Scientia Agricultura Sinica ›› 2019, Vol. 52 ›› Issue (3): 385-398.doi: 10.3864/j.issn.0578-1752.2019.03.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS •     Next Articles

Genome-Wide Association Analysis for Rice Submergence Seedling Rate

SUN Kai,LI DongXiu,YANG Jing,DONG JiChi,YAN XianCheng,LUO LiXin,LIU YongZhu,XIAO WuMing,WANG Hui,CHEN ZhiQiang,GUO Tao   

  1. National Plant Space Breeding Engineering Technology Research Center, South China Agricultural University, Guangzhou 510642
  • Received:2018-09-18 Accepted:2018-11-12 Online:2019-02-01 Published:2019-02-14

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Abstract:

【Background】 The low seedling rate of direct seeding rice is an important factor limiting its yield. Mining rice materials with high seed viability and low oxygen germination ability is the key to improving the seedling rate and solving the problem of seedlings in direct seeding rice. 【Objective】 The key phenotypic traits affecting the rate of emergence and tolerance of seedlings were analyzed, and the relevant genetic loci and candidate genes were mined to provide a theoretical and material basis for the study of direct seeding rice cultivars and the mechanism of resistance to flooding. 【Method】 Using 200 rice germplasms from a wide range of sources. The germination test was carried out in an aerobic environment, and the seed viability phenotype was measured including germination rate, germination index and viability index; The coleoptile length and coleoptile diameter were measured under hypoxic conditions. The flood-tolerant seedling experiment was carried out, the water depth was 10cm, and the flood-tolerant seedling rate was measured after 20d. The correlation between various traits was analyzed, and the key traits affecting the rate of tolerance to flooding were explored. Genome-wide association analysis was performed on the above six phenotypes by simplified genome sequencing, and SNP sites significantly associated with traits were identified and within the correlation interval. Screening candidate genes related to the research purpose; transcriptome detection under the conditions of aerobic, anaerobic and oxygen content conversion of 02428 and YZX two materials, combined with genome-wide association analysis results, analysis of differences in expression patterns of candidate genes. 【Result】 Seed viability, coleoptile phenotype and seedling rate showed extensive genetic variation among 200 materials. Among them, the variation of coleoptile length and viability index was the most abundant, and the coefficient of variation was the largest. At the same time, the results of correlation analysis showed that there was a significant positive correlation between the coleoptile length, viability index and the seedling rate. Through genome-wide association analysis, 8 sites significantly associated with the viability index and 15 sites significantly associated with the coleoptile length were identified. Based on the correlation of seed growth and development and stress resistance, six candidate genes related to viability index and seven candidate genes related to the coleoptile length were screened in the relevant interval. Further comparison of 13 genes in aerobic and anaerobic the expression patterns and expression changes under oxygen conversion conditions showed that the three genes Os02g0657000, Os03g0592500 and Os08g0380100 showed different expression patterns when the oxygen content changed, and the expression amount changed significantly, showing sensitivity to oxygen treatment. 【Conclusion】 Seed viability and coleoptile length were closely related to the rate of flooding and seedling emergence, which could be used as an important trait for screening flood-tolerant rice materials. Combining genome-wide association analysis, transcriptome analysis and gene expression pattern can improve the screening efficiency of candidate genes for hypoxia tolerance germination of rice seeds; flooding tolerance of rice seedlings may be regulated by genes related to stress and photosynthesis..

Key words: rice, seed vitality, hypoxia-resistant germination, genome-wide association analysis, transcriptome analysis

Table 1

Phenotype of rice strains"

性状
Trait		 极小值
Min		 极大值
Max		 均值
Average		 标准误
Standard error		 标准差
Standard deviation		 变异系数
Coefficient of variation
发芽率 Germination rate (%) 64.9515 100.0000 95.8427 0.3259 4.9420 5.1564
发芽指数 Germination index 32.6747 90.3761 59.6827 0.6815 10.3348 17.3162
活力指数 Vitality index 0.1376 0.9656 0.3345 0.0071 0.1079 32.2571
胚芽鞘长 Coleoptile length (cm) 0.9640 3.4622 2.3019 0.0302 0.4577 19.8836
胚芽鞘直径 Coleoptile diameter (mm) 0.4544 0.6576 0.5287 0.0026 0.0387 7.3198
成苗率 Seedling rate (%) 11.1111 97.7788 61.5295 1.3074 19.8212 32.2141

