Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers

Roh, Hee-Jong; Kim, Seung-Chang; Cho, Chang-Yeon; Lee, Jinwook; Jeon, Dayeon; Kim, Dong-Kyo; Kim, Kwan-Woo; Afrin, Fahmida; Ko, Yeoung-Gyu; Lee, Jun Heon; Batsaikhan, Solongo; Susanti, Triana; Hegay, Sergey; Kongvongxay, Siton; Gorkhali, Neena Amatya; Thi, Lan Anh Nguyen; Thao, Trinh Thi Thu; Manikku, Lakmalie

doi:10.5713/ajas.19.0958

Cited by 10 publications

(9 citation statements)

References 29 publications

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“…However, microsatellites and DNA barcodes still accepted as markers of choice because they are technically less demanding and cost-effective in evaluation. Ample literature is available on use of microsatellite markers in domestic chicken [29][30][31]. Nonetheless, uses of SNP markers and whole mitogenome sequencing have recently been appeared in the publication, which can be used to evaluate genetic diversity of domestic chicken.…”

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

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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.

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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

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“…This haplogroup is widely distributed in red junglefowl in Thailand [44], whereas it is comparatively rare in domestic chickens and has only been reported in a limited number of indigenous chickens in Indonesia [50] and Thailand [44]. These results thus indicate that In a number of previous studies, the genetic diversity of indigenous chickens in Southeast Asia has been investigated using microsatellite DNA markers [18,20,44,51]. For example, Cuc et al ( 2010) [18] examined the genetic diversity of nine indigenous chicken breeds in Vietnam and found that the mean number of alleles per locus (Na), observed heterozygosity (Ho), and expected heterozygosity (He) were 6.09, 0.60, and 0.63, respectively.…”

Section: A C C E P T E D a R T I C L Ementioning

confidence: 83%

“…and four breeds from Laos (0.62 to 0.69 and 0.64 to 0.68, respectively) [20] but were less than 0.60 in nine Thai indigenous chicken breeds (averaging 0.56 and 0.57, respectively) [44]. In…”

Section: A C C E P T E D a R T I C L Ementioning

confidence: 89%

“…In a number of previous studies, the genetic diversity of indigenous chickens in Southeast Asia has been investigated using microsatellite DNA markers [ 18 , 20 , 44 , 51 ]. For example, Cuc et al [ 18 ] examined the genetic diversity of nine indigenous chicken breeds in Vietnam and found that the mean number of alleles per locus ( Na ), observed heterozygosity ( Ho ), and expected heterozygosity ( He ) were 6.09, 0.60, and 0.63, respectively.…”

Section: Discussionmentioning

confidence: 99%

“…Similarly, owing to their high polymorphism, microsatellite markers are also among the most powerful molecular tools for estimating genetic diversity among chicken populations and their genetic structures [3,16], and microsatellite markers recommended by the Food and Agriculture Organization (FAO) are openly available [17]. Indeed, microsatellites have been successfully applied in analyses of the genetic diversity and population structure of chickens [3,[18][19][20].…”

Section: A C C E P T E D a R T I C L Ementioning

confidence: 99%

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Genetic diversity and population genetic structure of Cambodian indigenous chickens

Ren¹,

Nunome

Suzuki

et al. 2022

Anim Biosci

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Cambodia is located within the distribution range of the red junglefowl, the common ancestor of domestic chickens. Although a variety of indigenous chickens have been reared in Cambodia since ancient times, their genetic characteristics have yet to be sufficiently defined. Here, we conducted a large-scale population genetic study to investigate the genetic diversity and population genetic structure of Cambodian indigenous chickens and their phylogenetic relationships with other chicken breeds and native chickens worldwide. MethodsA Bayesian phylogenetic tree was constructed based on 625 mitochondrial DNA D-loop sequences, and Bayesian clustering analysis was performed for 666 individuals with 23 microsatellite markers, using samples collected from 28 indigenous chicken populations in 24 provinces and three commercial chicken breeds. ResultsA total of 92 haplotypes of mitochondrial D-loop sequences belonging to haplogroups A to F and J were detected in Cambodian chickens; in the indigenous chickens, haplogroup D (44.4%) was the most common, and haplogroups A (21.0%) and B (13.2%) were also dominant. However, haplogroup J, which is rare in domestic chickens but abundant in Thai red junglefowl, was found at a high frequency (14.5%), whereas the frequency of haplogroup E was considerably lower (4.6%). Population genetic structure analysis based on microsatellite markers revealed the presence of three major genetic clusters in Cambodian indigenous chickens. Their genetic diversity was A c c e p t e d A r t i c l e 4 relatively high, which was similar to findings reported for indigenous chickens from other Southeast Asian countries. ConclusionCambodian indigenous chickens are characterized by mitochondrial D-loop haplotypes that are common to indigenous chickens throughout Southeast Asia, and may retain many of the haplotypes that originated from wild ancestral populations. These chickens exhibit high population genetic diversity, and the geographical distribution of three major clusters may be attributed to interregional trade and poultry transportation routes within Cambodia or international movement between Cambodia and other countries.

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Designing and evaluating a cost‐effective single nucleotide polymorphism liquid array for Chinese native chickens

Liu,

Shan,

et al. 2023

Animal Research and One Health

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Genotyping plays an important role in breeding and population studies. Currently available genotyping technologies, including solid‐phase chips and sequencing, often have several limitations in their application to local chickens in China, including high costs, insufficient diversity, and poor universality. In the present study, we developed a chicken 5 K single nucleotide polymorphism (SNP) array suitable for breeding and genetic analysis using genotyping by targeted sequencing technology. The chip design was based on genomic data from 33 local breeds, and 5847 SNPs were selected for the final chip design. Among these SNPs, 3427 sites were associated with economic traits in broiler chickens. Our chip contained 25,000 high‐quality SNP markers captured from 5 K regions with highly efficient target site capture. Population analyses of the eight breeds showed high detection rates and minor allele frequencies for SNP markers on the array, enabling clear differentiation of different populations and families within populations. The genetic diversity trend obtained using the chip was consistent with the results obtained from microsatellite analyses. Additionally, the 5 K array was applied to a genome‐wide association study of broilers, resulting in the identification of several growth‐ and meat quality‐related loci. Therefore, the newly developed chip is efficient, cost‐effective, and well suited for application in local Chinese chickens, which will accelerate poultry breeding improvements and enhance conservation efforts.

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Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers

Cited by 10 publications

References 29 publications

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

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

Genetic diversity and population genetic structure of Cambodian indigenous chickens

Designing and evaluating a cost‐effective single nucleotide polymorphism liquid array for Chinese native chickens

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