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

Genetic diversity among two native Indian chicken populations using cytochrome c oxidase subunit I and cytochrome b DNA barcodes

BACKGROUND AND AIM

India has large varieties (recognized, unrecognized) of native chickens (Desi) scattered throughout the country, managed under scavenging system different from commercial chicken breeds. However, they are less investigated for genetic diversity they harbor. The present study was planned to evaluate genetic diversity among two native chicken populations of North Gujarat (proposed Aravali breed) and South Gujarat (Ankleshwar breed). Aravali chicken, a distinct population with unique characters different from the registered chicken breeds of India is under process to be registered as a new chicken breed of Gujarat, India.

MATERIALS AND METHODS

Two mitochondrial markers, namely, cytochrome oxidase c subunit I (COX I) and cytochrome b (Cyt b) genes were studied across 10 birds from each population. Methodology included sample collection (blood), DNA isolation (manual), polymerase chain reaction amplification of mitochondrial genes, Sanger sequencing, and purification followed by data analysis using various softwares.

RESULTS

Haplotype analysis of the COX I gene unveiled a total eight and three haplotypes from the Aravali and Ankleshwar populations, respectively, with haplotype diversity (Hd) of 92.70 % for the Aravali and 34.50% for the Ankleshwar breed. Haplotype analysis of the Cyt b gene revealed a total of four haplotypes from the Aravali population with 60% Hd and no polymorphism in Ankleshwar breed. The phylogenetic analysis uncovered Red Jungle Fowl and Gray Jungle Fowl as prime roots for both populations and all domestic chicken breeds.

CONCLUSION

Study findings indicated high genetic variability in Aravali chicken populations with COX I mitochondrial marker being more informative for evaluating genetic diversity in chickens.

Characterisation of the complete mitochondrial genome, genetic diversity and maternal origin of Huainan Partridge chicken

1. The objectives of the present study were to investigate the complete mitochondrial genome, genetic diversity and maternal origin of Huainan Partridge chicken (HPC).2. One complete mitochondrial genome and 37 complete D-loop regions of HPC were sequenced. Moreover, 400 mitochondrial genome D-loop sequences of Chinese native chicken were downloaded from the National Centre for Biotechnology Information database.3. The complete HPC genome was 16,785 bp in size, including 22 tRNA genes, two rRNA genes, 13 protein-coding genes and one non-coding control region. The haplotype diversity and nucleotide diversity of HPC were 0.964, and 0.00615, respectively. Twenty-three variable sites defining 22 haplotypes were identified, and the 22 haplotypes were distributed into three haplogroups (A, B, and C).4. In conclusion, HPC has a typical vertebrate mitochondrial genome, relatively high haplotype diversity, relatively low nucleotide diversity, and potentially three maternal lineages. HPC showed considerable genetic information exchange with Southwest Chinese chicken populations and had not admixed with European commercial breeds in the course of domestication.

Population structure, genetic diversity and phylogenetic analysis of different rural and commercial chickens of Pakistan using complete sequence of mtDNA D-loop

Chicken is the most important poultry bird in Pakistan that not only provides nutrition but also contributes to country's economy. The Pakistani chicken and its germplasm resources are not genetically characterized and explored. Here, we focused at rural and commercial chickens of Pakistan and explored genetic diversity, population structure and phylogeny. We first collected feather samples from Rural and Broiler populations of Pakistani chickens, isolated DNA and sequenced complete D-loop of mtDNA. The length of complete D-loop ranged from 1231 to 1234 bp in Pakistani chickens. The GC content was 39%. Hotspots of mutations were three hypervariable sites (HVS). Most of the variations (77%) were in HVS1. In a total, 26 polymorphic sites defined 12 haplotypes and all major haplogroups (A-I) in genetic structure of Pakistani chickens. Genetic diversity remained relatively very low in Broiler (Pi = 0.00212 ± 0.00136). There was a low sharing of matrilineages between the two populations (Fst = 0.170). With high Hd value (0.825 ± 0.051) and presence of all nine major haplogroups the rural chicken population showed relatively rich genepool. Finally we did molecular phylogenetic analysis and inferred phylogeny. Presence of subcontinent specific haplogroups E3 and I and clustering of Indian red junglefowl closely with Pakistani chickens in Bayesian inference tree, provide further evidence for an independent domestication event of chicken in subcontinent.

Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs

BACKGROUND

Maintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. Three chicken breeds (Baier Yellow Chicken (BEC), Beijing You Chicken (BYC) and Langshan Chicken (LSC)) are currently in conservation programs in China. Changes in genetic diversity were measured by heterozygosity, genomic inbreeding coefficients, and autozygosity, using estimates derived from runs of homozygosity (ROH) that were identified using SNPs.

RESULTS

Ninety DNA samples were collected from three generations for each breed. In the most recent generation, the highest genetic diversity was observed in LSC, followed by BEC and BYC. Inbreeding coefficients based on ROH for the three breeds declined slightly between the first and middle generations, and then rapidly increased. No inbreeding coefficients exceeded 0.1. Population structure assessments using neighbor-joining tree analysis, principal components analysis, and STRUCTURE analysis indicated that no genetic differentiation existed within breeds. LD decay and ROH at different cut-off lengths were used to identify traces left by recent or ancient inbreeding. Few long ROH were identified, indicating that inbreeding has been largely avoided with the current conservation strategy. The observed losses in genetic diversity and occurrences of inbreeding might be consequences of sub-optimal effective population sizes.

CONCLUSIONS

The conserved Chinese chicken populations have high genomic diversity under the current conservation program (R: F). Furthermore, this study highlights the need to monitor dynamic changes in genetic diversity in conserved breeds over successive generations. Our research provides new insights into genetic diversity dynamics in conserved populations, and lays a solid foundation for improving conservation schemes.