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

[1]	ZHANG H, WANG Z, LI X, et al. The IbBBX24-IbTOE3-IbPRX17 module enhances abiotic stress tolerance by scavenging reactive oxygen species in sweet potato[J]. New Phytologist, 2022, 233(3): 1133-1152. DOI URL
[2]	ZHANG H, GAO X R, ZHI Y H, et al. A non-tandem CCCH-type zinc-finger protein, IbC3H18, functions as a nuclear transcriptional activator and enhances abiotic stress tolerance in sweet potato[J]. New Phytologist, 2019, 223(4): 1918-1936. DOI PMID
[3]	ARUMUGANATHAN K, EARLE E D. Nuclear DNA content of some important plant species[J]. Plant Molecular Biology Reporter, 1991, 9(3): 208-218. DOI URL
[4]	SI Z Z, DU B, HUO J X, et al. A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas(L.) Lam.) genome composition[J]. BMC Genomics, 2016, 17(1): 945. DOI URL
[5]	何畅, 杨锦昌, 余纽, 等. 基于油楠(Sindora glabra)转录组测序的SSR分子标记的开发[J]. 分子植物育种, 2020, 18(7): 2280-2289.
	HE C, YANG J C, YU N, et al. Development of SSR molecular markers based on transcriptome sequencing of Sindora glabra[J]. Molecular Plant Breeding, 2020, 18(7): 2280-2289. (in Chinese with English abstract)
[6]	MONDEN Y, HARA T, OKADA Y, et al. Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing[J]. Breeding Science, 2015, 65(2): 145-153. DOI PMID
[7]	MENG Y S, ZHAO N, LI H, et al. SSR fingerprinting of 203 sweetpotato (Ipomoea batatas(L.) Lam.) varieties[J]. Journal of Integrative Agriculture, 2018, 17(1): 86-93. DOI URL
[8]	SASAI R M, TABUCHI H, SHIRASAWA K, et al. Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato[J]. DNA Research, 2019, 26(5): 399-409. DOI URL
[9]	FENG J Y, ZHAO S, LI M, et al. Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq[J]. Genomics, 2020, 112(2): 1978-1987. DOI PMID
[10]	MENG Y, SU W, MA Y, et al. Assessment of genetic diversity and variety identification based on developed retrotransposon-based insertion polymorphism (RBIP) markers in sweet potato (Ipomoea batatas(L.) Lam.)[J]. Scientific Reports, 2021, 11: 17116. DOI
[11]	MENG Y S, ZHENG C X, LI H, et al. Development of a high-density SSR genetic linkage map in sweet potato[J]. The Crop Journal, 2021, 9(6): 1367-1374. DOI URL
[12]	YANG J, MOEINZADEH M H, KUHL H, et al. Haplotype-resolved sweet potato genome traces back its hexaploidization history[J]. Nature Plants, 2017, 3 (9): 696-703. DOI PMID
[13]	JIANG S, CAI D Y, SUN Y W, et al. Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome[J]. Mobile DNA, 2016, 7: 1. DOI URL
[14]	GALINDO-GONZÁLEZ L, MHIRI C, DEYHOLOS M K, et al. LTR-retrotransposons in plants: engines of evolution[J]. Gene, 2017, 626: 14-25. DOI URL
[15]	OROZCO-ARIAS S, ISAZA G, GUYOT R. Retrotransposons in plant genomes: structure, identification, and classification through bioinformatics and machine learning[J]. International Journal of Molecular Sciences, 2019, 20(15): 3837. DOI URL
[16]	HUANG Y J, CHEN H, HAN J L, et al. Species-specific abundant retrotransposons elucidate the genomic composition of modern sugarcane cultivars[J]. Chromosoma, 2020, 129(1): 45-55. DOI PMID
[17]	NADEEM M A. Deciphering the genetic diversity and population structure of Turkish bread wheat germplasm using iPBS-retrotransposons markers[J]. Molecular Biology Reports, 2021, 48(10): 6739-6748. DOI PMID
[18]	WAUGH R, MCLEAN K, FLAVELL A J, et al. Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP)[J]. Molecular & General Genetics: MGG, 1997, 253(6): 687-694.
