Genome-Wide Population Genetic Analysis of Commercial, Indigenous, Game, and Wild Chickens Using 600K SNP Microarray Data

Zhang, Jinxin; Nie, Changsheng; Li, Xinghua; Ning, Zhonghua; Chen, Yu; Jia, Yaxiong; Han, Jianlin; Wang, Liang; Lv, Xueze; Yang, Weijia; Qu, Lujiang

doi:10.3389/fgene.2020.543294

Cited by 35 publications

(39 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is even higher than a previous study conducted on 14 French breeds in which they observed an overall Fst of 0.19 (Berthouly et al, 2008). However the observed genetic differentiation between French breeds is larger than the one observed in Chinese populations with overall Fst of 0.11 (Qu et al, 2006) and pairwise Fst ranging from 0.03 to 0.27 (Zhang et al, 2020) while we observed values from 0.13 to 0.43 for French local breeds. This indicates that management of French local breeds succeeded in conserving a large number of distinct breeds.…”

Section: Overall Breed Structurecontrasting

confidence: 94%

“…These values are larger than those observed in other European breeds with an observed heterozygosity 0.19 in breeds sampled in Germany (Malomane et al, 2019) and observed heterozygosity ranging from 0.16 to 0.29 in Dutch breeds (Bortoluzzi et al, 2018) . Reversely this level of within population diversity is very close to the one observed in Asian populations with values ranging from 0.29 to 0.36 (Zhang et al, 2020) . Interestingly this corresponds to the level of diversity observed in populations less structured like the Chinese ones in which gene flow occurs regularly between breeds ensuring the conservation of a high level of within-breed genetic diversity.…”

Section: Overall Diversitysupporting

confidence: 78%

See 1 more Smart Citation

Management programs as a key factor for genetic conservation of small populations : The case of French local chicken breeds

Restoux

Rognon

Vieaud

et al. 2021

Preprint

View full text Add to dashboard Cite

On-going climate change will drastically modify agriculture in the future, with a need for more sustainable systems, for animal production in particular. In this context, genetic diversity is a key factor for adaptation to new conditions: local breeds are likely to harbor unique adaptive features and represent a key component of diversity to reach resilience. Nevertheless, they are often suffering from small population size putting these valuable resources at risk of extinction. In chickens, management programs have been initiated a few decades ago in France, relying on a particular niche market aiming at promoting and protecting local breeds. We conducted a unique comprehensive study of 23 French local populations, along with 4 commercial lines, to evaluate their genetic conservation status and the efficiency of management programs. Using a 57K SNP chip we demonstrated that both between and within breeds genetic diversity were high in French populations. Diversity was mainly structured according to selection and breeds' history. Nevertheless, we observed a prominent sub-structuring of breeds according to farmer's practices in terms of exchange, leading to more or less isolated flocks. Analyzing demographic parameters as well as molecular information, we showed the efficiency of consistent management programs to conserve genetic diversity, since the earlier the breeds integrated programs the lower was the inbreeding. Finally we stressed that management programs can benefit from molecular markers and runs of homozygosity, ROH, in particular, as a valuable and affordable tool to monitor genetic diversity of local breeds which often lack pedigree information.

show abstract

Section: Overall Breed Structurecontrasting

confidence: 94%

Section: Overall Diversitysupporting

confidence: 78%

Management programs as a key factor for genetic conservation of small populations : The case of French local chicken breeds

Restoux

Rognon

Vieaud

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…However, considering the costs involved and assess to technology, barcoding markers were used in the present study. SNPs have been used for genomewide analysis to assess the conservation status and the genomic variability of Italian chicken breeds [22] as well as to understand genetic structures of these (indigenous, commercial, gamecock, and wild ancestral chicken) breeds under different selection pressure [23]. Furthermore, mitogenome sequences have been utilized to assess hereditary divergence between 22 Asian native breeds and seven native Indian chicken breeds [24], to investigate phylogenetic evolution and genetic diversity of Tibetan chicken [25], Tosa-Jidori of Japan [26], Huainan Partridge [27], and Huangshan Black [28] chickens of China.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity among two native Indian chicken populations using cytochrome c oxidase subunit I and cytochrome b DNA barcodes

