Cargando…
A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes
BACKGROUND: Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which,...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8428137/ https://www.ncbi.nlm.nih.gov/pubmed/34503452 http://dx.doi.org/10.1186/s12711-021-00664-9 |
_version_ | 1783750319978577920 |
---|---|
author | Rostamzadeh Mahdabi, Elaheh Esmailizadeh, Ali Ayatollahi Mehrgardi, Ahmad Asadi Fozi, Masood |
author_facet | Rostamzadeh Mahdabi, Elaheh Esmailizadeh, Ali Ayatollahi Mehrgardi, Ahmad Asadi Fozi, Masood |
author_sort | Rostamzadeh Mahdabi, Elaheh |
collection | PubMed |
description | BACKGROUND: Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (F(ST) and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken. RESULTS: Using whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1). CONCLUSIONS: Our findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-021-00664-9. |
format | Online Article Text |
id | pubmed-8428137 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-84281372021-09-10 A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes Rostamzadeh Mahdabi, Elaheh Esmailizadeh, Ali Ayatollahi Mehrgardi, Ahmad Asadi Fozi, Masood Genet Sel Evol Research Article BACKGROUND: Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (F(ST) and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken. RESULTS: Using whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1). CONCLUSIONS: Our findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-021-00664-9. BioMed Central 2021-09-09 /pmc/articles/PMC8428137/ /pubmed/34503452 http://dx.doi.org/10.1186/s12711-021-00664-9 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Rostamzadeh Mahdabi, Elaheh Esmailizadeh, Ali Ayatollahi Mehrgardi, Ahmad Asadi Fozi, Masood A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes |
title | A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes |
title_full | A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes |
title_fullStr | A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes |
title_full_unstemmed | A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes |
title_short | A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes |
title_sort | genome-wide scan to identify signatures of selection in two iranian indigenous chicken ecotypes |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8428137/ https://www.ncbi.nlm.nih.gov/pubmed/34503452 http://dx.doi.org/10.1186/s12711-021-00664-9 |
work_keys_str_mv | AT rostamzadehmahdabielaheh agenomewidescantoidentifysignaturesofselectionintwoiranianindigenouschickenecotypes AT esmailizadehali agenomewidescantoidentifysignaturesofselectionintwoiranianindigenouschickenecotypes AT ayatollahimehrgardiahmad agenomewidescantoidentifysignaturesofselectionintwoiranianindigenouschickenecotypes AT asadifozimasood agenomewidescantoidentifysignaturesofselectionintwoiranianindigenouschickenecotypes AT rostamzadehmahdabielaheh genomewidescantoidentifysignaturesofselectionintwoiranianindigenouschickenecotypes AT esmailizadehali genomewidescantoidentifysignaturesofselectionintwoiranianindigenouschickenecotypes AT ayatollahimehrgardiahmad genomewidescantoidentifysignaturesofselectionintwoiranianindigenouschickenecotypes AT asadifozimasood genomewidescantoidentifysignaturesofselectionintwoiranianindigenouschickenecotypes |