Information Mining of SNP Sites in the Leaf Transcriptome of Sunflower Drought-resistant Inbred Lines

doi:10.11924/j.issn.1000-6850.casb2022-0335

Abstract

Abstract:

In order to explore the transcriptome SNP markers in response to drought stress in sunflower, with the sunflower drought resistant inbred line 17062 as the experimental material, RNA-seq technology combined with bioinformatics analysis method was used to statistically analyze SNP markers. The results showed that in SNP type analysis, the conversion rate accounted for 62.82%, and the inversion rate accounted for 37.17%. In the conversion, the frequency of C/T was the highest, which was 31.51%. In the distribution of functional elements, the number of SNP distributed in exons was 178744.3, which was significantly more than that of other functional elements. The sequence annotation of SNP sites found that 76678 SNP genes had GO annotation and 4379 had KEGG annotation. The repeated SNP gene sequences in the Top30 GO annotation ranking (Top30) differential genes (DEGs) were screened, and 1542 genes were obtained, of which 650 gene sequences had GO annotation. These differential genes are involved in multiple biological functions and important metabolic pathways, which are of great significance for the development of SNP markers in sunflower transcriptome, the identification of drought resistant germplasm resources, and the selection of drought resistant “three-line” hybrids.

Key words: sunflower (Helianthus annuus L.), drought stress, leaf, SNP

WEN Yujie, ZHAO Yajie, ZHU Kongyan, ZHAO Rong, WANG Meng, QIAO Yimin, BAO Haizhu, GAO Julin. Information Mining of SNP Sites in the Leaf Transcriptome of Sunflower Drought-resistant Inbred Lines[J]. Chinese Agricultural Science Bulletin, 2023, 39(9): 106-114.

Figures/Tables 8

References 27

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样品	原始测序数目(M)	筛选后序列数目(M)	Q30/%	GC/%
CKAX1	53.42	52.04	92.51	45.55
CKAX2	44.38	43.23	92.65	45.63
CKAX3	54.05	52.68	92.61	45.63
TAX1	53.09	51.73	92.47	44.89
TAX2	52.24	50.91	92.60	44.97
TAX3	50.80	49.51	92.15	45.02

样品	原始测序数目(M)	筛选后序列数目(M)	Q30/%	GC/%
CKAX1	53.42	52.04	92.51	45.55
CKAX2	44.38	43.23	92.65	45.63
CKAX3	54.05	52.68	92.61	45.63
TAX1	53.09	51.73	92.47	44.89
TAX2	52.24	50.91	92.60	44.97
TAX3	50.80	49.51	92.15	45.02

类型		转换			颠换
类型		A/G	C/T	合计	A/T	A/C	G/C	G/T	合计
TAX1	SNP 数目	172896	174095	346991	61632	51422	41816	51452	206322
TAX1	概率	31.25%	31.46%	62.71%	11.14%	9.29%	7.56%	9.30%	37.29%
TAX2	SNP 数目	164653	165744	330396	58637	49052	39755	48626	196070
TAX2	概率	31.28%	31.48%	62.76%	11.14%	9.32%	7.55%	9.24%	37.24%
TAX3	SNP 数目	149502	149839	299341	52336	44252	36235	43563	176386
TAX3	概率	31.43%	31.50%	62.92%	11.00%	9.30%	7.62%	9.16%	37.08%
CKAX1	SNP 数目	158252	159520	317772	55763	47091	38414	46559	187827
CKAX1	概率	31.30%	31.55%	62.85%	11.03%	9.31%	7.60%	9.21%	37.15%
CKAX2	SNP 数目	139619	140748	280367	49027	41419	34115	41027	165588
CKAX2	概率	31.31%	31.56%	62.87%	10.99%	9.29%	7.65%	9.20%	37.13%
CKAX3	SNP 数目	151778	152704	304482	53439	46047	36879	44686	180051
CKAX3	概率	31.32%	31.52%	62.84%	11.03%	9.50%	7.61%	9.22%	37.16%

类型		转换			颠换
类型		A/G	C/T	合计	A/T	A/C	G/C	G/T	合计
TAX1	SNP 数目	172896	174095	346991	61632	51422	41816	51452	206322
TAX1	概率	31.25%	31.46%	62.71%	11.14%	9.29%	7.56%	9.30%	37.29%
TAX2	SNP 数目	164653	165744	330396	58637	49052	39755	48626	196070
TAX2	概率	31.28%	31.48%	62.76%	11.14%	9.32%	7.55%	9.24%	37.24%
TAX3	SNP 数目	149502	149839	299341	52336	44252	36235	43563	176386
TAX3	概率	31.43%	31.50%	62.92%	11.00%	9.30%	7.62%	9.16%	37.08%
CKAX1	SNP 数目	158252	159520	317772	55763	47091	38414	46559	187827
CKAX1	概率	31.30%	31.55%	62.85%	11.03%	9.31%	7.60%	9.21%	37.15%
CKAX2	SNP 数目	139619	140748	280367	49027	41419	34115	41027	165588
CKAX2	概率	31.31%	31.56%	62.87%	10.99%	9.29%	7.65%	9.20%	37.13%
CKAX3	SNP 数目	151778	152704	304482	53439	46047	36879	44686	180051
CKAX3	概率	31.32%	31.52%	62.84%	11.03%	9.50%	7.61%	9.22%	37.16%

GO条目（1级）	GO条目（2级）	SNP数量/个
生物过程	半乳糖醛酸酯的生物合成工艺	2
	光合作用	25
	细胞壁组织	41
	还原戊磷酸循环	12
	光合作用，光系统I中的光捕获	8
	光合作用、光收集	3
	细胞壁生物发生	5
	光刺激反应	22
	木聚糖代谢过程	4
	蛋白质发色团连锁	13
细胞成分	非原质体	48
	胞外区	82
	细胞壁	52
	叶绿体类囊体膜	52
	微管	38
	膜锚定组分	25
	叶绿体类囊体	32
	类囊体	30
	光合体系I	12
	植物型细胞壁	31
分子功能	转录抑制因子活性，金属离子调控序列特异性DNA结合	2
	磷酸酮激酶活性	0
	微管结合	37
	叶绿素结合	12
	蛋白激酶结合	10
	木葡聚糖：木葡聚糖转移酶活性	4
	核酮糖-二磷酸羧化酶的活性	5
	O-乙酰转移酶活性	9
	snoRNA结合	10
	微管运动活动	19