Origin of Hungarian indigenous chicken breeds inferred from mitochondrial DNA D-loop sequences

Japanese indigenous chickens have a long breeding history, possibly beginning 2000 years ago. Genetic characterization of Japanese indigenous chickens has been performed using mitochondrial D-loop region and microsatellite DNA markers. Their phylogenetic relationships with chickens worldwide and genetic variation within breeds have not yet been examined. In this study, the genetic characteristics of 38 Japanese indigenous chicken breeds were assessed by phylogenetic analyses of mitochondrial D-loop sequences compared with those of indigenous chicken breeds overseas. To evaluate the genetic relationships among Japanese indigenous chicken breeds, a STRUCTURE analysis was conducted using 27 microsatellite DNA markers. D-loop sequences of Japanese indigenous chickens were classified into five major haplogroups, A–E, among 15 haplogroups found in chickens worldwide. The haplogroup composition suggested that Japanese indigenous chickens originated mainly from China, with some originating from Southeast Asia. The STRUCTURE analyses revealed that Japanese indigenous chickens are genetically differentiated from chickens overseas; Japanese indigenous chicken breeds possess distinctive genetic characteristics, and Jidori breeds, which have been reared in various regions of Japan for a long time, are genetically close to each other. These results provide new insights into the history of chickens around Asia in addition to novel genetic data for the conservation of Japanese indigenous chickens.

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Genetic diversity of Jiangsu native chicken breeds assessed with the mitochondrial DNA D-loop region

British Poultry Science ◽

10.1080/00071668.2017.1395391 ◽

2017 ◽

Vol 59 (1) ◽

pp. 34-39 ◽

Cited By ~ 2

Author(s):

X. X. Jia ◽

J. X. Lu ◽

X. J. Tang ◽

Y. F. Fan ◽

S. H. Huang ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Loop Region ◽

Native Chicken ◽

D Loop ◽

Chicken Breeds

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Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region

Molecular Biology Reports ◽

10.1007/s11033-016-3976-0 ◽

2016 ◽

Vol 43 (5) ◽

pp. 415-425 ◽

Cited By ~ 7

Author(s):

Yuying Liao ◽

Guodong Mo ◽

Junli Sun ◽

Fengying Wei ◽

Dezhong Joshua Liao

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Loop Region ◽

D Loop ◽

Chicken Breeds

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Molecular Characterization of Sudanese and Southern Sudanese Chicken Breeds Using mtDNA D-Loop

Genetics Research International ◽

10.1155/2014/928420 ◽

2014 ◽

Vol 2014 ◽

pp. 1-8 ◽

Cited By ~ 6

Author(s):

Charles E. Wani ◽

Ibrahim A. Yousif ◽

Muntasir E. Ibrahim ◽

Hassan H. Musa

Keyword(s):

Genetic Variation ◽

Genetic Difference ◽

Genetic Relationships ◽

Indigenous Chicken ◽

Commercial Strain ◽

Pcr Product ◽

D Loop ◽

Chicken Breeds ◽

Networks Analysis

The objective of this study was to assess the genetic relationships and diversity and to estimate the amount of gene flow among the five chicken populations from Sudan and South Sudan and commercial strain of egg line White Leghorn chickens. The chicken populations were genotyped using mtDNA D-loop as a molecular marker. PCR product of the mtDNA D-loop segment was 600 bp and 14 haplotypes were identified. The neighbor-joining phylogenetic tree indicated that the indigenous Sudanese chickens can be grouped into two clades, IV and IIIa only. Median joining networks analysis showed that haplotype LBB49 has the highest frequency. The hierarchal analysis of molecular variance (AMOVA) showed that genetic variation within the population was 88.6% and the differentiation among the population was 11.4%. When the populations was redefined into two geographical zones, rich and poor Savanna, the results were fractioned into three genetic variations: between individuals within population 95.5%, between populations within the group 0.75%, and genetic variation between groups 3.75%. The pair wise Fst showed high genetic difference between Betwil populations and the rest with Fst ranging from 0.1492 to 0.2447. We found that there is large number of gene exchanges within the Sudanese indigenous chicken (Nm=4.622).

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Genetic diversity of local chicken breeds in East China based on mitochondrial DNA D-loop region

Biodiversity Science ◽

10.17520/biods.2017012 ◽

2017 ◽

Vol 25 (5) ◽

pp. 540-548

Author(s):

Xiaoxu Jia ◽

◽

Xiujun Tang ◽

Yanfeng Fan ◽

Junxian Lu ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

East China ◽

Loop Region ◽

D Loop ◽

Chicken Breeds ◽

Local Chicken

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GENETIC DIVERSITY OF VIETNAMESE NATIVE CHICKEN BREEDS BASED ON MITOCHONDRIAL DNA D-LOOP SEQUENCE

The Journal of Animal and Plant Sciences - February ◽

10.36899/japs.2022.3.0466 ◽

2021 ◽

Vol 32 (3) ◽

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Loop Sequence ◽

Native Chicken ◽

D Loop ◽

Chicken Breeds

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Genetic polymorphisms on heat-shock protein 70 gene and mitochondrial DNA d-loop variations: implications on selection for heat stress in indigenous chickens in Kenya

10.7287/peerj.preprints.27589v1 ◽

2019 ◽

Author(s):

Grace M Kennedy ◽

Philip M Panyako ◽

Philip A Oyier ◽

Emmanuel K Ndiema ◽

Jacqueline K Lichoti ◽

...