Fig. 1

Histogram of trait frequency distribution a: Germination rate; b: Germination index; c: Vitality index; d: Coleoptile length; e: Coleoptile diameter; f: Seedling rate"

Table 2

Correlation analysis of phenotype"

性状
Trait		 成苗率
Seedling rate		 发芽率
Germination rate		 发芽指数
Germination index		 活力指数
Vitality index		 胚芽鞘长
Coleoptile length		 胚芽鞘直径
Coleoptile diameter
成苗率 Seedling rate 1
发芽率 Germination rate 0.254** 1
发芽指数 Germination index 0.229** 0.422** 1
活力指数Vitality index 0.224** 0.129 0.518** 1
胚芽鞘长 Coleoptile length 0.271** 0.129* 0.287** 0.305** 1
胚芽鞘直径 Coleoptile diameter -0.078 -0.382** -0.226** 0.022 0.137* 1

Fig. 2

Phylogenetic tree and PCA analysis"

Fig. 3

Manhattan map and Q-Q map of vitality index"

Table 3

Associate loci of vitality index"

染色体 Chr. SNP位置 Position (bp) 等位基因 Allele 峰值 Peak value 已报道的位点 Known loci
1 13783629 C/T 6.322302731
2 26540479 A/G 6.142571185 [18-19]
5 3878312 A/G 6.384993065
6 5542656 C/T 8.912458149 [20]
10 13589547 C/T 6.960402683 [20-21]
11 4608768 A/G 7.710957603
11 26538371 G/T 6.863393569
12 23449435 T/C 6.103889317 [22-23]

Table 4

Candidate genes located in associate loci of vitality index"

SNP位置
SNP position		 基因编号
Gene ID		 基因注释
Gene annotation
Chr.01_13783629 Os01g0347500 木瓜蛋白酶样半胱氨酸蛋白酶 Papain-like cysteine proteinase
Chr.02_26540479 Os02g0657000 含AP2结构域的蛋白质 AP2 domain-containing protein
Chr.02_26540479 Os02g0658200 锌指,含有PHD型结构域的蛋白质 Zinc finger, PHD-type domain containing protein
Chr.02_26540479 Os02g0658400 Remorin,含有C末端结构域的蛋白质 Remorin, C-terminal domain containing protein
Chr.11_26538371 Os11g0660300 热激蛋白DnaJ,含有N-末端结构域的蛋白质 Heat shock protein DnaJ, N-terminal domain containing protein
Chr.11_26538371 Os11g0661200 糖苷水解酶 Glycoside hydrolasen

Fig. 4

Manhattan map and Q-Q map of coleoptile length"

Table 5

Associate loci of coleoptile length"

染色体 Chr. SNP位置 Position (bp) 等位基因 Allele 峰值 Peak value 已报道的位点 Known loci
3 22007803 C/T 5.023909483
4 6615471 A/G 4.342639196
4 23562335 T/C 4.028691488
5 15450007 G/A 4.777759954 [24]
6 757734 A/G 4.284055624
6 9693092 A/G 4.340712509
6 21932341 T/C 4.165186256 [25-26]
6 29822164 T/A 4.48136579 [27-28]
8 5689664 C/T 4.675971197 [29]
8 18019426 T/C 4.364278864
10 3160014 G/A 4.652868342
10 7504391 T/C 4.286580613
10 17384859 G/C 4.84143398
11 10896433 T/C 4.076205999
11 18620615 C/A 4.169961251

Table 6

Candidate genes located in associate loci of coleoptile length"

SNP位置 SNP Position 基因编号 Gene ID 基因注释 Gene annotation
Chr.03_22007803 Os03g0595600 谷胱甘肽转移酶 Glutathione transferase
Chr.03_22007803 Os03g0592500 叶绿素a-b结合蛋白 Chlorophyll a-b binding protein
Chr.06_29822164 Os06g0704300 锌指CCCH结构域的蛋白质 Zinc finger CCCH domain-containing protein
Chr.08_15689664 Os08g0198200 天冬氨酸蛋白酶CDR1 Aspartic proteinase CDR1
Chr.08_18019270 Os08g0380100 含有BURP结构域的蛋白质 BURP domain-containing protein
Chr.10_17384859 Os10g0466500 锌指蛋白CONSTANS-LIKE 4 Zinc finger protein CONSTANS-LIKE 4
Chr.11_10896433 Os11g0293900 植物含UBX结构域的蛋白质 Plant UBX domain-containing protein

Fig. 5

Expression heatmap of candidate genes"

Fig. 6

Expression profile of candidate genes"

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