Genetic Diversity and Population Genetic Structure of Cambodia Indigenous Chickens

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Genetic Diversity and Population Genetic Structure of
Cambodia Indigenous Chickens
（カンボジア在来鶏の遺伝的多様性と集団の遺伝構造）

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REN Theary

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The indigenous chicken is one of the most important animal species
worldwide since it provides higher proportion of animal protein in the human diet.
Indigenous chickens are also kept for income and sociocultural roles among the
Cambodia communities. The indigenous chickens are usually preferred o ver exotic
chickens due to their pigmentation, taste, flavor and leanness.
Physically, the diversity within indigenous domestic chicken is extensive
and this should provide a breeding base for animals that are adapted to a variety of
local environments. However, industrialization and globalization of chicken in the
21 st century have adversely affected distribution of chicken genetic resources
limiting breed composition to industrial breeds. As a result, many chicken breeds
are either extinct or seriously threatened with extinction. This study was
formulated to provide information on genetic diversity of the indigenous chickens
in Cambodia that would be important in designing effective selection and
conservation strategies.
Genetic variability among indigenous chicken population were tested using
23 microsatellite markers. Out of this study, the information on genetic diversity
in indigenous chicken populations that can be reveal genetic structures and
differentiation of indigenous chicken populations and al so to understand
phylogenetic relationships of the Cambodian indigenous chickens among the
chicken population in the world.
In chapter I, I conducted on a large-scale genetic study using
mitochondrial DNA D-loop sequences and 23 microsatellite DNA markers which
were selected from the 30 markers to investigate the genetic diversity of

indigenous chickens and 44 commercial chickens from three breeds (Isa Brown,
Rhode Island White and three-way hybrid chicken) indices were calculated for 28
villages in 26 districts of 24 provinces. In addition, recently examined the mtDNA
D-loop sequences of 585 Cambodian indigenous chickens, 89 haplotypes of
Cambodian indigenous chickens were hound and belonged to haplogroup A to F
and J, D was the most prevailed haplogroup in Cambodian indigenous chickens,
and A and B were the second and the third ones. J which is one of the rare
haplogroups of chickens in the world, was the fourth frequent haplogroups in
Cambodian indigenous chickens, haplopgroup E, which is the most dominant
haplogroup of chickens in the world, showed less than one –third frequency of J.
The 27 indigenous chickens having haplogroup E shared the same h aplotypes with
commercial chickens. The fact that haplogroups A, B, and D were major
haplogroups in Cambodian indigenous chickens was coincided with previously
known genetic characteristics of indigenous chickens in Southeast Asia.
Noteworthy findings of this study were comparatively high frequency of
haplogroup J and low frequency of haplogroup E in Cambodian indigenous
chickens, which are rare and the most dominant haplogroups in the world.
In chapter II, the variations in the physical features and the u seful
attributes of different populations of indigenous chickens , the indigenous chickens
have unique combinations of adaptive phenotypes and genotypes that respond to
the local environment condition and climate change in which they have developed
and evolved. I conducted genetic characterization of Cambodian indigenous
chickens to examine their phylogenetic relationships of Cambodian chickens with
other chicken breeds and native chickens in the world . In this chapter, 585
Cambodian individuals indigenous chicken were assessed by phylogenetic
analyses of mitochondrial DNA D-loop sequences compared with those of
indigenous chicken breeds overseas. To evaluate the genetic relationships among
Cambodian indigenous chicken breeds, a STRUCTURE analysis was conduct ed
using 23 microsatellite DNA markers also with 623 individual belonging to 28
villages from 24 provinces and 43 individuals of three commercial chicken breeds.
Structure Harvester analysis indicated that the highest and second highest delta K
values were K = 3 and K =5, respectively (Figure 3A). At K = 3 and K = 5,
indigenous chickens of Chamkar Ou village in Pursat (Pop 7-1), Preybanlek village
in Kampong Thom (Pop 8), and the three-way hybrid chicken breed were assigned
to the same cluster (shown in purple at K = 3 and K = 5 in Figure 3B). At K = 5,
the Toul Ta Aek village population in Battambang (Pop 6) was grouped the same
cluster as the two commercial chicken breeds, Isa Brown and Rhode Island White
(shown in green).

In Chapter III, different phylogenetic and evolutionary analyses were
performed for indigenous chickens and its genetic relatedness to available
commercial chickens based on DNA sequencing. As a consequence, different
phylogenetic trees were reconstructed providing evidences for a close
phylogenetic alliance among commercial chicken and indigenous chickens. On
investigation of the phylogenetic positions of Cambodian indigenous chicken in
the chicken population throughout the world. To understand the dispersal history
of chickens, I constructed a phylogenetic tree, a Bayesian BEAST with 165 D-loop
sequences. In addition, to examine a possible hypothesis of mitochondrial DNA
adaptation to various environments in chicken habitats, ami no acid mutations in
coding regions of mitochondrial genome were surveyed for each haplogroup. To
further establish the phylogenetic position of Cambodian indigenous chickens
from the standpoint of chicken gene pools in Southeast Asia, it will be necessary to
conduct additional comparative genome-wide analyses of indigenous chickens
from Cambodia and neighboring countries.