Phylogenetic Analysis of Native Chicken from Bangladesh and Neighboring Asian Countries Based on Complete Sequence of Mitochondrial DNA D-loop Region

Islam, MA; Nishibori, Masahide

doi:10.2141/jpsa.0120007

Cited by 9 publications

(9 citation statements)

References 29 publications

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“…Nucleotide sequence variation showed 9 haplotypes in CamRJFs, 6 haplotypes in MyaRJFs, 3 haplotypes in BanRJFs and 5 haplotypes in LaoNCs which was corroborated with Nishibori et al (2002) and Islam and Nishibori (2012). Nishibori et al (2002) reported that LaoNCs had low genetic variability based on mtDNA D-loop sequences.…”

Section: Mtdna D-loop Sequence Variation Of Camrjfs Myarjfs Banrjfssupporting

confidence: 67%

“…The other BanRJF2 was grouped with CamRJFs in Clade G. These results suggested that two types of RJF populations exist in Bangladesh, one is an unique in Bangladesh and the other is originated from neighbor countries. Islam and Nishibori (2012) reported that some individuals of Bangladesh chicken populations have a relationship with Japanese native and silky chickens, and also with South East Asian populations of China, Cambodia, Laos, Vietnam, Thailand and Indonesia. Srisulandari et al (2008) reported the five distinct clades within Indonesian native chickens.…”

Section: Banrjfsmentioning

confidence: 99%

“…Nishibori et al (2002) reported that LaoNCs had low genetic variability based on mtDNA D-loop sequences. Islam and Nishibori (2012) reported 16 haplotypes in Bangladesh native chickens and BanRJFs which were grouped into 6 clades. Adebambo et al (2009) found 16 haplotypes in Nigerian indigenous and Anaktitan chickens which were grouped under one clade 4.…”

Section: Mtdna D-loop Sequence Variation Of Camrjfs Myarjfs Banrjfsmentioning

confidence: 99%

“…They also showed that Bhutanese native chickens and Thai native chickens were related to G. g. spadiceus, and the red earlobed RJF. Islam and Nishibori (2012) studied the phylogenetic relationship between two populations of Bangladesh native chickens (full feathered and naked neck breeds) and BanRJF. Pham et al (2013) studied the genetic diversity of Vietnamese domestic chicken populations and found that Vietnamese local chickens exhibited a higher diversity than the chicken populations of Chinese origin.…”

Section: Laoncsmentioning

confidence: 99%

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Phylogenetic Analysis of South East Asian Countries Chickens Based on Mitochondrial DNA Variations

Osman

Nishibori

2014

J. Poult. Sci.

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Domestic chickens have long been important to human societies for food, religion, entertainment, and decorative uses, yet the origins and phylogeography of chickens through Asia remain uncertain. In this study, the complete mitochondrial (mtDNA) D-loop sequences were analyzed for a total of 27 individuals of Cambodia (n＝13), Myanmar (n＝6), Bangladesh (n＝3) Red junglefowls (RJFs) and Laos native chickens (n＝5). Sequences of mtDNA D-loop of these chickens were compared with 67 D-loop chicken sequences annotated in the GenBank; White Leghorn, RJFs and other Asiatic chickens to identify the phylogenetic relationship within and among Cambodia, Myanmar, Bangladesh RJFs and Laos native chickens for the conservation and improvement of chicken genetic resources. The nucleotide variation of sequence among 23 haplotypes for within and among populations of Cambodia RJFs, Myanmar RJFs, Bangladesh RJFs and Laos native chickens supported the phenotypic variation of individuals of the populations. The 38, 28, 24 and 23 sites of single nucleotide polymorphism (SNP) in Cambodia, Myanmar, Bangladesh RJFs and Laos native chickens, respectively were observed. All RJFs and Laos native chickens have nucleotide insertion in mtDNA D-loop region comparing with White Leghorn. A phylogenetic tree was constructed using the nucleotide sequences of the complete mtDNA D-loop region of the 28 RJFs, 25 other chicken breeds and the 41 chicken haplotypes. Phylogenetic analysis showed total of 94 individuals those were separated into 8 clades. The phylogenetic analysis showed the close genetic relationship within and between the populations of each country. The genetic information from this study is the initial investigation using these populations in Myanmar, Cambodia, Bangladesh and Laos which may be useful in developing future strategies for conservation and improvement of valuable genetic resource.Key words: Bangladesh, Cambodia, Laos, mtDNA, Myanmar, Red junglefowl J. Poult. Sci., 51: 248-261, 2014 Introduction Chickens are classified as: Galliformes, Phasianidae, Gallus (junglefowl). Domestication resulted the basic changes in behavior, physiology and production of birds, but still there are some similarities between the ancestor and the current chickens (Al-Nasser et al., 2007). It is widely accepted the currently recognized populations of domestic chicken descend from a single ancestor; the Red junglefowl (Gallus gallus; RJF) (Hashiguchi et al., 1981;Okada et al., 1984;Yamashita et al., 1994).One of the first attempts to look for the genealogical origin of the present domestic chicken at mitochondrial DNA (mtDNA) level was undertaken by Akishinonomiya et al. (1994Akishinonomiya et al. ( , 1996. They established the theory of monophyletic origin of the domestic chicken that descended mainly from RJF subspecies of Southeast Asia. This result was supported by the analysis of microsatellite DNAs (Hillel et al., 2003) and single nucleotide polymorphism (SNP) genotypes in a wide range of distant chicken populations (Twito et al., 2007). In add...

