Genetic Diversity and Population Structure Analysis Between Indian Red Jungle Fowl and Domestic Chicken Using Microsatellite Markers

Investigating genetic diversity and population phylogeny of five Chongqing local chicken populations autosomal using microsatellites

The genetic diversity and population structures of five Chongqing local chicken populations were investigated using by 24 microsatellite markers. Results revealed that the mean number of alleles (N_A) ranged from 7.08 (Daninghe chicken, DN) to 8.46 (Nanchuan chicken, NC). The highest observed heterozygosity (H_O) and expected heterozygosity (H_E) were observed in DN (H_O = 0.7252; H_E = 0.7409) and the lowest H_O and H_E were observed in XS (Xiushan native chicken [XS], H_O = 0.5910 and H_E = 0.6697). The inbreeding coefficient (F_IS) within population ranged from 0.022 (DN) to 0.119 (XS). Among the 24 microsatellite markers, four loci (MCW0111, MCW0016, ADL0278, and MCW0104) deviated from the Hardy-Weinberg equilibrium in all the studied populations. The results of population polygenetic analysis based on Nei's genetic distance and STRUCTURE software showed that the clustering of the five populations was incomplete consistent with geographical distribution. Moreover, a large number of gene flows were widespread among different populations, suggesting that genetic material exchanges occurred due to human activities and migration which was also verified by PCoA. In summary, this study preliminarily showed that Chongqing local chicken populations had rich genetic diversity and remarkable genetic divergence, but still high risk in conversion. These findings would be useful to the management of conservation strategies and the utilization of local chicken populations in further.

AFLP markers based genetic diversity and population structure analysis of Kadaknath: an indigenous black meat poultry breed of India

The current study is the first worldwide to assess the genetic diversity of Kadaknath poultry using amplified fragment length polymorphism (AFLP) markers. Out of total 96 accessions, four were outliers and 92 were Kadaknath accessions of which 30 were males, 62 were females. Of these, 74 were jet black, 7 penciled and 11 were golden feather color type of Kadaknath. High level of polymorphism (23.94%) was observed in 387 loci amplified using six AFLP primer combinations. The Jaccard's similarity coefficient ranged from 0.211 to 0.754 with an average dissimilarity of 0.517. Based on the neighbor-joining method of clustering, all accessions were clustered into seven major clusters which were not consistent with their respective geographical locations. The mean values of effective multiplex ratio, polymorphic information content, resolving power and marker index were 15.16, 0.38, 9.87 and 5.85 respectively. Further, the high log-likelihood score was produced when the number of populations (K) was set at 7 while carrying out the population STRUCTURE analysis, which was also congruent with clustering analysis based on genetic diversity. The extent of genetic diversity detected in this study could be used for germplasm selection and developing conservation strategies of pure breed of Kadaknath.

Effect of Quercetin on Oxidative Stress, Mitochondrial Activity, and Quality of Indian Red Jungle Fowl (Gallus gallus murghi) Sperm

Aim: The study was designed to elucidate the effects of quercetin in an extender on oxidative stress, mitochondrial activity and quality of Indian red jungle fowl (Gallus gallus murghi) sperm during cryopreservation. Materials and Methods: Semen was collected from seven adult males through abdominal massage and evaluated for semen volume, concentration, and motility. The qualifying semen ejaculates having >80% motility were diluted in red fowl extenders with 0 (control), 5, 10, 15, and 20 mM quercetin. Diluted semen was frozen following a glycerol-based protocol. Semen quality (motility, plasma membrane integrity, viability, acrosome integrity, and chromatin condensation status) and biochemical parameters (mitochondrial activity, ferric reducing antioxidant power, and malondialdehyde [MDA]) were determined at various stages of cryopreservation. Results: Sperm motility, plasma membrane integrity, viability, acrosome integrity, and chromatin condensation were recorded highest (p < 0.05) with 15 mM quercetin compared with 5, 10, and 20 mM quercetin and control at post-dilution, cooling, equilibration, and freeze-thawing. Nevertheless, mitochondrial activity and antioxidant potential were recorded highest with 15 mM quercetin compared with all experimental extenders at post-equilibration and freeze-thawing. MDA concentration in sperm and seminal plasma were recorded lowest (p < 0.05) in the extender having 15 mM quercetin at post-equilibration and freeze-thawing. Cryopreservation stages showed negative effects (p < 0.05) on semen quality parameters, irrespective of experimental extenders. Conclusions: It is concluded that quercetin (15 mM) supplementation in red fowl extender improves sperm motility, plasma membrane integrity, viability, acrosome integrity, chromatin condensation, and mitochondrial activity by elevating the total antioxidant potential and ameliorating lipid peroxidation during cryopreservation.