et al. 2021

View full text Add to dashboard Cite

Background and Aim: India has large varieties (recognized, unrecognized) of native chickens (Desi) scattered throughout the country, managed under scavenging system different from commercial chicken breeds. However, they are less investigated for genetic diversity they harbor. The present study was planned to evaluate genetic diversity among two native chicken populations of North Gujarat (proposed Aravali breed) and South Gujarat (Ankleshwar breed). Aravali chicken, a distinct population with unique characters different from the registered chicken breeds of India is under process to be registered as a new chicken breed of Gujarat, India. Materials and Methods: Two mitochondrial markers, namely, cytochrome c oxidase subunit I (COX I) and cytochrome b (Cyt b) genes were studied across 10 birds from each population. Methodology included sample collection (blood), DNA isolation (manual), polymerase chain reaction amplification of mitochondrial genes, Sanger sequencing, and purification followed by data analysis using various softwares. Results: Haplotype analysis of the COX I gene unveiled a total eight and three haplotypes from the Aravali and Ankleshwar populations, respectively, with haplotype diversity (Hd) of 92.70 % for the Aravali and 34.50% for the Ankleshwar breed. Haplotype analysis of the Cyt b gene revealed a total of four haplotypes from the Aravali population with 60% Hd and no polymorphism in Ankleshwar breed. The phylogenetic analysis uncovered Red Jungle Fowl and Gray Jungle Fowl as prime roots for both populations and all domestic chicken breeds. Conclusion: Study findings indicated high genetic variability in Aravali chicken populations with COX I mitochondrial marker being more informative for evaluating genetic diversity in chickens.

show abstract

“…ROH islands are widely observed in populations and can be used as a useful tool to identify the phenomenon called “selective sweeps”, genome regions undergone selection pressure ( Szmatoła et al 2019 ). ROH islands have been used to localize selection signatures in the genome of farm animals including sheep ( Purfield et al 2017 ; Mastrangelo et al 2017 ; Mastrangelo et al 2018 ; Luigi-Sierra et al 2019 ; Signer-Hasler et al 2019 ), goat ( Bertolini et al 2018 ; Onzima et al 2018 ), horse ( Metzger et al 2015 ; Grilz-Seger et al 2018 ; Ablondi et al 2019 ; Grilz-Seger et al 2019 ), cattle ( Goszczynski et al 2018 ; Peripolli et al 2018 ; Nandolo et al 2018 ; Szmatoła et al 2019 ; Peripolli et al 2020 ), pig ( Wang et al 2019 ; Xu et al 2019 ; Xie et al 2019 ; Gorssen et al 2020 ) and in chicken ( Marchesi et al 2018 ; Almeida et al 2019 ; Strillacci et al 2018 ; Zhang et al 2018 ; Zhang et al 2020 ).…”

mentioning

confidence: 99%

Runs of Homozygosity in Modern Chicken Revealed by Sequence Data

Talebi

Szmatoła

Mészáros

et al. 2020

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

Runs of homozygosity (ROH) are chromosomal stretches that in a diploid genome appear in a homozygous state and display identical alleles at multiple contiguous loci. This study aimed to systematically compare the genomic distribution of the ROH islands among five populations of wild vs. commercial chickens of both layer and broiler type. To this end, we analyzed whole genome sequences of 115 birds including white layer (WL, n=25), brown layer (BL, n=25), broiler line A (BRA, n=20), broiler line B (BRB, n=20) and Red Junglefowl (RJF, n=25). The ROH segments varied in size markedly among populations, ranging from 0.3 to 21.83 Mb reflecting their past genealogy. White layers contained the largest portion of the genome in homozygous state with an average ROH length of 432.1 Mb (±18.7) per bird, despite carrying it in short segments (0.3-1 Mb). Population-wise inbreeding measures based on Wright's (Fis) and genomic (FROH) metrics revealed highly inbred genome of layer lines relative to the broilers and Red Junglefowl. We further revealed the ROH islands, among commercial lines overlapped with QTLs related to limb development (GREM1, MEOX2), body weight (Meis2a.1, uc_338), eggshell color (GLCCI1, ICA1, UMAD1), antibody response to Newcastle virus (ROBO2), and feather pecking. Comparison of ROH landscape in sequencing resolution demonstrated that a sizable portion of genome of commercial lines segregates in homozygote state, reflecting many generations of assortative mating and intensive selection in their recent history. In contrary, wild birds carry shorter ROH segments, likely suggestive of older evolutionary events.

show abstract

Genome-Wide Population Genetic Analysis of Commercial, Indigenous, Game, and Wild Chickens Using 600K SNP Microarray Data

Cited by 35 publications

References 66 publications

Management programs as a key factor for genetic conservation of small populations : The case of French local chicken breeds

Management programs as a key factor for genetic conservation of small populations : The case of French local chicken breeds

Genetic diversity among two native Indian chicken populations using cytochrome c oxidase subunit I and cytochrome b DNA barcodes

Runs of Homozygosity in Modern Chicken Revealed by Sequence Data

Contact Info

Product

Resources

About