Assessment of genetic diversity and variety identification based on insertion site-based polymorphism (ISBP) markers developed in wild species related to sweet potato

doi:10.3969/j.issn.1004-1524.2023.03.01

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (3): 489-498.DOI: 10.3969/j.issn.1004-1524.2023.03.01

• Crop Science • Previous Articles Next Articles

Assessment of genetic diversity and variety identification based on insertion site-based polymorphism (ISBP) markers developed in wild species related to sweet potato

MENG Yusha¹^,²(), WANG Yin¹^,², LAI Qixian¹^,², LIU Lei¹^,², XIANG Chao³, WU Yonghua¹^,², ZHENG Yanran¹^,², GU Xingguo¹^,², FANG Hao¹^,², MIAO Miao¹^,², WU Liehong³, TANG Yong¹^,²^,^*()

1. Institute of Rural Development, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
2. Key Laboratory of Creative Agriculture, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
3. Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China

Received:2021-12-15 Online:2023-03-25 Published:2023-04-07

Abstract

Abstract:

Based on genome wide sequencing of wild species related to sweet potato Ipomoea triloba and Ipomoea trifida, 2 360 long terminal repeat retrotransposons (LTR-RT) sequences were identified. One hundred insertion-site-based polymorphisms (ISBP) primer pairs were developed and four sweet potato germplasm resources were used to evaluate the polymorphisms of ISBP primers. Twenty four pairs of ISBP primers were found to be highly polymorphic, which were then applied to genetic diversity analysis and variety identification of 56 sweet potato germplasm resources collected in Zhejiang province. The results showed that 24 pairs of ISBP primers generated 182 polymorphic bands in 56 germplasm resources, and each germplasm resource had unique fingerprint information. The genetic analysis results of NTsys, UPGMA and PCA showed that the genetic distance between different germplasm resources in the population ranged from 0.027 5 to 0.653 8, with an average of 0.373 2, the average of polymorphic information content (PIC) was 0.289 6, and these resources were divided into two populations containing 11 and 45 germplasm resources, respectively. Studies have shown that the genetic variation of this population is small and the genetic background among different germplasm resources is narrow. The ISBP primers developed in this study not only increased the number of transposon molecular markers, filled in the gap of application of ISBP markers in genetic analysis of sweet potato, but also provided a favorable tool for the identification, protection and utilization of sweet potato variety resources.

Key words: sweet potato, ISBP, LTR, molecular marker, genetic diversity, variety identification

CLC Number:

S531

MENG Yusha, WANG Yin, LAI Qixian, LIU Lei, XIANG Chao, WU Yonghua, ZHENG Yanran, GU Xingguo, FANG Hao, MIAO Miao, WU Liehong, TANG Yong. Assessment of genetic diversity and variety identification based on insertion site-based polymorphism (ISBP) markers developed in wild species related to sweet potato[J]. Acta Agriculturae Zhejiangensis, 2023, 35(3): 489-498.

Figures/Tables 6

References 35

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亚家族中LTR 的个数 LTR No. of subfamily	Ipomoea triloba				Ipomoea trifida
	Copia家族 Copia family		Gypsy家族 Gypsy family		Copia家族 Gypsy family		Gypsy家族 Gypsy family
		亚家族个数 No. of subfamily	LTR-RT 数量 LTR-RT No.	亚家族个数 No. of subfamily	LTR-RT 数量 LTR-RT No.	亚家族个数 No. of subfamily	LTR-RT 数量 LTR-RT No.	亚家族个数 No. of subfamily	LTR-RT 数量 LTR-RT No.
1	128	128	1 102	1 102	126	126	826	826
2	6	12	13	26	4	8	12	24
≥3	6	22	9	49	5	22	3	15
共计Total	149	162	1 124	1 177	135	156	841	865

亚家族中LTR 的个数 LTR No. of subfamily	Ipomoea triloba				Ipomoea trifida
	Copia家族 Copia family		Gypsy家族 Gypsy family		Copia家族 Gypsy family		Gypsy家族 Gypsy family
		亚家族个数 No. of subfamily	LTR-RT 数量 LTR-RT No.	亚家族个数 No. of subfamily	LTR-RT 数量 LTR-RT No.	亚家族个数 No. of subfamily	LTR-RT 数量 LTR-RT No.	亚家族个数 No. of subfamily	LTR-RT 数量 LTR-RT No.
1	128	128	1 102	1 102	126	126	826	826
2	6	12	13	26	4	8	12	24
≥3	6	22	9	49	5	22	3	15
共计Total	149	162	1 124	1 177	135	156	841	865

