Cargando…
Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing
Genetic characterization of Chinese indigenous pig breeds is essential to promote scientific conservation and sustainable development of pigs. Here, we systematically surveyed the genomes of 75 unrelated Diannan small-ear (DSE) pigs from three diverse regions (Yingjiang County, Jinping County, and S...
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/PMC7406676/ https://www.ncbi.nlm.nih.gov/pubmed/32849777 http://dx.doi.org/10.3389/fgene.2020.00733 |
_version_ | 1783567471831154688 |
---|---|
author | Wu, Fen Sun, Hao Lu, Shaoxiong Gou, Xiao Yan, Dawei Xu, Zhong Zhang, Zhenyang Qadri, Qamar Raza Zhang, Zhe Wang, Zhen Chen, Qiang Li, Mingli Wang, Xiaoyi Dong, Xinxing Wang, Qishan Pan, Yuchun |
author_facet | Wu, Fen Sun, Hao Lu, Shaoxiong Gou, Xiao Yan, Dawei Xu, Zhong Zhang, Zhenyang Qadri, Qamar Raza Zhang, Zhe Wang, Zhen Chen, Qiang Li, Mingli Wang, Xiaoyi Dong, Xinxing Wang, Qishan Pan, Yuchun |
author_sort | Wu, Fen |
collection | PubMed |
description | Genetic characterization of Chinese indigenous pig breeds is essential to promote scientific conservation and sustainable development of pigs. Here, we systematically surveyed the genomes of 75 unrelated Diannan small-ear (DSE) pigs from three diverse regions (Yingjiang County, Jinping County, and Sipsongpanna in Yunnan Province) to describe their population structures, genetic diversity, inbreeding coefficients, and selection signatures. First, these individuals were sequenced and genotyped using the genome reducing and sequencing (GGRS) protocol. A total of 438,038 autosomal single-nucleotide polymorphisms (SNPs) were obtained and used for subsequent statistical analysis. The results showed that these DSE pigs were clearly differentiated into three separate clades revealed by the population structure and principal component analysis, which is consistent with their geographical origins. Diannan small-ear pigs owned lower genetic diversity when compared with some other pig breeds, which demonstrated the need to strengthen the conservation strategies for DSE pigs. In addition, the inbreeding coefficients based on runs of homozygosity (ROH) length (F(ROH)) were calculated in each ROH length categories, respectively. And the results indicated that the ancient (up to 50 generations ago) inbreeding had greater impacts than recent (within the last five generations) inbreeding within DSE pigs. Some candidate selection signatures within the DSE pig population were detected through the ROH islands and integrated haplotype homozygosity score (iHS) methods. And genes associated with meat quality (COL15A1, RPL3L, and SLC9A3R2), body size (PALM2-AKAP2, NANS, TRAF7, and PACSIN1), adaptability (CLDN9 and E4F1), and appetite (GRM4) were identified. These findings can help to understand the genetic characteristics and provide insights into the molecular background of special phenotypes of DSE pigs to promote conservation and sustainability of the breed. |
format | Online Article Text |
id | pubmed-7406676 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-74066762020-08-25 Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing Wu, Fen Sun, Hao Lu, Shaoxiong Gou, Xiao Yan, Dawei Xu, Zhong Zhang, Zhenyang Qadri, Qamar Raza Zhang, Zhe Wang, Zhen Chen, Qiang Li, Mingli Wang, Xiaoyi Dong, Xinxing Wang, Qishan Pan, Yuchun Front Genet Genetics Genetic characterization of Chinese indigenous pig breeds is essential to promote scientific conservation and sustainable development of pigs. Here, we systematically surveyed the genomes of 75 unrelated Diannan small-ear (DSE) pigs from three diverse regions (Yingjiang County, Jinping County, and Sipsongpanna in Yunnan Province) to describe their population structures, genetic diversity, inbreeding coefficients, and selection signatures. First, these individuals were sequenced and genotyped using the genome reducing and sequencing (GGRS) protocol. A total of 438,038 autosomal single-nucleotide polymorphisms (SNPs) were obtained and used for subsequent statistical analysis. The results showed that these DSE pigs were clearly differentiated into three separate clades revealed by the population structure and principal component analysis, which is consistent with their geographical origins. Diannan small-ear pigs owned lower genetic diversity when compared with some other pig breeds, which demonstrated the need to strengthen the conservation strategies for DSE pigs. In addition, the inbreeding coefficients based on runs of homozygosity (ROH) length (F(ROH)) were calculated in each ROH length categories, respectively. And the results indicated that the ancient (up to 50 generations ago) inbreeding had greater impacts than recent (within the last five generations) inbreeding within DSE pigs. Some candidate selection signatures within the DSE pig population were detected through the ROH islands and integrated haplotype homozygosity score (iHS) methods. And genes associated with meat quality (COL15A1, RPL3L, and SLC9A3R2), body size (PALM2-AKAP2, NANS, TRAF7, and PACSIN1), adaptability (CLDN9 and E4F1), and appetite (GRM4) were identified. These findings can help to understand the genetic characteristics and provide insights into the molecular background of special phenotypes of DSE pigs to promote conservation and sustainability of the breed. Frontiers Media S.A. 2020-07-30 /pmc/articles/PMC7406676/ /pubmed/32849777 http://dx.doi.org/10.3389/fgene.2020.00733 Text en Copyright © 2020 Wu, Sun, Lu, Gou, Yan, Xu, Zhang, Qadri, Zhang, Wang, Chen, Li, Wang, Dong, Wang and Pan. 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 | Genetics Wu, Fen Sun, Hao Lu, Shaoxiong Gou, Xiao Yan, Dawei Xu, Zhong Zhang, Zhenyang Qadri, Qamar Raza Zhang, Zhe Wang, Zhen Chen, Qiang Li, Mingli Wang, Xiaoyi Dong, Xinxing Wang, Qishan Pan, Yuchun Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing |
title | Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing |
title_full | Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing |
title_fullStr | Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing |
title_full_unstemmed | Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing |
title_short | Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing |
title_sort | genetic diversity and selection signatures within diannan small-ear pigs revealed by next-generation sequencing |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7406676/ https://www.ncbi.nlm.nih.gov/pubmed/32849777 http://dx.doi.org/10.3389/fgene.2020.00733 |
work_keys_str_mv | AT wufen geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT sunhao geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT lushaoxiong geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT gouxiao geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT yandawei geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT xuzhong geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT zhangzhenyang geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT qadriqamarraza geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT zhangzhe geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT wangzhen geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT chenqiang geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT limingli geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT wangxiaoyi geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT dongxinxing geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT wangqishan geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing AT panyuchun geneticdiversityandselectionsignatureswithindiannansmallearpigsrevealedbynextgenerationsequencing |