scholarly journals 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

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.

scholarly journals 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

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.

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

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2074
Author(s):  
Ayano Hata ◽  
Atsushi Takenouchi ◽  
Keiji Kinoshita ◽  
Momomi Hirokawa ◽  
Takeshi Igawa ◽  
...  
Keyword(s):  
Dna Markers ◽  
Microsatellite Dna ◽  
Genetic Relationships ◽  
Indigenous Chicken ◽  
Genetic Characteristics ◽  
Indigenous Chickens ◽  
Loop Region ◽  
Microsatellite Dna Markers ◽  
D Loop ◽  
Chicken Breeds

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.

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

2010 ◽  
Vol 41 (5) ◽  
pp. 548-550 ◽  
Author(s):  
T. Revay ◽  
N. Bodzsar ◽  
V. E. Mobegi ◽  
O. Hanotte ◽  
A. Hidas
Keyword(s):  
Mitochondrial Dna ◽  
Indigenous Chicken ◽  
D Loop ◽  
Chicken Breeds

scholarly journals Evaluation of the genetic diversity of six Chinese indigenous chickens

2020 ◽  
Vol 33 (10) ◽  
pp. 1566-1572
Author(s):  
Yuzhu Sha ◽  
Caixia Gao ◽  
Meimei Liu ◽  
Shengguo Zhao
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Indian Subcontinent ◽  
Coastal Region ◽  
Principal Component ◽  
Sharp Decrease ◽  
Haplotype Sharing ◽  
Indigenous Chickens ◽  
D Loop ◽  
Commercial Chickens

Objective: The extensive breeding of commercial chickens has led to a sharp decrease in the resources of many indigenous chickens, especially the indigenous chickens in the southeastern coastal region, which are on the verge of extinction, and the indigenous chickens in the northwestern region of China, which are also at risk. However, there are few reports on the evaluation of genetic diversity and conservation of genetic resources of indigenous chickens in remote areas in the Northwest of China.Methods: In the present study, the genetic diversity and phylogenetic relationship of six indigenous chickens from different regions were studied based on variation in mitochondrial DNA control region (D-loop), and the degree of introgression from commercial breeds into these chickens was determined by the amount of haplotype sharing between indigenous and commercial breeds.Results: Twenty-five polymorphic sites and 25 haplotypes were detected in 206 individuals. Principal component analysis showed that the Jingning chicken had the highest genetic diversity among the six indigenous chickens. According to the degree of introgression, the six indigenous breeds may be involved in haplotype sharing with commercial breeds, and the introgression from commercial chickens into the Haidong chicken is the most serious.Conclusion: The genetic uniqueness of indigenous chickens has been eroded, so it is necessary to consider the protection of their genetic resources. Phylogenetic analysis suggests that the six indigenous chickens have two major matrilineal origins: one from Yunnan or its surrounding areas in China and the other from the Indian subcontinent.

scholarly journals Intermixing of Commercial Pure Breed Chickens with Indigenous (Sakini) Breed of Nepal

2021 ◽  
Vol 7 ◽  
pp. 92-96
Author(s):  
Neena Amatya Gorkhali ◽  
Chhiring Sherpa ◽  
Mana Raj Kolachhapati ◽  
Bhoj Raj Pokharel ◽  
Nirajan Bhattarai ◽  
...  
Keyword(s):  
Rhode Island ◽  
Genetic Erosion ◽  
Variable Region ◽  
Production Performance ◽  
Indigenous Chicken ◽  
Three Samples ◽  
The Status ◽  
D Loop ◽  
The Government ◽  
Commercial Chickens

The intermixing of pure breeds of commercial chickens with Nepalese indigenous flock of chickens has not been explored yet genetically. The study aims to investigate the status of interbreeding of Nepalese indigenous chickens with exotic breeds. Thirty three samples of indigenous chicken, Sakini, from three different ecological regions, Terai, mid-hill and high hill, were taken for the study. The 522 bp hyper-variable region of D loop mtDNA of each sampled population was PCR amplified and sequenced. The Neighbor joining tree revealed that most of Nepalese Sakini and commercial chickens such as New Hampshire, Rhode Island Red, White Leghorn, White Plymouth Rock and Barred Plymouth Rock lied in same clade. Our study provides first direct evidence that the Sakini was already bred with commercial breeds for the sake of enhancing production performance and also alarms the government to introduce proper strategies and policies to avoid such genetic erosion.

