Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds

Comparative peculiarities of genomic diversity in Gallus gallus domesticus chickens with decorative plumage: the muffs and beard phenotype

Throughout history, humans have been attempting to develop the ornamental features of domestic animals in addition to their productive qualities. Many chicken breeds have developed tufts of elongated feathers that jut out from the sides and bottom of the beak, leading to the phenotype known as muffs and beard. It is an incomplete autosomal dominant phenotype determined by the Mb locus localised on chromosome GGA27. This project aimed to analyse the genetic diversity of chicken breeds using full genomic genotyping with the Chicken 60K BeadChip. A total of 53,313 Single Nucleotide Polymorphisms were analysed. DNA was obtained from breeds with the muffs and beard as a marker phenotype: Faverolles (n = 20), Ukrainian Muffed (n = 18), Orloff (n = 20), Novopavlov White (n = 20), and Novopavlov Coloured (n = 15). The Russian White (n = 20) was selected as an alternative breed without the muffs and beard phenotype. The chickens are owned by the Centre of Collective Use "Genetic Collection of Rare and Endangered Breeds of Chickens" (St. Petersburg region, Pushkin), and are also included in the Core Shared Research Facility (CSRF) and/or Large-Scale Research Facility (LSRF). Multidimensional scaling revealed that the Novopavlov White and the Novopavlov Coloured populations formed a separate group. The Ukrainian Muffed and the Orloff have also been combined into a separate group. Based on cluster analysis, with the cross-validation error and the most probable number of clusters K = 4 taken into account, the Orloff was singled out as a separate group. The Ukrainian Muffed exhibited a notable similarity with the Orloff under the same conditions. At K = 5, the populations of the Novopavlov White and the Novopavlov Coloured diverged. Only at K = 6, a distinct and separate cluster was formed by the Ukrainian Muffed. The Russian White had the greatest number of short (1-2 Mb) homozygous regions. If the HOXB8 gene is located between 3.402 and 3.404 Mb on chromosome GGA27, homozygous regions are rarely found in the chickens with the muffs and beard phenotype. Scanning the chicken genome with the Chicken 60K BeadChip provided enough information about the genetic diversity of the chicken breeds for the peculiarities of the development of the ornamental muffs and beard phenotypes in them to be understood. For example, Phoenix bantams, whose tail feathers grow throughout their lives, require greater consideration of husbandry conditions.

Association between plasma L-carnitine levels and mitochondrial DNA copy number

Mitochondria are key cytoplasmic organelles in eukaryotic cells that generate adenosine triphosphate (ATP) through the electron transport chain and oxidative phosphorylation. Mitochondrial DNA (mtDNA) copy number (mtDNAcn) is considered a biomarker for both mitochondrial quantity and function as well as cellular oxidative stress level. Previous epidemiologic findings revealed that weight gain, higher body mass index (BMI), smoking, and high insulinemic potential of lifestyle were associated with lower leukocyte mtDNAcn. Carnitines are a group of compounds that play a critical role in energy production. We quantified the associations of plasma L-carnitine levels with leukocyte mtDNAcn. We then examined the association between mtDNAcn and L-carnitine (HMDB0000062) in 538 U.S. men without cancers, diabetes, or cardiovascular disease at blood collection from the Health Professionals Follow-Up Study (HPFS). We found a significant inverse association between L-carnitine and mtDNAcn (ρ = -0.1, P = 0.02). This implies that the carnitine metabolic pathway may be associated with mitochondrial function and oxidative stress.

Genome-Wide Re-Sequencing Data Reveals the Population Structure and Selection Signatures of Tunchang Pigs in China

