Cargando…

Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line

The advanced intercross line (AIL) that is created by successive generations of pseudo-random mating after the F(2) generation is a valuable resource, especially in agricultural livestock and poultry species, because it improves the precision of quantitative trait loci (QTL) mapping compared with tr...

Descripción completa

Detalles Bibliográficos
Autores principales: Wang, Yuzhe, Bu, Lina, Cao, Xuemin, Qu, Hao, Zhang, Chunyuan, Ren, Jiangli, Huang, Zhuolin, Zhao, Yiqiang, Luo, Chenglong, Hu, Xiaoxiang, Shu, Dingming, Li, Ning
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509424/
https://www.ncbi.nlm.nih.gov/pubmed/33033489
http://dx.doi.org/10.3389/fgene.2020.00894
_version_ 1783585592801492992
author Wang, Yuzhe
Bu, Lina
Cao, Xuemin
Qu, Hao
Zhang, Chunyuan
Ren, Jiangli
Huang, Zhuolin
Zhao, Yiqiang
Luo, Chenglong
Hu, Xiaoxiang
Shu, Dingming
Li, Ning
author_facet Wang, Yuzhe
Bu, Lina
Cao, Xuemin
Qu, Hao
Zhang, Chunyuan
Ren, Jiangli
Huang, Zhuolin
Zhao, Yiqiang
Luo, Chenglong
Hu, Xiaoxiang
Shu, Dingming
Li, Ning
author_sort Wang, Yuzhe
collection PubMed
description The advanced intercross line (AIL) that is created by successive generations of pseudo-random mating after the F(2) generation is a valuable resource, especially in agricultural livestock and poultry species, because it improves the precision of quantitative trait loci (QTL) mapping compared with traditional association populations by introducing more recombination events. The growth traits of broilers have significant economic value in the chicken industry, and many QTLs affecting growth traits have been identified, especially on chromosomes 1, 4, and 27, albeit with large confidence intervals that potentially contain dozens of genes. To promote a better understanding of the underlying genetic architecture of growth trait differences, specifically body weight and bone development, in this study, we report a nine-generation AIL derived from two divergent outbred lines: High Quality chicken Line A (HQLA) and Huiyang Bearded (HB) chicken. We evaluate the genetic architecture of the F(0), F(2), F(8), and F(9) generations of AIL and demonstrate that the population of the F(9) generation sufficiently randomized the founder genomes and has the characteristics of rapid linkage disequilibrium decay, limited allele frequency decline, and abundant nucleotide diversity. This AIL yielded a much narrower QTL than the F(2) generations, especially the QTL on chromosome 27, which was reduced to 120 Kb. An ancestral haplotype association analysis showed that most of the dominant haplotypes are inherited from HQLA but with fluctuation of the effects between them. We highlight the important role of four candidate genes (PHOSPHO1, IGF2BP1, ZNF652, and GIP) in bone growth. We also retrieved a missing QTL from AIL on chromosome 4 by identifying the founder selection signatures, which are explained by the loss of association power that results from rare alleles. Our study provides a reasonable resource for detecting quantitative trait genes and tracking ancestor history and will facilitate our understanding of the genetic mechanisms underlying chicken bone growth.
format Online
Article
Text
id pubmed-7509424
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-75094242020-10-07 Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line Wang, Yuzhe Bu, Lina Cao, Xuemin Qu, Hao Zhang, Chunyuan Ren, Jiangli Huang, Zhuolin Zhao, Yiqiang Luo, Chenglong Hu, Xiaoxiang Shu, Dingming Li, Ning Front Genet Genetics The advanced intercross line (AIL) that is created by successive generations of pseudo-random mating after the F(2) generation is a valuable resource, especially in agricultural livestock and poultry species, because it improves the precision of quantitative trait loci (QTL) mapping compared with traditional association populations by introducing more recombination events. The growth traits of broilers have significant economic value in the chicken industry, and many QTLs affecting growth traits have been identified, especially on chromosomes 1, 4, and 27, albeit with large confidence intervals that potentially contain dozens of genes. To promote a better understanding of the underlying genetic architecture of growth trait differences, specifically body weight and bone development, in this study, we report a nine-generation AIL derived from two divergent outbred lines: High Quality chicken Line A (HQLA) and Huiyang Bearded (HB) chicken. We evaluate the genetic architecture of the F(0), F(2), F(8), and F(9) generations of AIL and demonstrate that the population of the F(9) generation sufficiently randomized the founder genomes and has the characteristics of rapid linkage disequilibrium decay, limited allele frequency decline, and abundant nucleotide diversity. This AIL yielded a much narrower QTL than the F(2) generations, especially the QTL on chromosome 27, which was reduced to 120 Kb. An ancestral haplotype association analysis showed that most of the dominant haplotypes are inherited from HQLA but with fluctuation of the effects between them. We highlight the important role of four candidate genes (PHOSPHO1, IGF2BP1, ZNF652, and GIP) in bone growth. We also retrieved a missing QTL from AIL on chromosome 4 by identifying the founder selection signatures, which are explained by the loss of association power that results from rare alleles. Our study provides a reasonable resource for detecting quantitative trait genes and tracking ancestor history and will facilitate our understanding of the genetic mechanisms underlying chicken bone growth. Frontiers Media S.A. 2020-09-04 /pmc/articles/PMC7509424/ /pubmed/33033489 http://dx.doi.org/10.3389/fgene.2020.00894 Text en Copyright © 2020 Wang, Bu, Cao, Qu, Zhang, Ren, Huang, Zhao, Luo, Hu, Shu and Li. 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
Wang, Yuzhe
Bu, Lina
Cao, Xuemin
Qu, Hao
Zhang, Chunyuan
Ren, Jiangli
Huang, Zhuolin
Zhao, Yiqiang
Luo, Chenglong
Hu, Xiaoxiang
Shu, Dingming
Li, Ning
Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line
title Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line
title_full Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line
title_fullStr Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line
title_full_unstemmed Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line
title_short Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line
title_sort genetic dissection of growth traits in a unique chicken advanced intercross line
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509424/
https://www.ncbi.nlm.nih.gov/pubmed/33033489
http://dx.doi.org/10.3389/fgene.2020.00894
work_keys_str_mv AT wangyuzhe geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline
AT bulina geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline
AT caoxuemin geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline
AT quhao geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline
AT zhangchunyuan geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline
AT renjiangli geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline
AT huangzhuolin geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline
AT zhaoyiqiang geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline
AT luochenglong geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline
AT huxiaoxiang geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline
AT shudingming geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline
AT lining geneticdissectionofgrowthtraitsinauniquechickenadvancedintercrossline