Genomic characterization of three Vietnamese indigenous chicken varieties using mitochondrial D-loop sequences

2019 ◽  
Vol 99 (4) ◽  
pp. 833-839
Author(s):  
Son Quang Do ◽  
Lan Thi Phuong Nguyen ◽  
Thinh Hoang Nguyen ◽  
Trung Quoc Nguyen
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Diversity Indices ◽  
Fixation Index ◽  
Indigenous Chicken ◽  
Loop Region ◽  
Red Junglefowl ◽  
D Loop ◽  
Genomic Characterization

In this study, partial mitochondrial DNA (mtDNA) D-loop sequences of three Vietnamese indigenous chicken varieties, including Mong Tien Phong, To, and Sau Ngon, were analyzed to access genetic diversity and the maternal lineages of origin. A 525 bp fragment of the mtDNA D-loop region was sequenced from a total of 61 chickens of the three varieties. A neighbor-joining phylogenetic tree was assembled from the haplotypes obtained and reference sequences of mtDNA D-loop sequences of Red Junglefowl and domestic chickens from National Center for Biotechnology Information database. Genetic diversity indices and analysis of molecular variance were performed. Evaluation of genetic relationships between the three varieties was carried out with pairwise fixation index (FST). In total, 16 haplotypes were identified in the chickens studied. These haplotypes were classified in three haplogroups (A, B, and E) with the majority grouped in haplogroup B and haplogroup E. All three chicken varieties studied were distributed into 2–3 haplogroups and all three haplogroups found in this study are also represented by Red Junglefowl. In conclusion, all three Vietnamese indigenous chicken varieties have likely originated from multiple maternal lineages and potentially descended from the Red Junglefowl.

scholarly journals Mitochondrial DNA D-Loop Diversity of the Helmeted Guinea Fowls in Kenya and Its Implications on HSP70 Gene Functional Polymorphism

2018 ◽  
Vol 2018 ◽  
pp. 1-12
Author(s):  
Philip Murunga ◽  
Grace Moraa Kennedy ◽  
Titus Imboma ◽  
Phillista Malaki ◽  
Daniel Kariuki ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Wild Population ◽  
Profile Analysis ◽  
Demographic History ◽  
Genetic Profile ◽  
Hsp70 Gene ◽  
Functional Polymorphisms ◽  
Mtdna Haplotypes ◽  
D Loop

We analyzed variations in 90 mitochondrial DNA (mtDNA) D-loop and heat shock protein 70 (HSP70) gene sequences from four populations of domesticated helmeted Guinea fowls (70 individuals) and 1 population of wild helmeted Guinea fowls (20 individuals) in Kenya in order to get information about their origin, genetic diversity, and traits associated with heat stress. 90 sequences were assigned to 25 distinct mtDNA and 4 HSP70 haplotypes. Most mtDNA haplotypes of the domesticated helmeted Guinea fowls were grouped into two main haplogroups, HgA and HgB. The wild population grouped into distinct mtDNA haplogroups. Two mtDNA haplotypes dominated across all populations of domesticated helmeted Guinea fowls: Hap2 and Hap4, while the dominant HSP70 haplotype found in all populations was CGC. Higher haplotype diversities were generally observed. The HSP70 haplotype diversities were low across all populations. The nucleotide diversity values for both mtDNA and HSP70 were generally low. Most mtDNA genetic variations occurred among populations for the three hierarchical categories considered while most variations in the HSP70 gene occurred among individuals within population. The lack of population structure among the domestic populations could suggest intensive genetic intermixing. The differentiation of the wild population may be due to a clearly distinct demographic history that shaped its genetic profile. Analysis of the Kenyan Guinea fowl population structure and history based on mtDNA D-loop variations and HSP70 gene functional polymorphisms complimented by archaeological and linguistic insight supports the hypothesis that most domesticated helmeted Guinea fowls in Kenya are related to the West African domesticated helmeted Guinea fowls. We recommend more molecular studies on this emerging poultry species with potential for poverty alleviation and food security against a backdrop of climate change in Africa.

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