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

Ajibike, A. B.; Adeleye, O.O.; Ilori, Babatunde Moses; Osinbowale, Damilola A.; Adeniyi, O.A.; Durosaro, Samuel O.; Sanda, A. J.; Adebambo, O. A.; Adebambo, A.O.

doi:10.1007/s12041-017-0860-1

Cited by 4 publications

(9 citation statements)

References 28 publications

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“…Nucleotide diversity (π) across all individuals was estimated at 0.00062, and the haplotype diversity ( Hd ) was determined at 0.288. These values are markedly low, in accordance with those reported for other indigenous Nigerian populations, especially from the southwestern part of the country, where the lowest haplotype diversity was detected (Hd = 0.25) ( Ajibike et al., 2017 ). The entire Nigerian population reached a mean haplotype diversity value of 0.673.…”

Section: Resultssupporting

confidence: 88%

“…The other southwestern samples shared 4 haplotypes with north-central Nigeria, 2 haplotypes with the northeastern region, and 2 other haplotypes (including both Fulani and Yoruba) with the northwestern area. Conversely, the commercial egg line strains (Anak titan, Giriraja, and Yaffa by Ajibike et al., 2017 ) occurred separately.…”

Section: Resultsmentioning

confidence: 97%

“…Recently, Herrera et al. (2017) described a phylogenetic link between haplogroups of chickens from East Africa and South Asia, and Ajibike et al. (2017) described the lack of phylogeographic structuring in Nigerian village chickens without mentioning specific ecotypes.…”

Section: Resultsmentioning

confidence: 99%

“…The evolutionary relationships among the haplotypes were visualized through the construction of a median-joining network using Network 4.6 (Fluxus Technology Ltd., Colchester, England), in which redundant parallel mutations at nucleotide positions 217, 243, 261, 269, and 310 were downweighted to reduce excess reticulations. The network included both Yoruba and Fulani ecotypes and all available sequences from Nigerian chickens retrieved from GenBank, including the commercial line, which was used as an outgroup ( Ajibike et al., 2017 ).…”

Section: Methodsmentioning

confidence: 99%

“…The available genetic studies concern only the characterization of adaptive genes ( Ojo, 2002 , Fayeye et al., 2006 , Fayeye and Oketoyin, 2006 ) and not the identification of genetic diversity among populations. In a recent study, Ajibike et al. (2017) assessed the first phylogenetic evaluation based on mitochondrial DNA ( mtDNA ) variation in indigenous chickens from different areas of Nigeria, but that study lacked information on specific breeds and types.…”

Section: Introductionmentioning

confidence: 99%

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Mitochondrial diversity of Yoruba and Fulani chickens: A biodiversity reservoir in Nigeria

et al. 2020

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Poultry are the most widely distributed type of livestock in Nigeria. Indigenous chickens are extremely common throughout the country. Indeed, approximately 83 million chickens are raised in extensive systems and 60 million in semi-intensive systems. To provide the first comprehensive overview of the maternal lineages in Southwest Nigeria, we analyzed 96 mitochondrial DNA control region sequences from 2 indigenous chicken ecotypes: Fulani and Yoruba. All samples belonged to the most frequent haplogroup (E) in Africa and Europe and showed noticeably low haplotype diversity. Although only 11 different haplotypes were detected, with 2 of them never found before in Nigeria, the presence of unique sequences among our indigenous samples testified to their status as an important genetic resource to be preserved. Furthermore, a total of 7,868 published sequences were included in the comparative analysis, which revealed an east-west geographic pattern of haplogroup distribution and led to the conclusion that the gene flow from Southeastern Asia mainly involved one mitochondrial clade. Moreover, owing to the extensive genetic intermixing among Nigerian chickens, conservation efforts are required to safeguard the extant mitochondrial variability in these indigenous ecotypes and establish future improvement and selection programs.

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Section: Resultssupporting

confidence: 88%

Section: Resultsmentioning

confidence: 97%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mitochondrial diversity of Yoruba and Fulani chickens: A biodiversity reservoir in Nigeria

et al. 2020

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Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress

Rachman,

Bamidele,

Dessie

et al. 2024

Sci Rep

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Indigenous poultry breeds from Africa can survive in harsh tropical environments (such as long arid seasons, excessive rain and humidity, and extreme heat) and are resilient to disease challenges, but they are not productive compared to their commercial counterparts. Their adaptive characteristics are in response to natural selection or to artificial selection for production traits that have left selection signatures in the genome. Identifying these signatures of positive selection can provide insight into the genetic bases of tropical adaptations observed in indigenous poultry and thereby help to develop robust and high-performing breeds for extreme tropical climates. Here, we present the first large-scale whole-genome sequencing analysis of Nigerian indigenous chickens from different agro-climatic conditions, investigating their genetic diversity and adaptation to tropical hot climates (extreme arid and extreme humid conditions). The study shows a large extant genetic diversity but low level of population differentiation. Using different selection signature analyses, several candidate genes for adaptation were detected, especially in relation to thermotolerance and immune response (e.g., cytochrome P450 2B4-like, TSHR, HSF1, CDC37, SFTPB, HIF3A, SLC44A2, and ILF3 genes). These results have important implications for conserving valuable genetic resources and breeding improvement of chickens for thermotolerance.

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

Cited by 4 publications

References 28 publications

Mitochondrial diversity of Yoruba and Fulani chickens: A biodiversity reservoir in Nigeria

Mitochondrial diversity of Yoruba and Fulani chickens: A biodiversity reservoir in Nigeria

Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress

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

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