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

Indian Red Jungle fowl reveals a genetic relationship with South East Asian Red Jungle fowl and Indian native chicken breeds as evidenced through whole mitochondrial genome sequences

Background: Native chickens are dispersed in a wide geographical range and have hereditary assets that are kept by farmers for various purposes. Mitochondrial DNA (mtDNA) is a widely utilized marker in molecular studies because of its quick advancement, matrilineal legacy, and simple molecular structure. Method and Results: We performed NGS sequencing to investigate mitochondrial genomes and to evaluate the hereditary connections, diversity, and measure of gene stream estimation in Indian native chicken breeds and Red Jungle fowl. The chicken breeds were genotyped using the D-loop region and 23 haplotypes were identified. When compared to Indian native breeds, more haplotypes were identified in the NADH dehydrogenase subunits, Cytochrome c oxidase, Cytochrome b, ATP synthase subunit 6, and Ribosomal RNA genes. The phylogenetic examination indicated that the analyzed chicken breeds were divided into six significant clades, namely A, B, C, D, E, and F, of which the F clade indicated the domestication of chicken breeds in India. Additionally, our work affirmed that the Indian Red Jungle Fowl is the origin for both reference Red Jungle Fowl as well as all Indian breeds, which is reflected in the dendrogram as well as network analysis based on the whole mtDNA and D-loop region. Indian Red Jungle Fowl is distributed as an outgroup, suggesting that this ancestry was reciprocally monophyletic. Conclusion: The mtDNA sequences of Indian native chickens provided novel insights into adaptation mechanisms and the significance of important mtDNA variations in understanding the maternal lineages of native birds.

Leveraging Available Resources and Stakeholder Involvement for Improved Productivity of African Livestock in the Era of Genomic Breeding

The African continent is home to diverse populations of livestock breeds adapted to harsh environmental conditions with more than 70% under traditional systems of management. Animal productivity is less than optimal in most cases and is faced with numerous challenges including limited access to adequate nutrition and disease management, poor institutional capacities and lack of adequate government policies and funding to develop the livestock sector. Africa is home to about 1.3 billion people and with increasing demand for animal proteins by an ever growing human population, the current state of livestock productivity creates a significant yield gap for animal products. Although a greater section of the population, especially those living in rural areas depend largely on livestock for their livelihoods; the potential of the sector remains underutilized and therefore unable to contribute significantly to economic development and social wellbeing of the people. With current advances in livestock management practices, breeding technologies and health management, and with inclusion of all stakeholders, African livestock populations can be sustainably developed to close the animal protein gap that exists in the continent. In particular, advances in gene technologies, and application of genomic breeding in many Western countries has resulted in tremendous gains in traits like milk production with the potential that, implementation of genomic selection and other improved practices (nutrition, healthcare, etc.) can lead to rapid improvement in traits of economic importance in African livestock populations. The African livestock populations in the context of this review are limited to cattle, goat, pig, poultry, and sheep, which are mainly exploited for meat, milk, and eggs. This review examines the current state of livestock productivity in Africa, the main challenges faced by the sector, the role of various stakeholders and discusses in-depth strategies that can enable the application of genomic technologies for rapid improvement of livestock traits of economic importance.

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

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.

Genetic evidence from mitochondrial DNA corroborates the origin of Tibetan chickens

Chicken is the most common poultry species and is important to human societies. Tibetan chicken (Gallus gallus domesticus) is a breed endemic to China that is distributed mainly on the Qinghai-Tibet Plateau. However, its origin has not been well characterized. In the present study, we sequenced partial mitochondrial DNA (mtDNA) control region of 239 and 283 samples from Tibetan and Sichuan indigenous chickens, respectively. Incorporating 1091 published sequences, we constructed the matrilineal genealogy of Tibetan chickens to further document their domestication history. We found that the genetic structure of the mtDNA haplotypes of Tibetan chickens are dominated by seven major haplogroups (A-G). In addition, phylogenetic and network analyses showed that Tibetan chickens are not distinguishable from the indigenous chickens in surrounding areas. Furthermore, some clades of Tibetan chickens may have originated from game fowls. In summary, our results collectively indicated that Tibetan chickens may have diverged from indigenous chickens in the adjacent regions and hybridized with various chickens.

Deeper insight into maternal genetic assessments and demographic history for Egyptian indigenous chicken populations using mtDNA analysis

This study principally sought to reveal the demographic expansion of Egyptian indigenous chickens (EIC) using representative breeds: Sinai (North), Fayoumi (Middle) and Dandarawi (South) of Egypt as well as to deeply clarify their genetic diversity, possible matrilineal origin and dispersal routes. A total of 33 partial mitochondrial DNA sequences were generated from EIC and compared with a worldwide reference dataset of 1290 wild and domestic chicken sequences. Study populations had 12 polymorphic variable sites and 7 haplotypes. A lack of maternal substructure between EIC was detected (F ST  = 0.003). The unimodal mismatch distribution and negative values of Tajima's D (-0.659) and Fu's Fs (-0.157) indicated demographic expansion among EIC and pointed to Fayoumi as the oldest EIC population. Egyptian haplotypes were clustered phylogenetically into two divergent clades. Their phylogeography revealed an ancient single maternal lineage of Egyptian chickens likely derived from Indian-Subcontinent. Moreover, a recent maternal commercial heritage possibly originated in Yunnan-Province and/or surrounding areas was admixed restrictedly into Sinai. It is implied that Egypt was an entry point for Indian chicken into Africa and its further dispersal route to Europe. This study provides a clue supporting the previous assumption that urged utilizing consistent founder populations having closely related progenitors for synthetizing a stabilized homogenous crossbreed as a sustainable discipline in breeding program.

Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective population sizes particularly in the conservation flocks. The utility and limitations of the iselect chicken SNP60K in village chicken populations is discussed.