SSR and SNP in Salt Tolerant Sweet Potato: Characteristics Analysis Based on Transcriptome Sequencing

doi:10.11923/j.issn.2095-4050.cjas2021-0124

Abstract

Abstract:

The aims are to mine and analyze the potential SSR and SNP loci in sweet potato transcriptome under salt stress, and enrich the molecular markers of sweet potato. Based on the transcriptome sequences of different salt tolerant sweet potato varieties, the SSR and SNP were analyzed by MISA and GATK software. The results showed that, a total of 33192 SSR loci were identified in 24323 Unigenes with a frequency of 21.11%. 6271 Unigenes contained more than one SSR locus. Mono-nucleotide repeat SSR and di-nucleotide repeat SSR were the main types. The two repeat motifs, A/T and AG/CT, had the highest proportion and were the dominant motifs of sweet potato SSR. After searching SNP loci in 157252 Unigenes, 7691906 SNP loci were identified with a distribution density of 0.08 SNP per bp. The predicted SNPs included 4729922 transitions and 2961984 transversions. C/T and A/G were the main types, accounting for 32.34% and 29.15% of all the SNPs. Taken together, the transcriptome of sweet potato has abundant SSR and SNP markers with high polymorphism, and the study could lay a theoretical basis for the selection of stress resistant varieties and germplasm cultivation of sweet potato.

Key words: sweet potato, salt stress, transcriptome, SSR, SNP

CLC Number:

S531

ZHANG Xiaohong, PENG Qiong, YAN Zheng. SSR and SNP in Salt Tolerant Sweet Potato: Characteristics Analysis Based on Transcriptome Sequencing[J]. Journal of Agriculture, 2022, 12(11): 55-61.

Figures/Tables 6

References 43

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项目	数量
评估的序列数目	157252
评估的序列总碱基数 (bp)	90649057
识别的SSR总数	33192
包含SSR的序列数目	24323
包含1个以上SSR的序列数目	6271
以复合物形式存在的SSR数目	4471
单核苷酸重复SSR数目	18718
双核苷酸重复SSR数目	8121
三核苷酸重复SSR数目	5565
四核苷酸重复SSR数目	601
五核苷酸重复SSR数目	129
六核苷酸重复SSR数目	58

项目	数量
评估的序列数目	157252
评估的序列总碱基数 (bp)	90649057
识别的SSR总数	33192
包含SSR的序列数目	24323
包含1个以上SSR的序列数目	6271
以复合物形式存在的SSR数目	4471
单核苷酸重复SSR数目	18718
双核苷酸重复SSR数目	8121
三核苷酸重复SSR数目	5565
四核苷酸重复SSR数目	601
五核苷酸重复SSR数目	129
六核苷酸重复SSR数目	58

重复类型	重复基元类型总数	重复基元	数量	占比/%
单核苷酸重复	2	A/T	18391	55.41
单核苷酸重复	2	C/G	327	0.99
双核苷酸重复	4	AG/CT	3706	11.17
		AT/AT	3185	9.60
		AC/GT	1220	3.68
		CG/CG	10	0.03
三核苷酸重复	10	AAT/ATT	1606	4.84
		AAG/CTT	1325	3.99
		ATC/ATG	603	1.82
		CCG/CGG	585	1.76
		AAC/GTT	459	1.38
		剩余三核苷酸重复基元	987	2.97
四核苷酸重复	28	AAAT/ATTT	231	0.70
		AAAG/CTTT	89	0.27
		ACAT/ATGT	65	0.20
		AAAC/GTTT	56	0.17
		剩余四核苷酸重复基元	160	0.48
五核苷酸重复	40	AAAAT/ATTTT	31	0.09
		AAAAC/GTTTT	28	0.08
		AAAAG/CTTTT	9	0.03
		AAGAG/CTCTT	9	0.03
		剩余五核苷酸重复基元	52	0.16
六核苷酸重复	36	AAAAAC/GTTTTT	6	0.02
		AAAAAT/ATTTTT	6	0.02
		AAAGAG/CTCTTT	3	0.01
		AAAGGC/CCTTTG	2	0.01
		剩余六核苷酸重复基元	41	0.12

重复类型	重复基元类型总数	重复基元	数量	占比/%
单核苷酸重复	2	A/T	18391	55.41
单核苷酸重复	2	C/G	327	0.99
双核苷酸重复	4	AG/CT	3706	11.17
		AT/AT	3185	9.60
		AC/GT	1220	3.68
		CG/CG	10	0.03
三核苷酸重复	10	AAT/ATT	1606	4.84
		AAG/CTT	1325	3.99
		ATC/ATG	603	1.82
		CCG/CGG	585	1.76
		AAC/GTT	459	1.38
		剩余三核苷酸重复基元	987	2.97
四核苷酸重复	28	AAAT/ATTT	231	0.70
		AAAG/CTTT	89	0.27
		ACAT/ATGT	65	0.20
		AAAC/GTTT	56	0.17
		剩余四核苷酸重复基元	160	0.48
五核苷酸重复	40	AAAAT/ATTTT	31	0.09
		AAAAC/GTTTT	28	0.08
		AAAAG/CTTTT	9	0.03
		AAGAG/CTCTT	9	0.03
		剩余五核苷酸重复基元	52	0.16
六核苷酸重复	36	AAAAAC/GTTTTT	6	0.02
		AAAAAT/ATTTTT	6	0.02
		AAAGAG/CTCTTT	3	0.01
		AAAGGC/CCTTTG	2	0.01
		剩余六核苷酸重复基元	41	0.12

重复类型	重复次数									总计
重复类型	5	6	7	8	9	10	11	12	>12	总计
单核苷酸	0	0	0	0	0	5667	3174	2122	7755	18718
双核苷酸	0	2679	1579	1104	711	512	536	590	410	8121
三核苷酸	2930	1283	591	265	59	71	58	52	256	5565
四核苷酸	415	146	12	11	4	6	2	3	2	601
五核苷酸	99	16	9	4	0	0	1	0	0	129
六核苷酸	26	15	10	4	1	0	1	0	1	58
总计	3470	4139	2201	1388	775	6256	3772	2767	8424	33192