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Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data
SIMPLE SUMMARY: Rabbit breeding is an important branch of agricultural animal breeding; their fur color and weight are desirable traits for artificial breeding. Polymorphism can provide potential molecular markers for studying rabbit traits and improve rabbit breeds with such markers in the future....
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9404428/ https://www.ncbi.nlm.nih.gov/pubmed/36009642 http://dx.doi.org/10.3390/ani12162052 |
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author | Li, Congyan Li, Yuying Zheng, Jie Guo, Zhiqiang Mei, Xiuli Lei, Min Ren, Yongjun Zhang, Xiangyu Zhang, Cuixia Yang, Chao Tang, Li Ji, Yang Yang, Rui Yu, Jifeng Xie, Xiaohong Kuang, Liangde |
author_facet | Li, Congyan Li, Yuying Zheng, Jie Guo, Zhiqiang Mei, Xiuli Lei, Min Ren, Yongjun Zhang, Xiangyu Zhang, Cuixia Yang, Chao Tang, Li Ji, Yang Yang, Rui Yu, Jifeng Xie, Xiaohong Kuang, Liangde |
author_sort | Li, Congyan |
collection | PubMed |
description | SIMPLE SUMMARY: Rabbit breeding is an important branch of agricultural animal breeding; their fur color and weight are desirable traits for artificial breeding. Polymorphism can provide potential molecular markers for studying rabbit traits and improve rabbit breeds with such markers in the future. In this study, single-nucleotide polymorphism markers in genotyping-by-sequencing data were used to analyze rabbit traits. In total, three genes were identified to be associated with fur color and four with weight. The results of this study provide a data base for the research and improvement of rabbit breeding program. ABSTRACT: The domestic rabbit (Oryctolagus cuniculus f. domesticus) is a very important variety in biomedical research and agricultural animal breeding. Due to the different geographical areas in which rabbit breeds originated, and the long history of domestication/artificial breeding, rabbits have experienced strong selection pressure, which has shaped many traits of most rabbit varieties, such as color and weight. An efficient genome-wide single-nucleotide polymorphism (SNP) detection strategy is genotyping-by-sequencing (GBS), which has been widely used in many organisms. This study attempted to explore bi-allelic SNPs associated with fur color and weight-related traits using GBS in five rabbit breeds. The data consisted of a total 831,035 SNPs in 150 individuals from Californian rabbits (CF), German Zika rabbits (ZK), Qixing rabbits (QX), Sichuan grey rabbits (SG), and Sichuan white rabbits (SW). In addition, these five breeds of rabbits were obviously independent populations, with high genetic differentiation among breeds and low genetic diversity within breeds. A total of 32,144 SNP sites were identified by selective sweep among the different varieties. The genes that carried SNP loci in these selected regions were related to important traits (fur color and weight) and signal pathways, such as the MAPK/ERK signaling pathway and the Hippo signaling pathway. In addition, genes related to fur color and weight were identified, such as ASIPs, MITFs and KITs, ADCY3s, YAPs, FASs, and ACSL5s, and they had more SNP sites. The research offers the foundation for further exploration of molecular genetic markers of SNPs that are related to traits. |
format | Online Article Text |
id | pubmed-9404428 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-94044282022-08-26 Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data Li, Congyan Li, Yuying Zheng, Jie Guo, Zhiqiang Mei, Xiuli Lei, Min Ren, Yongjun Zhang, Xiangyu Zhang, Cuixia Yang, Chao Tang, Li Ji, Yang Yang, Rui Yu, Jifeng Xie, Xiaohong Kuang, Liangde Animals (Basel) Article SIMPLE SUMMARY: Rabbit breeding is an important branch of agricultural animal breeding; their fur color and weight are desirable traits for artificial breeding. Polymorphism can provide potential molecular markers for studying rabbit traits and improve rabbit breeds with such markers in the future. In this study, single-nucleotide polymorphism markers in genotyping-by-sequencing data were used to analyze rabbit traits. In total, three genes were identified to be associated with fur color and four with weight. The results of this study provide a data base for the research and improvement of rabbit breeding program. ABSTRACT: The domestic rabbit (Oryctolagus cuniculus f. domesticus) is a very important variety in biomedical research and agricultural animal breeding. Due to the different geographical areas in which rabbit breeds originated, and the long history of domestication/artificial breeding, rabbits have experienced strong selection pressure, which has shaped many traits of most rabbit varieties, such as color and weight. An efficient genome-wide single-nucleotide polymorphism (SNP) detection strategy is genotyping-by-sequencing (GBS), which has been widely used in many organisms. This study attempted to explore bi-allelic SNPs associated with fur color and weight-related traits using GBS in five rabbit breeds. The data consisted of a total 831,035 SNPs in 150 individuals from Californian rabbits (CF), German Zika rabbits (ZK), Qixing rabbits (QX), Sichuan grey rabbits (SG), and Sichuan white rabbits (SW). In addition, these five breeds of rabbits were obviously independent populations, with high genetic differentiation among breeds and low genetic diversity within breeds. A total of 32,144 SNP sites were identified by selective sweep among the different varieties. The genes that carried SNP loci in these selected regions were related to important traits (fur color and weight) and signal pathways, such as the MAPK/ERK signaling pathway and the Hippo signaling pathway. In addition, genes related to fur color and weight were identified, such as ASIPs, MITFs and KITs, ADCY3s, YAPs, FASs, and ACSL5s, and they had more SNP sites. The research offers the foundation for further exploration of molecular genetic markers of SNPs that are related to traits. MDPI 2022-08-11 /pmc/articles/PMC9404428/ /pubmed/36009642 http://dx.doi.org/10.3390/ani12162052 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Li, Congyan Li, Yuying Zheng, Jie Guo, Zhiqiang Mei, Xiuli Lei, Min Ren, Yongjun Zhang, Xiangyu Zhang, Cuixia Yang, Chao Tang, Li Ji, Yang Yang, Rui Yu, Jifeng Xie, Xiaohong Kuang, Liangde Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data |
title | Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data |
title_full | Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data |
title_fullStr | Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data |
title_full_unstemmed | Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data |
title_short | Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data |
title_sort | trait analysis in domestic rabbits (oryctolagus cuniculus f. domesticus) using snp markers from genotyping-by-sequencing data |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9404428/ https://www.ncbi.nlm.nih.gov/pubmed/36009642 http://dx.doi.org/10.3390/ani12162052 |
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