引物名称 Primer name	Ne^*	H^*	I^*	PIC
IbISBP4	1.300 5	0.204 4	0.342 1	0.257 8
IbISBP14	1.563 0	0.335 8	0.503 4	0.326 4
IbISBP17	1.266 8	0.185 6	0.309 8	0.250 0
IbISBP18	1.490 8	0.288 4	0.433 7	0.281 5
IbISBP19	1.595 8	0.349 9	0.521 4	0.339 6
IbISBP26	1.620 2	0.356 5	0.527 8	0.319 2
IbISBP30	1.677 8	0.379 0	0.552 5	0.260 4
IbISBP31	1.448 1	0.286 3	0.445 0	0.314 5
IbISBP32	1.359 7	0.224 3	0.356 6	0.266 8
IbISBP57	1.557 2	0.323 0	0.479 4	0.318 4
IbISBP60	1.801 4	0.436 8	0.626 0	0.271 2
IbISBP67	1.604 5	0.345 7	0.511 6	0.288 7
IbISBP69	1.593 6	0.341 5	0.506 1	0.305 0
IbISBP70	1.619 2	0.345 3	0.508 9	0.294 4
IbISBP71	1.559 8	0.335 6	0.508 5	0.338 8
IbISBP72	1.670 8	0.377 7	0.555 0	0.326 6
IbISBP74	1.526 4	0.301 6	0.448 2	0.278 8
IbISBP79	1.582 3	0.320 5	0.459 9	0.200 8
IbISBP80	1.707 6	0.399 4	0.581 4	0.296 5
IbISBP107	1.523 4	0.314 5	0.476 9	0.314 5
IbISBP112	1.558 1	0.324 3	0.479 0	0.240 5
IbISBP120	1.251 4	0.172 6	0.283 8	0.233 7
IbISBP129	1.823 9	0.445 0	0.635 2	0.334 0
IbISBP135	1.531 9	0.314 8	0.474 2	0.291 2

引物名称 Primer name	Ne^*	H^*	I^*	PIC
IbISBP4	1.300 5	0.204 4	0.342 1	0.257 8
IbISBP14	1.563 0	0.335 8	0.503 4	0.326 4
IbISBP17	1.266 8	0.185 6	0.309 8	0.250 0
IbISBP18	1.490 8	0.288 4	0.433 7	0.281 5
IbISBP19	1.595 8	0.349 9	0.521 4	0.339 6
IbISBP26	1.620 2	0.356 5	0.527 8	0.319 2
IbISBP30	1.677 8	0.379 0	0.552 5	0.260 4
IbISBP31	1.448 1	0.286 3	0.445 0	0.314 5
IbISBP32	1.359 7	0.224 3	0.356 6	0.266 8
IbISBP57	1.557 2	0.323 0	0.479 4	0.318 4
IbISBP60	1.801 4	0.436 8	0.626 0	0.271 2
IbISBP67	1.604 5	0.345 7	0.511 6	0.288 7
IbISBP69	1.593 6	0.341 5	0.506 1	0.305 0
IbISBP70	1.619 2	0.345 3	0.508 9	0.294 4
IbISBP71	1.559 8	0.335 6	0.508 5	0.338 8
IbISBP72	1.670 8	0.377 7	0.555 0	0.326 6
IbISBP74	1.526 4	0.301 6	0.448 2	0.278 8
IbISBP79	1.582 3	0.320 5	0.459 9	0.200 8
IbISBP80	1.707 6	0.399 4	0.581 4	0.296 5
IbISBP107	1.523 4	0.314 5	0.476 9	0.314 5
IbISBP112	1.558 1	0.324 3	0.479 0	0.240 5
IbISBP120	1.251 4	0.172 6	0.283 8	0.233 7
IbISBP129	1.823 9	0.445 0	0.635 2	0.334 0
IbISBP135	1.531 9	0.314 8	0.474 2	0.291 2

Assessment of genetic diversity and variety identification based on insertion site-based polymorphism (ISBP) markers developed in wild species related to sweet potato

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