Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region

Teinlek, Piyanat; Siripattarapravat, Kannika; Tirawattanawanich, Chanin

doi:10.5713/ajas.17.0611

Cited by 36 publications

(38 citation statements)

References 22 publications

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“…In the present study, as was previously reported in the Chilean chicken [4], haplotypes belonging to the geographically broad type E were found; this haplogroup has been identified in European animals (Plymouth Rock, White Plymouth Rock, White Leghorn, and New Hampshire), as well as in the Middle East, India, and China [45]. Regarding the haplogroup F, it is mainly concentrated in the southwest of China and in native breeds from Japan, in which Haplogroup F was reported in the Shamo breed from Okinawa [48].…”

Section: Discussionmentioning

confidence: 99%

Deciphering the Patterns of Genetic Admixture and Diversity in the Ecuadorian Creole Chicken

Vargas

León²,

Menor

et al. 2019

Animals

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Simple SummaryIn Ecuador, the production of Ecuadorian Creole chicken is of crucial importance in the economy and for the nutrition of families. These chickens represent a focal point in scientific research for three main reasons: (1) they are an unknown genetic resource derived from 500 years of environmental and human selection and represent an important reservoir of genetic variability and adaptability; (2) Ecuadorian Creole chicken production is normally familiar, in a marginal dimension, and it is an important source of economic input for medium–low income communities; and (3) being a local genetic resource, it is available to local communities without intermediary international enterprises and represents the starting point for food sovereignty. We aimed to measure the level of genetic diversity and its phylogenetic position compared with other outgroup breeds using information from microsatellite and mitochondrial markers. Our results showed that these chicken populations represent a great reservoir of genetic variability; however, the genetic fragmentation owing to the high geographical diversity of the country could compromise the conservation status and, therefore, the establishment of an official breeding program is needed for the conservation and valuation of these avian populations, with this genetic characterization being a first step.AbstractLatin American Creole chickens are generally not characterized; this is the case in Ecuador, where the lack of scientific information is contributing to their extinction. Here, we developed a characterization of the genetic resources of Ecuadorian chickens located in three continental agroecosystems (Pacific coastal, Andean, and Amazonian). Blood samples of 234 unrelated animals were collected in six provinces across Ecuador: Bolívar, Chimborazo, Cotopaxi, Guayas, Morona Santiago, and Tungurahua, in order to perform a genetic characterization and population structure assessment using the AVIANDIV project microsatellites panel (30 loci) and D-loop sequences of mitochondrial DNA and comparing with reference data from other breeds or genetic lines. The results indicate that Ecuadorian Creole chickens are the result of the admixture of different genetic groups that occurred during the last five centuries. While the influence of South Spanish breeds is demonstrated in the colonial age, genetic relationships with other breeds (Leghorn, Spanish fighter cock) cannot be discarded. The geographical configuration of the country and extreme climate variability have influenced the genetic isolation of groups constituting a homogeneous genetic status into the whole population. This is not only a source of genetic variation, but also a critical point because genetic drift produces a loss of genetic variants.

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Section: Discussionmentioning

confidence: 99%

Deciphering the Patterns of Genetic Admixture and Diversity in the Ecuadorian Creole Chicken

Vargas

León²,

Menor

et al. 2019

Animals

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“…In Miao et al 5 and other reports cited in their study 18 , 19 , 23 , 32 red junglefowls (AB009432 and AB009441 in Miyake et al, 1997, direct submission to the international database GenBank [NCBI], HM462194 to HM462217 18 , D82900, D829001, and D82906 to D82908 19 ) and indigenous chicken individuals (AB007724 in Miyake et al, direct submission to the international database GenBank [NCBI]; D82922 19 ; FJ914360 and FJ914361 23 ) from Thailand were included. In addition, Teinlek et al 24 recently examined the mtDNA D-loop sequences of 220 Thai indigenous chickens consisting of four breeds (Pradu-hang-dam, Leung-hang-khao Chee, and Dang). Although Thailand may be one of the regions where chicken domestication occurred 3 , the data regarding the genetic diversity of red junglefowls and indigenous chickens in Thailand are still insufficient to accurately elucidate the origin and process of chicken domestication.…”