Keyword(s):

Mitochondrial Dna ◽

Heat Stress ◽

Heat Shock Protein 70 ◽

Diversity Indices ◽

Hsp70 Gene ◽

Indigenous Chicken ◽

Turkana Basin ◽

Indigenous Chickens ◽

D Loop ◽

Commercial Chickens

Background: Climate change resulting in heat stress, is one of the most challenging environmental conditions affecting poultry. Studying thermotolerance is crucial in the prevention of heat stress in chickens because it may lead to the identification of genetic lines that can withstand adverse effects of heat stress. This study aimed at investigating polymorphisms in heat shock protein 70 (HSP70) gene in indigenous chicken ecotypes. We also analyzed the mitochondrial DNA (mtDNA) D-loop of indigenous chickens to assess their origins and genetic diversity. Methods: We collected samples From Turkana basin, Mt. Elgon catchment, Lake Victoria basin and Lamu chicken ecotypes in Kenya. Genomic DNA was extracted from 280 chicken samples. The first 360 bp region of HSP70 and the first 760 bp region of the mtDNA were then amplified via PCR. These were later sequenced using Sanger ABI 3730 method. Results: We reveal through a detailed analysis of the HSP70 gene fragment in 20 indigenous chickens the presence of three HSP70 haplotypes (GC, AC, and AG) and 28 mtDNA haplotypes. Phylogenetic analysis of HSP70 revealed the presence of the ancestral haplotype GC which dominated in Turkana basin ecotype. The 28 mtDNA haplotypes clustered in haplogroups A, B, C, D, E and I. Haplogroup E which has never been reported in commercial chickens dominated in Turkana basin ecotype indicating no admixture with commercial chickens. mtDNA haplogroups were shown to have originated from various parts of South and Southeast Asia. Lack of population structure in indigenous chicken ecotypes could be an indication of genetic admixture. The mtDNA nucleotide and haplotype diversity indices were low for Turkana basin ecotype and high for Lamu ecotype. High HSP70 nucleotide diversity indices were recorded in Turkana basin ecotype, while low values were recorded in Lamu ecotype. Most of the mtDNA genetic variations occurred within individuals for the three hierarchical categories considered while most variations in HSP70 gene occurred within populations. Conclusions: This is the first study to analyze the HSP70 polymorphisms in indigenous chickens in Africa and results obtained should pave the way for further in-depth studies on heat stress.

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Genetic polymorphisms on heat-shock protein 70 gene and mitochondrial DNA d-loop variations: implications on selection for heat stress in indigenous chickens in Kenya

10.7287/peerj.preprints.27589 ◽

2019 ◽

Author(s):

Grace M Kennedy ◽

Philip M Panyako ◽

Philip A Oyier ◽

Emmanuel K Ndiema ◽

Jacqueline K Lichoti ◽

...

Keyword(s):

Mitochondrial Dna ◽

Heat Stress ◽

Heat Shock Protein 70 ◽

Diversity Indices ◽

Hsp70 Gene ◽

Indigenous Chicken ◽

Turkana Basin ◽

Indigenous Chickens ◽

D Loop ◽

Commercial Chickens

Background: Climate change resulting in heat stress, is one of the most challenging environmental conditions affecting poultry. Studying thermotolerance is crucial in the prevention of heat stress in chickens because it may lead to the identification of genetic lines that can withstand adverse effects of heat stress. This study aimed at investigating polymorphisms in heat shock protein 70 (HSP70) gene in indigenous chicken ecotypes. We also analyzed the mitochondrial DNA (mtDNA) D-loop of indigenous chickens to assess their origins and genetic diversity. Methods: We collected samples From Turkana basin, Mt. Elgon catchment, Lake Victoria basin and Lamu chicken ecotypes in Kenya. Genomic DNA was extracted from 280 chicken samples. The first 360 bp region of HSP70 and the first 760 bp region of the mtDNA were then amplified via PCR. These were later sequenced using Sanger ABI 3730 method. Results: We reveal through a detailed analysis of the HSP70 gene fragment in 20 indigenous chickens the presence of three HSP70 haplotypes (GC, AC, and AG) and 28 mtDNA haplotypes. Phylogenetic analysis of HSP70 revealed the presence of the ancestral haplotype GC which dominated in Turkana basin ecotype. The 28 mtDNA haplotypes clustered in haplogroups A, B, C, D, E and I. Haplogroup E which has never been reported in commercial chickens dominated in Turkana basin ecotype indicating no admixture with commercial chickens. mtDNA haplogroups were shown to have originated from various parts of South and Southeast Asia. Lack of population structure in indigenous chicken ecotypes could be an indication of genetic admixture. The mtDNA nucleotide and haplotype diversity indices were low for Turkana basin ecotype and high for Lamu ecotype. High HSP70 nucleotide diversity indices were recorded in Turkana basin ecotype, while low values were recorded in Lamu ecotype. Most of the mtDNA genetic variations occurred within individuals for the three hierarchical categories considered while most variations in HSP70 gene occurred within populations. Conclusions: This is the first study to analyze the HSP70 polymorphisms in indigenous chickens in Africa and results obtained should pave the way for further in-depth studies on heat stress.

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