SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.)
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 gen...
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2024-12-01
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| Online Access: | https://doi.org/10.1186/s12864-024-11139-8 |
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| author | Feiyang Yang Tao Lang Jingyu Wu Cong Zhang Huijuan Qu Zhigang Pu Fan Yang Ma Yu Junyan Feng |
| author_facet | Feiyang Yang Tao Lang Jingyu Wu Cong Zhang Huijuan Qu Zhigang Pu Fan Yang Ma Yu Junyan Feng |
| author_sort | Feiyang Yang |
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| description | 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. |
| format | Article |
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| institution | Kabale University |
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| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-8d2c6bca7c2d4794afb75f49b6e230072024-12-29T12:11:01ZengBMCBMC Genomics1471-21642024-12-0125111710.1186/s12864-024-11139-8SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.)Feiyang Yang0Tao Lang1Jingyu Wu2Cong Zhang3Huijuan Qu4Zhigang Pu5Fan Yang6Ma Yu7Junyan Feng8Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural SciencesBiotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural SciencesBiotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural SciencesBiotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural SciencesBiotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural SciencesBiotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural SciencesBiotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural SciencesSchool of life science and engineering, Southwest University of Science and TechnologyBiotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural SciencesAbstract 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.https://doi.org/10.1186/s12864-024-11139-8SweetpotatoRAD-seqSNPKASP markerDNA fingerprinting |
| spellingShingle | Feiyang Yang Tao Lang Jingyu Wu Cong Zhang Huijuan Qu Zhigang Pu Fan Yang Ma Yu Junyan Feng SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.) BMC Genomics Sweetpotato RAD-seq SNP KASP marker DNA fingerprinting |
| title | SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.) |
| title_full | SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.) |
| title_fullStr | SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.) |
| title_full_unstemmed | SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.) |
| title_short | SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.) |
| title_sort | snp loci identification and kasp marker development system for genetic diversity population structure and fingerprinting in sweetpotato ipomoea batatas l |
| topic | Sweetpotato RAD-seq SNP KASP marker DNA fingerprinting |
| url | https://doi.org/10.1186/s12864-024-11139-8 |
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