Section: Introductionmentioning

confidence: 99%

Origin and evolutionary history of domestic chickens inferred from a large population study of Thai red junglefowl and indigenous chickens

Hata

Nunome

Suwanasopee

et al. 2021

Sci Rep

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In this study, we aimed to elucidate the origin of domestic chickens and their evolutionary history over the course of their domestication. We conducted a large-scale genetic study using mitochondrial DNA D-loop sequences and 28 microsatellite DNA markers to investigate the diversity of 298 wild progenitor red junglefowl (Gallus gallus) across two subspecies (G. g. gallus and G. g. spadiceus) from 12 populations and 138 chickens from 10 chicken breeds indigenous to Thailand. Twenty-nine D-loop sequence haplotypes were newly identified: 14 and 17 for Thai indigenous chickens and red junglefowl, respectively. Bayesian clustering analysis with microsatellite markers also revealed high genetic diversity in the red junglefowl populations. These results suggest that the ancestral populations of Thai indigenous chickens were large, and that a part of the red junglefowl population gene pool was not involved in the domestication process. In addition, some haplogroups that are distributed in other countries of Southeast Asia were not observed in either the red junglefowls or the indigenous chickens examined in the present study, suggesting that chicken domestication occurred independently across multiple regions in Southeast Asia.

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“…Mitochondrial DNA (mtDNA) is a critical tool for tracing evolutionary and population genetics of most domesticated animals. Also, mtDNA diversity is vital in assessing the maternal origin, phylogeny, and population structure of all domestic animals [8][9][10][11][12][13]. Previous studies of goat mtDNA (control region) revealed a total of six haplogroups (also known as lineages; A, B, and C by Luikart et al [14]; D by Sultana et al [15]; F by Sardina et al [16]; and G by Naderi et al [6]).…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial DNA variation and phylogeography of native Mongolian goats

Ganbold

Lee

Paek

et al. 2020

Asian-Australas J Anim Sci

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Objective: Mongolia is one of a few countries that supports over 25 million goats, but genetic diversity, demographic history, and the origin of goat populations in Mongolia have not been well studied. This study was conducted to assess the genetic diversity, phylogenetic status and population structure of Mongolian native goats, as well as to discuss their origin together with other foreign breeds from different countries using hypervariable region 1 (HV1) in mtDNA.Methods: In this study, we examined the genetic diversity and phylogenetic status of Mongolian native goat populations using a 452 base-pair long fragment of HVI of mitochondrial DNA from 174 individuals representing 12 populations. In addition, 329 previously published reference sequences from different regions were included in our phylogenetic analyses.Results: Investigated native Mongolian goats displayed relatively high genetic diversities. After sequencing, we found a total of 109 polymorphic sites that defined 137 haplotypes among investigated populations. Of these, haplotype and nucleotide diversities of Mongolian goats were calculated as 0.997±0.001 and 0.0283±0.002, respectively. These haplotypes clearly clustered into four haplogroups (A, B, C, and D), with the predominance of haplogroup A (90.8%). Estimates of pairwise differences (Fst) and the analysis of molecular variance values among goat populations in Mongolia showed low genetic differentiation and weak geographical structure. In addition, Kazakh, Chinese (from Huanghuai and Leizhou), and Arabian (Turkish and Baladi breeds) goats had smaller genetic differentiation compared to Mongolian goats.Conclusion: In summary, we report novel information regarding genetic diversity, population structure, and origin of Mongolian goats. The findings obtained from this study reveal that abundant haplogroups (A to D) occur in goat populations in Mongolia, with high levels of haplotype and nucleotide diversity.

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Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region

Cited by 36 publications

References 22 publications

Deciphering the Patterns of Genetic Admixture and Diversity in the Ecuadorian Creole Chicken

Deciphering the Patterns of Genetic Admixture and Diversity in the Ecuadorian Creole Chicken

Origin and evolutionary history of domestic chickens inferred from a large population study of Thai red junglefowl and indigenous chickens

Mitochondrial DNA variation and phylogeography of native Mongolian goats

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