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Genetic diversity of wild rice accessions (Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection

Oryza rufipogon Griff. is a valuable germplasm resource for rice genetic improvement. However, natural habitat loss has led to the erosion of the genetic diversity of wild rice populations. Genetic diversity analysis of O. rufipogon accessions and development of the core collection are crucial for c...

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Autores principales: Zhang, Jing, Pan, Dajian, Fan, Zhilan, Yu, Hang, Jiang, Liqun, Lv, Shuwei, Sun, Bingrui, Chen, Wenfeng, Mao, Xingxue, Liu, Qing, Li, Chen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9576158/
https://www.ncbi.nlm.nih.gov/pubmed/36262660
http://dx.doi.org/10.3389/fpls.2022.999454
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author Zhang, Jing
Pan, Dajian
Fan, Zhilan
Yu, Hang
Jiang, Liqun
Lv, Shuwei
Sun, Bingrui
Chen, Wenfeng
Mao, Xingxue
Liu, Qing
Li, Chen
author_facet Zhang, Jing
Pan, Dajian
Fan, Zhilan
Yu, Hang
Jiang, Liqun
Lv, Shuwei
Sun, Bingrui
Chen, Wenfeng
Mao, Xingxue
Liu, Qing
Li, Chen
author_sort Zhang, Jing
collection PubMed
description Oryza rufipogon Griff. is a valuable germplasm resource for rice genetic improvement. However, natural habitat loss has led to the erosion of the genetic diversity of wild rice populations. Genetic diversity analysis of O. rufipogon accessions and development of the core collection are crucial for conserving natural genetic diversity and providing novel traits for rice breeding. In the present study, we developed 1,592 SNPs by multiplex PCR and next-generation sequencing (NGS) technology and used them to genotype 998 O. rufipogon accessions from 14 agroclimatic zones in Guangdong and Hainan Provinces, China. These SNPs were mapped onto 12 chromosomes, and the average MAF value was 0.128 with a minimum of 0.01 and a maximum of 0.499. The O. rufipogon accessions were classified into ten groups. The mean Nei’s diversity index and Shannon–Wiener index (I) were 0.187 and 0.308, respectively, in all populations, indicating that O. rufipogon accessions had rich genetic diversity. There were also differences in the genetic diversity of O. rufipogon resources in the 14 regions. Hainan populations possessed higher levels of genetic diversity, whereas the Guangzhou population had lower levels of genetic diversity than did the other populations. Phylogenetic analysis revealed that the genetic relationship among the distribution sites of O. rufipogon was closely related to geographical location. Based on genetic distance, a core collection of 299 accessions captured more than 99% of the genetic variation in the germplasm. This study provides insights into O. rufipogon conservation, and the constructed core collection provides valuable resources for future research and genomics-assisted breeding of rice.
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spelling pubmed-95761582022-10-18 Genetic diversity of wild rice accessions (Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection Zhang, Jing Pan, Dajian Fan, Zhilan Yu, Hang Jiang, Liqun Lv, Shuwei Sun, Bingrui Chen, Wenfeng Mao, Xingxue Liu, Qing Li, Chen Front Plant Sci Plant Science Oryza rufipogon Griff. is a valuable germplasm resource for rice genetic improvement. However, natural habitat loss has led to the erosion of the genetic diversity of wild rice populations. Genetic diversity analysis of O. rufipogon accessions and development of the core collection are crucial for conserving natural genetic diversity and providing novel traits for rice breeding. In the present study, we developed 1,592 SNPs by multiplex PCR and next-generation sequencing (NGS) technology and used them to genotype 998 O. rufipogon accessions from 14 agroclimatic zones in Guangdong and Hainan Provinces, China. These SNPs were mapped onto 12 chromosomes, and the average MAF value was 0.128 with a minimum of 0.01 and a maximum of 0.499. The O. rufipogon accessions were classified into ten groups. The mean Nei’s diversity index and Shannon–Wiener index (I) were 0.187 and 0.308, respectively, in all populations, indicating that O. rufipogon accessions had rich genetic diversity. There were also differences in the genetic diversity of O. rufipogon resources in the 14 regions. Hainan populations possessed higher levels of genetic diversity, whereas the Guangzhou population had lower levels of genetic diversity than did the other populations. Phylogenetic analysis revealed that the genetic relationship among the distribution sites of O. rufipogon was closely related to geographical location. Based on genetic distance, a core collection of 299 accessions captured more than 99% of the genetic variation in the germplasm. This study provides insights into O. rufipogon conservation, and the constructed core collection provides valuable resources for future research and genomics-assisted breeding of rice. Frontiers Media S.A. 2022-10-03 /pmc/articles/PMC9576158/ /pubmed/36262660 http://dx.doi.org/10.3389/fpls.2022.999454 Text en Copyright © 2022 Zhang, Pan, Fan, Yu, Jiang, Lv, Sun, Chen, Mao, Liu and Li https://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
Zhang, Jing
Pan, Dajian
Fan, Zhilan
Yu, Hang
Jiang, Liqun
Lv, Shuwei
Sun, Bingrui
Chen, Wenfeng
Mao, Xingxue
Liu, Qing
Li, Chen
Genetic diversity of wild rice accessions (Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection
title Genetic diversity of wild rice accessions (Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection
title_full Genetic diversity of wild rice accessions (Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection
title_fullStr Genetic diversity of wild rice accessions (Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection
title_full_unstemmed Genetic diversity of wild rice accessions (Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection
title_short Genetic diversity of wild rice accessions (Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection
title_sort genetic diversity of wild rice accessions (oryza rufipogon griff.) in guangdong and hainan provinces, china, and construction of a wild rice core collection
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9576158/
https://www.ncbi.nlm.nih.gov/pubmed/36262660
http://dx.doi.org/10.3389/fpls.2022.999454
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