Genetic diversity of Bangladeshi native chickens based on complete sequence of mitochondrial DNA D-loop region

Islam, MA; Osman, Sayed; Nishibori, Masahide

doi:10.1080/00071668.2019.1655708

Cited by 9 publications

(14 citation statements)

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“…Genetic diversity and relationships among chicken breeds have been studied widely in the past decade using mitochondrial sequences [ 6 – 12 , 18 , 22 ]. This current study is the first to address the origin of the Tosa-Jidori breed, indigenous to Kochi Prefecture, using complete D-loop and mitogenome sequences.…”

Section: Resultsmentioning

confidence: 99%

“…Haplogroup E is widely considered to have originated from the Indian subcontinent and is now prevalent in chicken populations worldwide [ 7 , 10 – 13 , 22 , 25 – 28 ]. There are non-negligible proportions of Sub-haplogroup E1 found in East China, North China and Northeast China (geographically close to Japan), as reported in a previous study [ 13 ].…”

Section: Resultsmentioning

confidence: 99%

“…In addition, only one mitogenome of any JNC breed (Silkie or Ukokkei) has been reported prior to this study [ 22 ]. The Silkie breed habituated in Japan before the beginning of the Edo period (1603 through 1867) [ 30 ]; it has many genetic features distinct from those observed in other chicken breeds, and does not belong to any of the three major JNC groups [ 2 ].…”

Section: Resultsmentioning

confidence: 99%

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Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens

2021

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14 15 ORCID 16 Sayed A.-M. Osman: https://orcid.org/0000-0001-6925-9414 ABSTRACT 27 Objective: In Japan, approximately 50 breeds of indigenous domestic chicken, called Japanese native 28 chickens (JNCs), have been developed. JNCs gradually became established based on three major 29 original groups, "Jidori", "Shoukoku" and "Shamo". Tosa-Jidori is a breed of Jidori, and archival 30 records as well as its morphologically primitive characters suggest an ancient origin. Although Jidori 31 is thought to have been introduced from East Asia, a previous study based on mitochondrial D-loop s 32 equences demonstrated that Tosa-Jidori belongs to haplogroup D, which is abundant in Southeast Asia 33 but rare in other regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The 34 relatively small size of the D-loop region offers limited resolution in comparison with mitogenome 35 phylogeny. This study was conducted to determine the phylogenetic position of the Tosa-Jidori breed 36 based on complete mitochondrial D-loop and mitogenome sequences, and to clarify its 37 evolutionary relationships, possible maternal origin and routes of introduction into Japan.38 Methods: Maximum parsimony trees were based on 133 chickens, and consisted of 86 mitogenome 39 sequences as well as 47 D-loop sequences.40Results: This is the first report of the complete mitogenome not only for the Tosa-Jidori breed, but 41 also for a member of one of the three major original groups of JNCs. Our phylogenetic analysis based 42 on D-loop and mitogenome sequences suggests that Tosa-Jidori individuals characterized in this study 43 belong to the haplogroup D as well as the sub-haplogroup E1. 44 Conclusion: \The sub-haplogroup E1 is relatively common in East Asia, and so although the 45 Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-46 Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC 47 breeds.48 49 A c c e p t e d A r t i c l e 53 Given the unique geographical location of Japan in the East Asian peripheral region, with 54 water surrounding it on all sides, Japanese native chicken (JNC) breeds of Gallus gallus have been 55 profoundly influenced by continental breeds, but at the same time, they have developed indigenously. 56 There are approximately 50 breeds of Japanese native chickens [1]. Until 1867, most of them were 57 developed for their special plumage, crowing and cockfighting, while subsequently, from the end of 58 the 19th century to the early stages of the 20th century, some new breeds were created to produce eggs 59 and/or meat. 60 Most of today's JNC breeds were established from members of three major original groups or 61 breeds: "Jidori", "Shoukoku", and "Shamo" [2]. Jidori does not specify a breed, but is a generic name 62 used for various local primitive chickens whose ancestors are thought to have been introduced to 63 Japan in the Yayoi period (300 BC-300 AD) via Korea. The Jidori group includes the three well-64 kn...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens

2021

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“…Notably, haplogroup E, which is the predominant type in domestic chickens, was found at low frequencies in Cambodian indigenous chickens. The frequency of haplogroup E is also low in indigenous chickens in Laos, Vietnam, and Myanmar [ 7 , 18 , 41 , 42 ], although it is frequently distributed among indigenous chickens in Thailand (10.9% and 23.2%) [ 43 , 44 ] and Bangladesh (33.3%) [ 45 ]. Haplogroup E is believed to have originated in India and is widely distributed in Western countries [ 7 ], which tends to indicate that it has not spread extensively in Southeast Asia.…”

Section: Discussionmentioning

confidence: 99%

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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“…Genetic diversity was evaluated from haplotype and nucleotide diversities calculated from mitochondrial D‐loop sequences. In previous studies, complete mitochondrial D‐loop sequences have been successfully applied to clarify the genetic information of native chicken populations such as genetic diversity and phylogenetic analysis (Godinez et al, 2019; Islam et al, 2019; Miao et al, 2013; Oka et al, 2007; Osman et al, 2016; Teinlek et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic analysis of Myanmar indigenous chickens using mitochondrial D‐loop sequence reveals their characteristics as a genetic resource

Mon

Lwin

Maw

et al. 2021

Animal Science Journal

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Myanmar indigenous chickens play important roles in food, entertainment, and farm business for the people of Myanmar. In this study, complete mitochondrial D‐loop sequences (1232 bp) were analyzed using 176 chickens, including three indigenous breeds, two fighting cock populations, and three indigenous populations to elucidate genetic diversity and accomplish a phylogenetic analysis of Myanmar indigenous chickens. The average haplotype and nucleotide diversities were 0.948 ± 0.009 and 0.00814 ± 0.00024, respectively, exhibiting high genetic diversity of Myanmar indigenous chickens. Sixty‐four haplotypes were classified as seven haplogroups, with the majority being haplogroup F. The breeds and populations except Inbinwa had multiple maternal haplogroups, suggesting that they experienced no recent purifying selection and bottleneck events. All breeds and populations examined shared haplogroup F. When 232 sequences belonging to haplogroup F (79 from Myanmar and 153 deposited sequences from other Asian countries/region) were analyzed together, the highest genetic diversity was observed in Myanmar indigenous chickens. Furthermore, Myanmar indigenous chickens and red junglefowls were observed in the center of the star‐like median‐joining network of 37 F‐haplotypes, suggesting that Myanmar is one of the origins of haplogroup F. These findings revealed the unique genetic characteristic of Myanmar indigenous chickens as important genetic resources.

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Genetic diversity of Bangladeshi native chickens based on complete sequence of mitochondrial DNA D-loop region

Cited by 9 publications

References 39 publications

Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens

Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens

Genetic diversity and population genetic structure of Cambodian indigenous chickens

Phylogenetic analysis of Myanmar indigenous chickens using mitochondrial D‐loop sequence reveals their characteristics as a genetic resource

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