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

Abstract

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.

Geographic Origin and Genetic Characteristics of Japanese Indigenous Chickens Inferred from Mitochondrial D-Loop Region and Microsatellite DNA Markers

“…Komiyama et al (2003) [23] hypothesized that the origin of Haplogroup H (described as "Group A" in their study) was China because Haplogroup H was not found in other areas in the world when the paper was published. Since their study, Haplogroup H has been found in Southern China, Vietnam, and Thailand [10,11,19,20] (Dich et al, 2011, Direct submission to GenBank). These results were congruent with previous hypotheses regarding the northern and southern introduction routes of Japanese indigenous chickens [30,31].…”

“…Haplogroups F and G are found to be restricted to Southwestern China and Southeast Asia [11,12,18]. Haplogroup H consists of chickens in restricted regions in southwestern China, Japan, and Thailand [11,19,20], and haplogroups I and J have been reported only for a few indigenous chickens in Northeast India and Southeast Asia [11,18,20] and wild red junglefowls in Southeast Asia [11,20]. Haplogroups K and W-Z have been rarely found in wild red junglefowls in Northeast India and Southwestern China, respectively [11].…”

Genetic diversity and population genetic structure of Cambodian indigenous chickens

“…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…”

“…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.…”

Development of lymphocyte subpopulations in local breed chickens

“…However, it is equally important to understand the immune regulation system in local breeds of chicken, particularly in developing countries. Indigenous breeds of chickens stand in an intermediate position between wild and commercial breeds [ 24 ].…”