Tunchang pig is one population of Hainan pig in the Hainan Province of China, with the characteristics of delicious meat, strong adaptability, and high resistance to diseases. To explore the genetic diversity and population structure of Tunchang pigs and uncover their germplasm characteristics, 10 unrelated Tunchang pigs were re-sequenced using the Illumina NovaSeq 150 bp paired-end platform with an average depth of 10×. Sequencing data from 36 individuals of 7 other pig breeds (including 4 local Chinese pig breeds (5 Jinhua, 5 Meishan, 5 Rongchang, and 6 Wuzhishan), and 3 commonly used commercial pig breeds (5 Duorc, 5 Landrace, and 5 Large White)) were downloaded from the NCBI public database. After analysis of genetic diversity and population structure, it has been found that compared to commercial pigs, Tunchang pigs have higher genetic diversity and are genetically close to native Chinese breeds. Three methods, FST, θπ, and XP-EHH, were used to detect selection signals for three breeds of pigs: Tunchang, Duroc, and Landrace. A total of 2117 significantly selected regions and 201 candidate genes were screened. Gene enrichment analysis showed that candidate genes were mainly associated with good adaptability, disease resistance, and lipid metabolism traits. Finally, further screening was conducted to identify potential candidate genes related to phenotypic traits, including meat quality (SELENOV, CBR4, TNNT1, TNNT3, VPS13A, PLD3, SRFBP1, and SSPN), immune regulation (CD48, FBL, PTPRH, GNA14, LOX, SLAMF6, CALCOCO1, IRGC, and ZNF667), growth and development (SYT5, PRX, PPP1R12C, and SMG9), reproduction (LGALS13 and EPG5), vision (SLC9A8 and KCNV2), energy metabolism (ATP5G2), cell migration (EPS8L1), and olfaction (GRK3). In summary, our research results provide a genomic overview of the genetic variation, genetic diversity, and population structure of the Tunchang pig population, which will be valuable for breeding and conservation of Tunchang pigs in the future.

Genome-wide re-sequencing data reveals the genetic diversity and population structure of Wenchang chicken in China

Wenchang (WC) chicken, the only indigenous chicken breed listed in Chinese genetic resources in Hainan province, is well known for its excellent meat quality and is sold all over southeast Asia. In recent years, the number of WC has decreased sharply with considerable variability in the quality at market. To explore the genetic diversity and population structure of WC chickens, the whole-genome data of 235 WC individuals from three conservation farms were obtained using the Illumina 150 bp paired-end platform and used in conjunction with the sequencing data from 123 individuals from other chicken breeds (including eight Chinese indigenous chicken breeds and three foreign or commercial breeds) downloaded from a public database. A total of 12 111 532 SNPs were identified, of which 11 541 878 SNPs were identified in WC. The results of gene enrichment analyses revealed that the SNPs harbored in WC genomes are mainly related to environmental adaptation, disease resistance and meat quality traits. Genetic diversity statistics, quantified by expected heterozygosity, observed heterozygosity, linkage disequilibrium, nucleotide diversity and fixation statistics, indicated that WC displays high genetic diversity compared with other Chinese indigenous chicken breeds. Genetic structure analyses showed that each population displayed great differentiation between WC and the other breeds, indicating the uniqueness of WC. In conclusion, the results of our study provide the first genomic overview of genetic variants, genetic diversity and population structure of WC from three conservation farms. This information will be valuable for the future breeding and conservation of WC and other surveyed populations.

Population Genetic Structure and Contribution of Philippine Chickens to the Pacific Chicken Diversity Inferred From Mitochondrial DNA

The Philippines is considered one of the biodiversity hotspots for animal genetic resources. In spite of this, population genetic structure, genetic diversity, and past population history of Philippine chickens are not well studied. In this study, phylogeny reconstruction and estimation of population genetic structure were based on 107 newly generated mitochondrial DNA (mtDNA) complete D-loop sequences and 37 previously published sequences of Philippine chickens, consisting of 34 haplotypes. Philippine chickens showed high haplotypic diversity (Hd = 0.915 ± 0.011) across Southeast Asia and Oceania. The phylogenetic analysis and median-joining (MJ) network revealed predominant maternal lineage haplogroup D classified throughout the population, while support for Philippine-Pacific subclade was evident, suggesting a Philippine origin of Pacific chickens. Here, we observed Philippine red junglefowls (RJFs) at the basal position of the tree within haplogroup D indicating an earlier introduction into the Philippines potentially via mainland Southeast Asia (MSEA). Another observation was the significantly low genetic differentiation and high rate of gene flow of Philippine chickens into Pacific chicken population. The negative Tajima's D and Fu's Fs neutrality tests revealed that Philippine chickens exhibited an expansion signal. The analyses of mismatch distribution and neutrality tests were consistent with the presence of weak phylogeographic structuring and evident population growth of Philippine chickens (haplogroup D) in the islands of Southeast Asia (ISEA). Furthermore, the Bayesian skyline plot (BSP) analysis showed an increase in the effective population size of Philippine chickens, relating with human settlement, and expansion events. The high level of genetic variability of Philippine chickens demonstrates conservation significance, thus, must be explored in the future.

