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Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies
Dearth of genomic resources particularly, microsatellite markers in nutritionally and commercially important fruit crop, guava necessitate the development of the novel genomic SSR markers through the library enrichment techniques. Three types of 3’ -biotinylated oligonucleotide probes [(CT)(14), (GT...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431106/ https://www.ncbi.nlm.nih.gov/pubmed/32804981 http://dx.doi.org/10.1371/journal.pone.0237538 |
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author | Kumar, Chavlesh Kumar, Ramesh Singh, Sanjay Kumar Goswami, Amit Kumar Nagaraja, A. Paliwal, Ritu Singh, Rakesh |
author_facet | Kumar, Chavlesh Kumar, Ramesh Singh, Sanjay Kumar Goswami, Amit Kumar Nagaraja, A. Paliwal, Ritu Singh, Rakesh |
author_sort | Kumar, Chavlesh |
collection | PubMed |
description | Dearth of genomic resources particularly, microsatellite markers in nutritionally and commercially important fruit crop, guava necessitate the development of the novel genomic SSR markers through the library enrichment techniques. Three types of 3’ -biotinylated oligonucleotide probes [(CT)(14), (GT)(12), and (AAC)(8)] were used to develop microsatellite enriched libraries. A total of 153 transformed colonies were screened of which 111 positive colonies were subjected for Sanger sequencing. The clones having more than five motif repeats were selected for primer designing and a total of 38 novel genomic simple sequence repeats could be identified. The g-SSRs had the motif groups ranging from monomer to pentamer out of which dimer group occurred the most (89.47%). Out of 38 g-SSRs markers developed, 26 were found polymorphic, which showed substantial genetic diversity among the guava genotypes including wild species. The average number of alleles per locus, major allele frequency, gene diversity, expected heterozygosity and polymorphic information content of 26 SSRs were 3.46, 0.56, 0.53, 0.29 and 0.46, respectively. The rate of cross-species transferability of the developed g-SSR loci varied from 38.46 to 80.77% among the studied wild Psidium species. Generation of N-J tree based on 26 SSRs grouped the 40 guava genotypes into six clades with two out-groups, the wild guava species showed genetic distinctness from cultivated genotypes. Furthermore, population structure analysis grouped the guava genotypes into three genetic groups, which were partly supported by PCoA and N-J tree. Further, AMOVA and PCoA deciphered high genetic diversity among the present set of guava genotypes including wild species. Thus, the developed novel g-SSRs were found efficient and informative for diversity and population structure analyses of the guava genotypes. These developed novel g-SSR loci would add to the new genomic resource in guava, which may be utilized in genomic-assisted guava breeding. |
format | Online Article Text |
id | pubmed-7431106 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-74311062020-08-20 Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies Kumar, Chavlesh Kumar, Ramesh Singh, Sanjay Kumar Goswami, Amit Kumar Nagaraja, A. Paliwal, Ritu Singh, Rakesh PLoS One Research Article Dearth of genomic resources particularly, microsatellite markers in nutritionally and commercially important fruit crop, guava necessitate the development of the novel genomic SSR markers through the library enrichment techniques. Three types of 3’ -biotinylated oligonucleotide probes [(CT)(14), (GT)(12), and (AAC)(8)] were used to develop microsatellite enriched libraries. A total of 153 transformed colonies were screened of which 111 positive colonies were subjected for Sanger sequencing. The clones having more than five motif repeats were selected for primer designing and a total of 38 novel genomic simple sequence repeats could be identified. The g-SSRs had the motif groups ranging from monomer to pentamer out of which dimer group occurred the most (89.47%). Out of 38 g-SSRs markers developed, 26 were found polymorphic, which showed substantial genetic diversity among the guava genotypes including wild species. The average number of alleles per locus, major allele frequency, gene diversity, expected heterozygosity and polymorphic information content of 26 SSRs were 3.46, 0.56, 0.53, 0.29 and 0.46, respectively. The rate of cross-species transferability of the developed g-SSR loci varied from 38.46 to 80.77% among the studied wild Psidium species. Generation of N-J tree based on 26 SSRs grouped the 40 guava genotypes into six clades with two out-groups, the wild guava species showed genetic distinctness from cultivated genotypes. Furthermore, population structure analysis grouped the guava genotypes into three genetic groups, which were partly supported by PCoA and N-J tree. Further, AMOVA and PCoA deciphered high genetic diversity among the present set of guava genotypes including wild species. Thus, the developed novel g-SSRs were found efficient and informative for diversity and population structure analyses of the guava genotypes. These developed novel g-SSR loci would add to the new genomic resource in guava, which may be utilized in genomic-assisted guava breeding. Public Library of Science 2020-08-17 /pmc/articles/PMC7431106/ /pubmed/32804981 http://dx.doi.org/10.1371/journal.pone.0237538 Text en © 2020 Kumar et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Kumar, Chavlesh Kumar, Ramesh Singh, Sanjay Kumar Goswami, Amit Kumar Nagaraja, A. Paliwal, Ritu Singh, Rakesh Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies |
title | Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies |
title_full | Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies |
title_fullStr | Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies |
title_full_unstemmed | Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies |
title_short | Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies |
title_sort | development of novel g-ssr markers in guava (psidium guajava l.) cv. allahabad safeda and their application in genetic diversity, population structure and cross species transferability studies |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431106/ https://www.ncbi.nlm.nih.gov/pubmed/32804981 http://dx.doi.org/10.1371/journal.pone.0237538 |
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