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Section: Mtdna D-loop Sequence Variation Of Camrjfs Myarjfs Banrjfssupporting

confidence: 67%

Section: Banrjfsmentioning

confidence: 99%

Section: Mtdna D-loop Sequence Variation Of Camrjfs Myarjfs Banrjfsmentioning

confidence: 99%

Section: Laoncsmentioning

confidence: 99%

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Phylogenetic Analysis of South East Asian Countries Chickens Based on Mitochondrial DNA Variations

Osman

Nishibori

2014

J. Poult. Sci.

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“…Kanginakudru et al (2008) found the evidence for domestication of Indian chickens, which were originated from Gallus gallus spadiceus, Gallus gallus gallus and Gallus gallus murghi. Islam and Nishibori (2012) also reported that native fowls in Bangladesh were strongly influenced from Gallus gallus murughi. The domestication of chickens was occurred in Southeast Asia, South China and Indian subcontinent (Liu et al, 2006;Oka et al, 2007).…”

Section: Introductionmentioning

confidence: 96%

Genetic Diversity Analysis of Egyptian Native Chickens Using mtDNA D-loop Region

et al. 2014

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This study was aimed to evaluate the genetic diversity of Egyptian native chickens by using mtDNA sequence polymorphism. A 546-bp fragment of the mtDNA D-loop region was sequenced for a total of 36 Egyptian native chickens with 14 reference sequences from DNA databank. Of the Egyptian chickens 5 haplotypes were identified. Haplotype diversity and nucleotide diversity of the Egyptian native chickens were 0.5635±0.0845 and 0.00123± 0.00108, respectively. The Egyptian native chickens were distributed within one clade, which were closed to the haplotypes from Indian subcontinent and Southeast Asia. Most of Egyptian native chickens were classified into the haplotype E1, which contains 63.9% of individuals followed by E4 (16.6%), E5 (11.1%), E2 (5.5%) and E3 (2.7%), respectively. These findings indicate that the maternal lineages was involved in the origin of domestic chicken in Egypt may have roots in Indian subcontinent and other Southeast Asia. The genetic information from this study will probably pave the way to further studies for evaluation, preservation and improvement of Egyptian native chickens as genetic resources in the future.

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Genetic diversity, phylogeographic structure and effect of selection at the mitochondrial hypervariable region of Nigerian chicken populations

Ajibike

Adeleye

Ilori

et al. 2017

J Genet

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In this study, the maternal genetic diversity, phylogenetic relationship and effect of natural selection on indigenous chickens from Nigeria were assessed. A total of 397-bp fragment of the mitochondrial DNA (mtDNA) D-loop region of 171 indigenous chickens from four populations of Nigeria and four commercial egg line strains (two Anak titan, one Giriraja and one Yaffa) as out-groups were analysed. Thirty-one haplotypes (28 from Nigerian chickens and three from commercial strains) and 34 polymorphic sites were identified. The mean haplotypic and nucleotide diversity were found to be 0.39 ± 0.05 and 0.02 ± 0.02, respectively. Majority of Nigerian chicken haplotypes observed were grouped into haplogroup D which originated from Indian subcontinent, suggesting a single maternal lineage. Genetic variation within and between populations accounted for 97.30 and 2.70% of the total genetic variation, respectively, which is in agreement with a recent and maternal founding effect. High number (4) of negatively selected sites observed based on single likelihood ancestral counting (SLAC) model indicated that the sampled Nigerian chicken populations were undergoing purifying selection. This study concluded that there was relatively high genetic diversity and differentiation, thus, this information will probably paveway for further evaluation studies, preservation and improvement of Nigerian chickens as genetic resources towards ensuring food security.

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Phylogenetic Analysis of Native Chicken from Bangladesh and Neighboring Asian Countries Based on Complete Sequence of Mitochondrial DNA D-loop Region

Cited by 9 publications

References 29 publications

Phylogenetic Analysis of South East Asian Countries Chickens Based on Mitochondrial DNA Variations

Phylogenetic Analysis of South East Asian Countries Chickens Based on Mitochondrial DNA Variations

Genetic Diversity Analysis of Egyptian Native Chickens Using mtDNA D-loop Region

Genetic diversity, phylogeographic structure and effect of selection at the mitochondrial hypervariable region of Nigerian chicken populations

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