Mitochondrial DNA diversity and demographic history of Black-boned chickens in China

Black-boned chickens (Gallus domesticus, herein abbreviated BBCs) are well known for their unique appearance and medicinal properties and have a long breeding history in China. However, the genetic diversity and demographic history of BBCs remain unclear. In this study, we analyzed 844 mitochondrial DNA D-loop sequences, including 346 de novo sequences and 498 previously published sequences from 20 BBC breeds. We detected a generally high level of genetic diversity among the BBCs, with average haplotype and nucleotide diversities of 0.917 ± 0.0049 and 0.01422, respectively. Nucleotide diversity was highest in populations from Southwest China (0.01549 ± 0.00026), particularly in Yunnan Province (0.01624 ± 0.00025). Significant genetic divergence was detected between most breeds, particularly between Yunnan chickens and those from all other provinces. Haplogroups F and G had the highest levels of genetic diversity and were restricted to Southwest China, particularly Yunnan Province. Based on neutrality tests and mismatch distribution analyses, we did not obtain evidence for rapid population expansions and observed similar demographic histories in BBCs and local non-BBCs. Our results suggest that Chinese BBCs have complex breeding histories and may be selected in situ from local domestic chickens. These results improve our understanding of the genetic heritage and breeding histories of these desirable chickens.

Identification of Target Chicken Populations by Machine Learning Models Using the Minimum Number of SNPs

A marker combination capable of classifying a specific chicken population could improve commercial value by increasing consumer confidence with respect to the origin of the population. This would facilitate the protection of native genetic resources in the market of each country. In this study, a total of 283 samples from 20 lines, which consisted of Korean native chickens, commercial native chickens, and commercial broilers with a layer population, were analyzed to determine the optimal marker combination comprising the minimum number of markers, using a 600 k high-density single nucleotide polymorphism (SNP) array. Machine learning algorithms, a genome-wide association study (GWAS), linkage disequilibrium (LD) analysis, and principal component analysis (PCA) were used to distinguish a target (case) group for comparison with control chicken groups. In the processing of marker selection, a total of 47,303 SNPs were used for classifying chicken populations; 96 LD-pruned SNPs (50 SNPs per LD block) served as the best marker combination for target chicken classification. Moreover, 36, 44, and 8 SNPs were selected as the minimum numbers of markers by the AdaBoost (AB), Random Forest (RF), and Decision Tree (DT) machine learning classification models, which had accuracy rates of 99.6%, 98.0%, and 97.9%, respectively. The selected marker combinations increased the genetic distance and fixation index (Fst) values between the case and control groups, and they reduced the number of genetic components required, confirming that efficient classification of the groups was possible by using a small number of marker sets. In a verification study including additional chicken breeds and samples (12 lines and 182 samples), the accuracy did not significantly change, and the target chicken group could be clearly distinguished from the other populations. The GWAS, PCA, and machine learning algorithms used in this study can be applied efficiently, to determine the optimal marker combination with the minimum number of markers that can distinguish the target population among a large number of SNP markers.

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.

Genetic diversity of Bangladeshi native chickens based on complete sequence of mitochondrial DNA D-loop region

1. The aim of this study was to explore genetic diversity and possible origin of Bangladeshi (BD) native chickens. The complete mtDNA D-loop region was sequenced in 60 chickens representing five populations; naked neck, full feathered, Aseel, Hilly and autosomal dwarf. The 61 reference sequences representing different domestic chicken clades in China, India, Laos, Indonesia, Myanmar, and other Eurasian regions were included. The mtDNA D-loop sequence polymorphism and maternal origin of five BD populations were analysed.2. A total of 35 polymorphic sites, and 21 haplotypes were detected in 60 mtDNA D-loop sequences. The haplotype and nucleotide diversity of the five populations were 0.921 ± 0.018 and 0.0061 ± 0.0019, respectively. Both mtDNA network and phylogenetic analysis indicated four clades (four haplogroups) in BD populations (21 haplotypes) along with 61 reference haplotypes. Clade E contained the most individuals (20) and haplotypes (11) of BD chickens, followed by clade D (17, 6), clade C (12, 2) and clade F (11, 2), respectively.3. The higher number of unique haplotypes found in Yunnan, China, suggested that the origin of BD chickens was in this region. The haplotypes from different haplogroups were introduced in Bangladeshi chickens from India, China and Myanmar. The phylogenetic tree showed a close relationship of BD chickens with the clusters from India, China, Myanmar and Laos, and indicated the dispersion of BD chickens from these sources. The phylogenetic information revealed high genetic diversity of BD chickens because of their origin from different lineages with high genetic variation and distance, which was determined from four cluster and neighbour-joining trees.4. In conclusion, BD populations had high genetic diversity. The mtDNA network profiles and phylogenetic trees showed multiple maternal origins of BD chickens from India, China, Myanmar and Laos.

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.