SNP Loci Identification and KASP Marker Development System for Genetic Diversity, Population Structure, and Fingerprinting in Sweetpotato (Ipomoea Batatas L.)

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2024 Dec 24

PMID 39719557

Authors

Feiyang Yang

Tao Lang

Jingyu Wu

Cong Zhang

Huijuan Qu

Zhigang Pu

Fan Yang

Ma Yu

Junyan Feng

Affiliations

Soon will be listed here.

Abstract

Sweetpotato (Ipomoea batatas L.), an important food and industrial crop in the world, has a highly heterozygous hexaploid genome, making the development of single nucleotide polymorphism (SNP) markers challenging. Identifying SNP loci and developing practical SNP markers are crucial for genomic and genetic research on sweetpotato. A restriction site-associated DNA sequencing analysis of 60 sweetpotato accessions in this study yielded about 7.97 million SNPs. Notably, 954 candidate SNPs were obtained from 21,681 high-quality SNPs. Based on their stability and polymorphism, 274 kompetitive allele specific PCR (KASP) markers were then developed and uniformly distributed on chromosomes. The 274 KASP markers were used to genotype 93 sweetpotato accessions to evaluate their utility for assessing germplasm and analyzing genetic diversity and population structures. These markers had respective mean values of 0.24, 0.34, 0.31, and 0.25 for minor allele frequency, heterozygosity, gene diversity, and polymorphic information content (PIC). Their genetic pedigree led to the division of all accessions into three primary clusters, which were found to be both interrelated and independent. Finally, 74 KASP markers with PIC values greater than 0.35 were selected as core markers. These markers were used to construct the DNA fingerprints of 93 sweetpotato accessions and were able to differentiate between all accessions. To the best of our knowledge, this is the first attempt at the development and application of KASP markers in sweetpotato. However, due to sweetpotato's polyploidy, heterozygosity and the complex genome, the KASP marker conversion rate in this study was relatively low. To improve the KASP marker conversion rate, and accuracies in SNP discovery and marker validation, further studies including more accessions from underrepresented regions are needed in sweetpotato.

References

Grewal S, Hubbart-Edwards S, Yang C, Devi U, Baker L, Heath J . Rapid identification of homozygosity and site of wild relative introgressions in wheat through chromosome-specific KASP genotyping assays. Plant Biotechnol J. 2019; 18(3):743-755. PMC: 7004896. DOI: 10.1111/pbi.13241. View

Clevenger J, Chavarro C, Pearl S, Ozias-Akins P, Jackson S . Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations. Mol Plant. 2015; 8(6):831-46. DOI: 10.1016/j.molp.2015.02.002. View

Yang Y, Lyu M, Liu J, Wu J, Wang Q, Xie T . Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars. BMC Plant Biol. 2022; 22(1):522. PMC: 9647966. DOI: 10.1186/s12870-022-03920-2. View

Yan M, Li M, Wang Y, Wang X, Moeinzadeh M, Quispe-Huamanquispe D . Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato. Mol Plant. 2023; 17(2):277-296. DOI: 10.1016/j.molp.2023.12.019. View

Feng J, Zhao S, Li M, Zhang C, Qu H, Li Q . Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq. Genomics. 2019; 112(2):1978-1987. DOI: 10.1016/j.ygeno.2019.11.010. View

Xiao X, Zhang N, Jin H, Si H . Genetic Analysis of Potato Breeding Collection Using Single-Nucleotide Polymorphism (SNP) Markers. Plants (Basel). 2023; 12(9). PMC: 10181131. DOI: 10.3390/plants12091895. View

Deschamps S, Llaca V, May G . Genotyping-by-Sequencing in Plants. Biology (Basel). 2014; 1(3):460-83. PMC: 4009820. DOI: 10.3390/biology1030460. View

Hirakawa H, Okada Y, Tabuchi H, Shirasawa K, Watanabe A, Tsuruoka H . Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don. DNA Res. 2015; 22(2):171-9. PMC: 4401327. DOI: 10.1093/dnares/dsv002. View

Wang Y, Lv H, Xiang X, Yang A, Feng Q, Dai P . Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China. Front Plant Sci. 2021; 12:618133. PMC: 7943628. DOI: 10.3389/fpls.2021.618133. View

10.

Shen Y, Wang J, Shaw R, Yu H, Sheng X, Zhao Z . Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli ( L. var. ) in China. Front Plant Sci. 2021; 12:655254. PMC: 8213352. DOI: 10.3389/fpls.2021.655254. View

11.

Makhoul M, Rambla C, Voss-Fels K, Hickey L, Snowdon R, Obermeier C . Overcoming polyploidy pitfalls: a user guide for effective SNP conversion into KASP markers in wheat. Theor Appl Genet. 2020; 133(8):2413-2430. PMC: 7360542. DOI: 10.1007/s00122-020-03608-x. View

12.

Wang S, Nie S, Zhu F . Chemical constituents and health effects of sweet potato. Food Res Int. 2017; 89(Pt 1):90-116. DOI: 10.1016/j.foodres.2016.08.032. View

13.

Yang G, Chen S, Chen L, Sun K, Huang C, Zhou D . Development of a core SNP arrays based on the KASP method for molecular breeding of rice. Rice (N Y). 2019; 12(1):21. PMC: 6453994. DOI: 10.1186/s12284-019-0272-3. View

14.

Rasheed A, Wen W, Gao F, Zhai S, Jin H, Liu J . Development and validation of KASP assays for genes underpinning key economic traits in bread wheat. Theor Appl Genet. 2016; 129(10):1843-60. DOI: 10.1007/s00122-016-2743-x. View

15.

Hale M, McCormick C, Jackson J, DeWoody J . Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics. 2009; 10:203. PMC: 2688523. DOI: 10.1186/1471-2164-10-203. View

16.

Agarwal G, Kavalappara S, Gautam S, da Silva A, Simmons A, Srinivasan R . Field Screen and Genotyping of against Two Begomoviruses in Georgia, USA. Insects. 2021; 12(1). PMC: 7827361. DOI: 10.3390/insects12010049. View

17.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

18.

Si Z, Du B, Huo J, He S, Liu Q, Zhai H . A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition. BMC Genomics. 2016; 17(1):945. PMC: 5117676. DOI: 10.1186/s12864-016-3302-1. View

19.

Anglin N, Robles R, Rossel G, Alagon R, Panta A, Jarret R . Genetic Identity, Diversity, and Population Structure of CIP's Sweetpotato () Germplasm Collection. Front Plant Sci. 2021; 12:660012. PMC: 8589021. DOI: 10.3389/fpls.2021.660012. View

20.

Wu B, Zhong Y, Wu Q, Chen F, Zhong G, Cui Y . Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars. Front Plant Sci. 2020; 11:563452. PMC: 7509436. DOI: 10.3389/fpls.2020.563452. View