Authentication of poultry products at the breed level using genetic markers

The Oravka tawny is a Slovak national breed of chicken. This breed has combined utility, which means it is valuable for both its meat and eggs. The Oravka tawny is linked to a specific region, Orava, and therefore these products could be protected by European geographical indication. The labeling and sale of chicken meat by the traditional breed of origin are widely used to promote quality and attract those products in the marketplace. For that use, we created the system and method of authentication that can reliably distinguish between the Oravka tawny, other chicken breeds, and other of Oravka”™s colorful characters. In our research, we analyzed 153 chicken feathers from the Oravka breed as well as from breeds used in the process of breeding the Oravka to their current state. They were divided into nine populations. To separate those populations, we used seven microsatellite markers recommended by FAO (Food and Agriculture Organization) and other authors. To create separate clusters of individual breeds, we used DAPC (discriminant analysis of principal components) analysis.

Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data

The wealth of information deliverable from transcriptome sequencing (RNA-seq) is significant, however current applications for variant detection still remain a challenge due to the complexity of the transcriptome. Given the ability of RNA-seq to reveal active regions of the genome, detection of RNA-seq SNPs can prove valuable in understanding the phenotypic diversity between populations. Thus, we present a novel computational workflow named VAP (Variant Analysis Pipeline) that takes advantage of multiple RNA-seq splice aware aligners to call SNPs in non-human models using RNA-seq data only. We applied VAP to RNA-seq from a highly inbred chicken line and achieved high accuracy when compared with the matching whole genome sequencing (WGS) data. Over 65% of WGS coding variants were identified from RNA-seq. Further, our results discovered SNPs resulting from post transcriptional modifications, such as RNA editing, which may reveal potentially functional variation that would have otherwise been missed in genomic data. Even with the limitation in detecting variants in expressed regions only, our method proves to be a reliable alternative for SNP identification using RNA-seq data. The source code and user manuals are available at https://modupeore.github.io/VAP/.

Variabilidade genética de 12 loci de microssatélites em galinhas crioulas Canela-Preta

RESUMO Esta pesquisa foi realizada com o objetivo de se conhecer a variabilidade genética de 12 loci de microssatélites em galinhas crioulas Canela-Preta. Foram coletadas amostras de sangue de 118 galinhas crioulas Canela-Preta, provenientes de três municípios do estado do Piauí (Oeiras, Queimada Nova e Teresina). Após extração do DNA, foram utilizados marcadores para 12 loci de microssatélites: LEI0192, LEI0209, LEI0212, LEI0217, LEI0221, LEI0234, LEI0237, LEI0248, LEI0258, MCW0081, MCW0183 e MCW0213, que foram amplificados pela técnica de reação em cadeia da polimerase (PCR). Foram obtidos 408 alelos (somando os alelos dos 12 loci), com os fragmentos variando entre 50 e 460 pares de bases. O número de alelos variou de 15 (MCW0081) a 52 (LEI0212), com média de 31,5 alelos por locus. A média de heterozigosidade esperada e o conteúdo de informações polimórficas foram, respectivamente, 0,887 e 0,909. Foram observados desvios no equilíbrio de Hardy-Weinberg e valores positivos do índice de fixação com excesso de homozigotos. Os microssatélites utilizados mostraram-se polimórficos e podem ser usados para investigações genéticas em galinhas Canela-Preta. As galinhas dos plantéis avaliados apresentam grande variabilidade gênica, o que as qualifica como importante fonte de recursos genéticos e, consequentemente, faculta a utilização delas em programas de melhoramento genético animal.

Effect of season and age on Indian red jungle fowl (Gallus gallus murghi) semen characteristics: A 4-year retrospective study

The reproductive potential of the adult males is expected to vary with age/season and largely differ not only in closely related avian species but even in subspecies, breeds and/or strains of the same species. Thus, it is pre-requisite to have knowledge of seminal parameters to achieve maximum production potential of at-risk species for ex situ in vitro conservation programs. A 4-year study was designed to evaluate the effect of age and season (spring, summer, autumn and winter) on semen characteristics of Indian red jungle fowl (Gallus gallus murghi) in a retrospective manner. Semen ejaculates (n = 1148) were regularly collected from eight adult cocks 6 to 54 months of age. Quantitative and qualitative semen parameters viz; volume (μL), concentration (1 × 10⁹ mL^-1), total sperm number per ejaculate (1 × 10⁹ mL^-1), motility (%), viability (%), plasma membrane integrity (%), acrosome integrity (%) and semen quality factor were recorded. A chronological increasing trend with age of most sperm quantitative and qualitative traits (semen volume, sperm concentration, total sperm number per ejaculate, plasma membrane integrity, viability, acrosomal integrity and semen quality factor) was observed. The highest values were observed at four years of age (P < 0.05) with the exception of sperm motility that was not affected by the age. Spring was the best season for sperm parameters viz; volume, motility, plasma membrane integrity, viability and acrosomal integrity (P < 0.05), however a remarkable sperm production was noticed all over the year. It is concluded that Indian red jungle fowl exhibits an evolution of sperm production that greatly differs in many points from other fowl sub-species. It is suggested that semen ejaculates of highest quality achieved for semen banking at the age of four year in the spring season.