Cargando…
Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars
High throughput sequencing was used to reveal the distribution of whole-genome variations in cultivated Morella rubra (Sieb. et Zucc.). A total of 3,151,123 SNPs, 371,757 small indels, and 15,904 SVs were detected in 52 accessions. Verification by Sanger sequencing demonstrated that the positive rat...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509436/ https://www.ncbi.nlm.nih.gov/pubmed/33013982 http://dx.doi.org/10.3389/fpls.2020.563452 |
_version_ | 1783585595614822400 |
---|---|
author | Wu, Bo Zhong, Yun Wu, Qianqian Chen, Fangyong Zhong, Guangyan Cui, Yiping |
author_facet | Wu, Bo Zhong, Yun Wu, Qianqian Chen, Fangyong Zhong, Guangyan Cui, Yiping |
author_sort | Wu, Bo |
collection | PubMed |
description | High throughput sequencing was used to reveal the distribution of whole-genome variations in cultivated Morella rubra (Sieb. et Zucc.). A total of 3,151,123 SNPs, 371,757 small indels, and 15,904 SVs were detected in 52 accessions. Verification by Sanger sequencing demonstrated that the positive rate of the SNPs was approximately 97.3%. Search for more genetic variations was expanded to 141 red bayberry accessions, most of which were cultivars, by sequencing 19 selected genomic segments (SEG1-19). The results showed that each segment harbored, on average, 7.8 alleles (haplotypes), a haplotype diversity of 0.42, and a polymorphic information content (PIC) of 0.40. Seventy-two different genotypes were identified from the 141 accessions, and statistical analysis showed that the accessions with duplicated genotypes were either somatic mutants or simply synonyms. Core set selection results showed that a minimum of 34 genotypes could already have covered all the alleles on the segments. A DNA fingerprinting system was developed for red bayberry, which used the diversity information of only 8 DNA segments yet still achieved a very high efficiency without losing robustness. No large clade was robustly supported by hierarchical clustering, and well-supported small clusters mainly included close relatives. These results should lead to an improved understanding of the genetic diversity of red bayberry and be valuable for future molecular breeding and variety protection. |
format | Online Article Text |
id | pubmed-7509436 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-75094362020-10-02 Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars Wu, Bo Zhong, Yun Wu, Qianqian Chen, Fangyong Zhong, Guangyan Cui, Yiping Front Plant Sci Plant Science High throughput sequencing was used to reveal the distribution of whole-genome variations in cultivated Morella rubra (Sieb. et Zucc.). A total of 3,151,123 SNPs, 371,757 small indels, and 15,904 SVs were detected in 52 accessions. Verification by Sanger sequencing demonstrated that the positive rate of the SNPs was approximately 97.3%. Search for more genetic variations was expanded to 141 red bayberry accessions, most of which were cultivars, by sequencing 19 selected genomic segments (SEG1-19). The results showed that each segment harbored, on average, 7.8 alleles (haplotypes), a haplotype diversity of 0.42, and a polymorphic information content (PIC) of 0.40. Seventy-two different genotypes were identified from the 141 accessions, and statistical analysis showed that the accessions with duplicated genotypes were either somatic mutants or simply synonyms. Core set selection results showed that a minimum of 34 genotypes could already have covered all the alleles on the segments. A DNA fingerprinting system was developed for red bayberry, which used the diversity information of only 8 DNA segments yet still achieved a very high efficiency without losing robustness. No large clade was robustly supported by hierarchical clustering, and well-supported small clusters mainly included close relatives. These results should lead to an improved understanding of the genetic diversity of red bayberry and be valuable for future molecular breeding and variety protection. Frontiers Media S.A. 2020-09-09 /pmc/articles/PMC7509436/ /pubmed/33013982 http://dx.doi.org/10.3389/fpls.2020.563452 Text en Copyright © 2020 Wu, Zhong, Wu, Chen, Zhong and Cui http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Wu, Bo Zhong, Yun Wu, Qianqian Chen, Fangyong Zhong, Guangyan Cui, Yiping Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars |
title | Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars |
title_full | Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars |
title_fullStr | Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars |
title_full_unstemmed | Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars |
title_short | Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars |
title_sort | genetic diversity, pedigree relationships, and a haplotype-based dna fingerprinting system of red bayberry cultivars |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509436/ https://www.ncbi.nlm.nih.gov/pubmed/33013982 http://dx.doi.org/10.3389/fpls.2020.563452 |
work_keys_str_mv | AT wubo geneticdiversitypedigreerelationshipsandahaplotypebaseddnafingerprintingsystemofredbayberrycultivars AT zhongyun geneticdiversitypedigreerelationshipsandahaplotypebaseddnafingerprintingsystemofredbayberrycultivars AT wuqianqian geneticdiversitypedigreerelationshipsandahaplotypebaseddnafingerprintingsystemofredbayberrycultivars AT chenfangyong geneticdiversitypedigreerelationshipsandahaplotypebaseddnafingerprintingsystemofredbayberrycultivars AT zhongguangyan geneticdiversitypedigreerelationshipsandahaplotypebaseddnafingerprintingsystemofredbayberrycultivars AT cuiyiping geneticdiversitypedigreerelationshipsandahaplotypebaseddnafingerprintingsystemofredbayberrycultivars |