significantly associated with rice salt tolerance, 13 regions overlapped with previously identified or cloned salt tolerance genes. The significantly associated region Chr. 8:10,564,948-10,733,175 was reported for the first time and named qGR8. There were 53 genes in qGR8 region, 34 of which were compared with transcriptome data to obtain the expression profiles. We compared the expression profiles and speculated that LOC_Os08g17370 was a candidate gene. This gene is a member of transmembrane 9 superfamily and is up-regulated in roots and leaves of salt-tolerant parent. Thus, this gene might be a novel salt-tolerant gene in qGR8 region at germination stage in rice. These results lay a foundation for cloning new genes of salt-tolerant and provide new genetic resources for breeding salt-tolerant rice varieties.

Key words: Oryza sativa L., core germplasm, germination, salt tolerance, genome-wide association study

XIA Xiu-Zhong, ZHANG Zong-Qiong, YANG Xing-Hai, ZHUANG Jie, ZENG Yu, DENG Guo-Fu, SONG Guo-Xian, HUANG Yu-Xiao, NONG Bao-Xuang, LI Dan-Ting. Genome wide association study of salt tolerance at the germination stage for core Germplasm of rice landrace in Guangxi, China[J].Acta Agronomica Sinica, 2022, 48(8): 2007-2015.

Figures/Tables 6

Fig. 1

Fig. 2

Fig. 3

Table 1

Transcriptional abundance of 34 genes at germination stage"

基因名称 Gene ID	转录丰度 Transcript abundances	描述 Description
LOC_Os08g17160	高High	Plastocyanin-like domain containing protein, putative, expressed
LOC_Os08g17294	高High	PSF3-Putative GINS complex subunit, expressed
LOC_Os08g17320	高High	Protein kinase family protein, putative, expressed
LOC_Os08g17370	高High	Transmembrane 9 superfamily member, putative, expressed
LOC_Os08g17410	高High	BRASSINOSTEROID INSENSITIVE 1 precursor, putative, expressed
LOC_Os08g17510	高High	Sulfotransferase domain containing protein, expressed
LOC_Os08g17600	高High	SNARE domain containing protein, putative, expressed
LOC_Os08g17610	高High	Expressed protein
LOC_Os08g17650	高High	LYR motif containing protein, putative, expressed
LOC_Os08g17680	高High	Stromal cell-drived factor 2-like protein precursor, putative, expressed
LOC_Os08g17150	低Low	Expressed protein
LOC_Os08g17390	低Low	Expressed protein
LOC_Os08g17400	低Low	WRKY89, expressed
LOC_Os08g17430	低Low	Expressed protein
LOC_Os08g17450	低Low	Retrotransposon protein, putative, undassified, expressed
LOC_Os08g17500	低Low	CinnamoyI-CoA reductase, putative, expressed
LOC_Os08g17520	低Low	Flavanol sulfotransferase-like, putative, expressed
LOC_Os08g17655	低Low	Expressed protein
LOC_Os08g17110	无No	Expressed protein
LOC_Os08g17120	无No	Transposon protein, putative, CACTA En/Spm sub-dass
LOC_Os08g17210	无No	Transposon protein, putative, CACTA En/Spm sub-dass
LOC_Os08g17220	无No	Uncharacterized PE-PGRS family protein PE PGRS54 precursor, putative, expressed
LOC_Os08g17270	无No	Expressed protein
LOC_Os08g17330	无No	Expressed protein
LOC_Os08g17340	无No	Hypothetical protein
LOC_Os08g17350	无No	Expressed protein
LOC_Os08g17360	无No	Hypothetical protein
LOC_Os08g17440	无No	Expressed protein
LOC_Os08g17560	无No	Expressed protein
LOC_Os08g17580	无No	Hypothetical protein
LOC_Os08g17620	无No	Expressed protein
LOC_Os08g17630	无No	Expressed protein
LOC_Os08g17640	无No	Z0S8-02-C2H2 zinc finger protein, expressed
LOC_Os08g17690	无No	Retrotransposon protein, putative, unclassified