[19]	KALENDAR R, GROB T, REGINA M, et al. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques[J]. Theoretical and Applied Genetics, 1999, 98(5): 704-711. DOI URL
[20]	SMýKAL P, BAČOVÁ-KERTESZOVÁ N, KALENDAR R, et al. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers[J]. Theoretical and Applied Genetics, 2011, 122(7): 1385-1397. DOI URL
[21]	MELNIKOVA N V, KUDRYAVTSEVA A V, SPERANSKAYA A S, et al. The FaRE1 LTR-retrotransposon based SSAP markers reveal genetic polymorphism of strawberry (Fragaria×ananassa) cultivars[J]. Journal of Agricultural Science, 2012, 4(11): 111.
[22]	NASRI S, ABDOLLAHI MANDOULAKANI B, DARVISHZADEH R, et al. Retrotransposon insertional polymorphism in Iranian bread wheat cultivars and breeding lines revealed by IRAP and REMAP markers[J]. Biochemical Genetics, 2013, 51(11/12): 927-943. DOI URL
[23]	PAUX E, FAURE S, CHOULET F, et al. Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat[J]. Plant Biotechnology Journal, 2010, 8(2): 196-210. DOI PMID
[24]	LIU J, ZHOU R J, WANG W X, et al. A copia-like retrotransposon insertion in the upstream region of the SHATTERPROOF1 gene, BnSHP1.A9, is associated with quantitative variation in pod shattering resistance in oilseed rape[J]. Journal of Experimental Botany, 2020, 71(18): 5402-5413. DOI PMID
[25]	GHONAIM M, KALENDAR R, BARAKAT H, et al. High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis[J]. Molecular Biology Reports, 2020, 47(3): 1589-1603. DOI PMID
[26]	GHONAIM M M, MOHAMED H I, OMRAN A A A. Evaluation of wheat (Triticum aestivum L.) salt stress tolerance using physiological parameters and retrotransposon-based markers[J]. Genetic Resources and Crop Evolution, 2021, 68(1): 227-242. DOI
[27]	BUTELLI E, LICCIARDELLO C, ZHANG Y, et al. Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges[J]. The Plant Cell, 2012, 24(3): 1242-1255. DOI PMID
[28]	KASHINO-FUJII M, YOKOSHO K, YAMAJI N, et al. Retrotransposon insertion and DNA methylation regulate aluminum tolerance in European barley accessions[J]. Plant Physiology, 2018, 178(2): 716-727. DOI URL
[29]	ROY N S, LEE S I, NKONGOLO K, et al. Retrotransposons in Betula nana, and interspecific relationships in the Betuloideae, based on inter-retrotransposon amplified polymorphism (IRAP) markers[J]. Genes & Genomics, 2018, 40(5): 511-519.
[30]	WU S, LAU K H, CAO Q, et al. Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement[J]. Nature Communications, 2018, 9: 4580. DOI PMID
[31]	VOS P, HOGERS R, BLEEKER M, et al. AFLP: a new technique for DNA fingerprinting[J]. Nucleic Acids Research, 1995, 23(21): 4407-4414. DOI PMID
[32]	李慧. 甘薯SSR分子连锁图谱的构建和块根产量相关QTL的定位[D]. 北京: 中国农业大学, 2014.
	LI H. Development of SSR genetic linkage maps and mapping of QTLs for storage root yield in sweetpotato, Ipomoea batatas(L.) Lam[D]. Beijing: China Agricultural University, 2014. (in Chinese with English abstract)
[33]	WU J, WANG Z W, SHI Z B, et al. The genome of the pear (Pyrus bretschneideri Rehd.)[J]. Genome Research, 2013, 23(2): 396-408. DOI URL
[34]	SCHNABLE P S, WARE D, FULTON R S, et al. The B73 maize genome: complexity, diversity, and dynamics[J]. Science, 2009, 326(5956): 1112-1115. DOI PMID
[35]	PIEGU B, GUYOT R, PICAULT N, et al. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice[J]. Genome Research, 2006, 16(10): 1262-1269. DOI URL

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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