Table 1

Fig. 4

Table 2

14 Associated QTLs and candidate genes related to salt tolerance at germination stage"

QTL	SNP数量 Number of SNPs	范围 Range	峰值SNP Peak SNP	P值 P-value	候选基因 Candidate gene	基因描述 Gene description
qGR1.1	2	23,752,956-23,786,838	23,752,956	2.33E-08	SIDP361^[23]	DUF1644蛋白 DUF1644 protein gene
qGR1.2	6	31,534,965-31,593,365	31,534,965	1.09E-07	OsERF922^[24]	ERF转录因子 ERF transcription factor
qGR3.1	3	1,874,033-1,874,036	1,874,033	2.22E-07	ONAC022^[25]	胁迫响应型NAC转录因子基因 Overexpression of a stress-responsive NAC
qGR3.2	16	16,671,741-17,432,153	16,671,952	2.81E-10	OsHAP2E^[26]	血红素激活蛋白; 核因子Y; CCAAT结合因子 Heme activator protein gene; nuclear factor Y; CCAAT binding factor
qGR3.3	2	20,621,667-20,925,341	20,621,667	2.00E-07	OsHAK16^[27,28]	钾转运蛋白 Potassium transporter
qGR3.4	3	26,339,090-26,393,672	26,339,090	2.89E-09	OsBIHD1^[29]	同源异型基因 Rice homeodomain gene
qGR3.5	5	31,937,083-32,488,239	31,982,396	1.32E-10	OsGASR1^[30]	赤霉素刺激转录基因 GA-stimulated transcript-related gene; Oryza sativa gibberellic acid stimulated rice 1
qGR4.1	5	17,564,210-19,871,791	17,626,425	8.53E-08	OsHAK1^[31]	钾离子转运蛋白 Potassium transporter
qGR4.2	5	24,215,216-24,282,470	24,282,470	2.26E-08	OsBADH1^[32]	甜菜碱醛脱氢酶 Betaine aldehyde dehydrogenase
qGR4.3	43	27,473,283-27,958,451	27,907,711	9.60E-13	OsGPX1^[33]	线粒体谷胱甘肽过氧化物酶 Mitochondrial glutathione peroxidase
qGR5	9	19,208,151-19,330,003	19,329,999	7.44E-08	SERF1^[34]	盐应答的ERF转录因子 Salt-responsive ERF 1
qGR6	12	1,607,061-1,822,395	1,661,829	1.07E-09	OsSIK1^[35]	类受体激酶基因; 胁迫诱导的蛋白激酶基因 Receptor-like kinase; stress-induced protein kinase gene 1
qGR8	4	10,564,948-10,733,175	10,564,948	4.24E-08	New gene	未知 Unknown
qGR12	3	21,374,803-22,039,414	21,374,803	7.63E-08	WSL12^[36]	白色条纹叶基因 White stripe leaf 12

Table 2

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Genome wide association study of salt tolerance at the germination stage for core Germplasm of rice landrace in Guangxi, China

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[4]	ZHENG Chong-Ke, ZHOU Guan-Hua, NIU Shu-Lin, HE Ya-Nan, SUN wei, XIE Xian-Zhi. Phenotypic characterization and gene mapping of an early senescence leaf H5(esl-H5) mutant in rice (Oryza sativa L.) [J]. Acta Agronomica Sinica, 2022, 48(6): 1389-1400.
[5]	LEI Xin-Hui, WAN Chen-Xi, TAO Jin-Cai, LENG Jia-Jun, WU Yi-Xin, WANG Jia-Le, WANG Peng-Ke, YANG Qing-Hua, FENG Bai-Li, GAO Jin-Feng. Effects of soaking seeds with MT and EBR on germination and seedling growth in buckwheat under salt stress [J]. Acta Agronomica Sinica, 2022, 48(5): 1210-1221.
[6]	SONG Shi-Qin, YANG Qing-Long, WANG Dan, LYU Yan-Jie, XU Wen-Hua, WEI Wen-Wen, LIU Xiao-Dan, YAO Fan-Yun, CAO Yu-Jun, WANG Yong-Jun, WANG Li-Chun. Relationship between seed morphology, storage substance and chilling tolerance during germination of dominant maize hybrids in Northeast China [J]. Acta Agronomica Sinica, 2022, 48(3): 726-738.
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[9]	ZHENG Xiang-Hua, YE Jun-Hua, CHENG Chao-Ping, WEI Xing-Hua, YE Xin-Fu, YANG Yao-Long. Xian-geng identification by SNP markers in Oryza sativa L. [J]. Acta Agronomica Sinica, 2022, 48(2): 342-352.
[10]	HU Liang-Liang, WANG Su-Hua, WANG Li-Xia, CHENG Xu-Zhen, CHEN Hong-Lin. Identification of salt tolerance and screening of salt tolerant germplasm of mungbean (Vigna radiate L.) at seedling stage [J]. Acta Agronomica Sinica, 2022, 48(2): 367-379.
[11]	LI Zhen-Hua, WANG Xian-Ya, LIU Yi-Ling, ZHAO Jie-Hong. NtPHYB1 interacts with light and temperature signal to regulate seed germination in Nicotiana tabacum L. [J]. Acta Agronomica Sinica, 2022, 48(1): 99-107.
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[13]	HAO Xi, CUI Ya-Nan, ZHANG Jun, LIU Juan, ZANG Xiu-Wang, GAO Wei, LIU Bing, DONG Wen-Zhao, TANG Feng-Shou. Effects of hydrogen peroxide soaking on germination and physiological metabolism of seeds in peanut [J]. Acta Agronomica Sinica, 2021, 47(9): 1834-1840.
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