Harnessing the untapped potential of indigenous cow milk in producing set-type yoghurts: case of Thamankaduwa White and Lankan cattle.

This research paper assessed textural, microstructural, sensory and colour properties of set-yoghurts produced using milk from two indigenous cattle types, Thamankaduwa White (TW) and Lankan cattle (LC) compared to two generic cattle breeds, Friesian and Jersey. Instrumental texture profile (firmness, adhesiveness, cohesiveness and springiness), colour space (L* a* b*) and scanning electron micrographs of set-yoghurts during 21 d of storage (4 ± 1°C) were evaluated. Sensory quality attributes were evaluated with 40 untrained panellists using a five-point hedonic scale. Set-yoghurts prepared using indigenous cow milk showed higher (P < 0.05) firmness, cohesiveness and apparent viscosity values compared to those prepared using generic cow milk. As revealed by micrographs, set-yoghurts made from TW milk had lesser and smaller void spaces and a dense protein gel network than gels made from LC and the two generic breeds. The gel network made from Friesian milk showed a comparatively larger porous gel structure and thinner protein strands resulting in a weaker gel than other milk gels. The highest lightness (L*) and yellowness (b*) were observed from set-yoghurt produced from Friesian and LC milk, respectively. Set-yoghurts from TW milk had the highest (P < 0.05) sensory scores for all sensory attributes. The lowest sensory acceptance was recorded in set-yoghurt made from Friesian milk. Thus, milk from TW and LC is likely to be suitable in producing set-yoghurts with superior textural, microstructural and sensory properties, compared to milk from Jersey and Friesian. Our results suggest the merits of using indigenous cow milk in producing set-yoghurts and, thereby, prioritizing the preservation of the genetic pool of these indigenous breeds.

High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers.

Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (F IS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative F IS were observed. The positive F IS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.

The wild species genome ancestry of domestic chickens.

BACKGROUND: Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes. RESULTS: In this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wild Gallus species. We first assess the genome-wide phylogeny and divergence time across the genus Gallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii. Both species form a clade that is sister to the Red junglefowl G. gallus, with the Green junglefowl G. varius the most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system. CONCLUSIONS: Our study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range.

Whole-Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species.

The red junglefowl Gallus gallus is the main progenitor of domestic chicken, the commonest livestock species, outnumbering humans by an approximate ratio of six to one. The genetic control for production traits have been well studied in commercial chicken, but the selection pressures underlying unique adaptation and production to local environments remain largely unknown in indigenous village chicken. Likewise, the genome regions under positive selection in the wild red junglefowl remain untapped. Here, using the pool heterozygosity approach, we analyzed indigenous village chicken populations from Ethiopia, Saudi Arabia, and Sri Lanka, alongside six red junglefowl, for signatures of positive selection across the autosomes. Two red junglefowl candidate selected regions were shared with all domestic chicken populations. Four candidates sweep regions, unique to and shared among all indigenous domestic chicken, were detected. Only one region includes annotated genes (TSHR and GTF2A1). Candidate regions that were unique to each domestic chicken population with functions relating to adaptation to temperature gradient, production, reproduction and immunity were identified. Our results provide new insights on the consequence of the selection pressures that followed domestication on the genome landscape of the domestic village chicken.

Responses of Sri Lankan indigenous goats and their Jamnapari crosses to artificial challenge with Haemonchus contortus.

Goat farming plays an important role in the Sri Lankan rural economy. Sri Lankan indigenous (SLI) goats and their crossbreds are reared mainly under extensive management and indiscriminately exposed to pathogens and parasites. This study was designed to evaluate resistance to haemonchosis in SLI goats and their Jamnapari crossbreds (JCB) in the dry zone of Sri Lanka. Twenty SLI and 20 JCB 4-month-old male goats were artificially challenged with 5000 H. contortus L3 larvae. Faecal egg counts (FEC), body weights, FAffa MAlan CHArt (FAMACHA®) scores, packed cell volumes (PCV), red blood cell counts, total and differential white blood cell counts, blood haemoglobin contents, serum total protein and albumin contents, and serum pepsinogen and antibody levels were determined at 0, 21, 28, 35 and 42days after challenge. Effects of measurement time were significant for all variables (P<0.05). Breed effects approached significance (P=0.06) and measurement time×breed interaction was significant (P<0.05) for FEC. Peak FEC occurred at day 35 in both goat types, and JCB goats had higher FEC than SLI goats at days 28 (P<0.001), 35 (P<0.10), and 42 (P<0.10). Means for FEC at day 35 were 1783±446 eggs per gram of feces (epg) for SLI kids and 3329±850 epg for JCB kids. Haematological parameters, serum chemistry, and FAMACHA scores suggested that SLI goats were recovering from parasitic infection by day 42, whereas JCB goats had increasing severity of anaemia. Means for PCV in SLI goats decreased from 26.8±0.7% at day 0 to 19.7±0.9% at day 35 and thereafter increased to 20.2±0.9% at day 42. Means for PCV in JCB goats declined from 25.9±0.6% at day 0 to 17.2±0.9% at day 42. Eosinophilia was observed in both genotypes. The JCB goats were heavier than SLI goats and had higher antibody titres, reflecting higher levels of parasitism. Both goat types significantly increased in body weight during the experiment and therefore tolerated parasite infection without severe production losses. We concluded that SLI goats were more resistant to haemonchosis than JCB goats, but that JCB goats were somewhat resilient to parasitic infection. Substantial variability in measurements associated with parasite infection in both breeds indicated potential to improve parasite resistance. Phenotypic information should be coupled with genomic information to identify appropriate breeding goals for future selection programs.

Mitochondrial DNA-Based Analyses of Relatedness Among Turkeys, Meleagris gallopavo.

The domesticated turkey, Meleagris gallopavo, is believed to be a single breed with several varieties whose relatedness and origins remain poorly understood. Using the mitochondrial genome sequence (GenBank accession no. EF153719) that our group first reported, we investigated the relationships among 15 of the most widely occurring turkey varieties using D-loop and 16S RNA sequences. We included, as a non-traditional outgroup, mtDNA sequence information from wild turkey varieties. A total of 24 SNPs, including 18 in the D-loop and 6 in the 16S rRNA, was identified, validated and used. Of the 15 haplotypes detected based on these SNPs, 7 were unique to wild turkeys. Nucleotide diversity estimates were relatively low when compared to those reported for chickens and other livestock. Network and phylogenetic analyses showed a closer relationship among heritage varieties than between heritage and wild turkeys. The mtDNA data provide additional evidence that suggest a recent divergence of turkey varieties.

Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken.

BACKGROUND: The chicken (Gallus gallus), like most avian species, has a very distinct karyotype consisting of many micro- and a few macrochromosomes. While it is known that recombination frequencies are much higher for micro- as compared to macrochromosomes, there is limited information on differences in linkage disequilibrium (LD) and haplotype diversity between these two classes of chromosomes. In this study, LD and haplotype diversity were systematically characterized in 371 birds from eight chicken populations (commercial lines, fancy breeds, and red jungle fowl) across macro- and microchromosomes. To this end we sampled four regions of approximately 1 cM each on macrochromosomes (GGA1 and GGA2), and four 1.5 -2 cM regions on microchromosomes (GGA26 and GGA27) at a high density of 1 SNP every 2 kb (total of 889 SNPs). RESULTS: At a similar physical distance, LD, haplotype homozygosity, haploblock structure, and haplotype sharing were all lower for the micro- as compared to the macrochromosomes. These differences were consistent across populations. Heterozygosity, genetic differentiation, and derived allele frequencies were also higher for the microchromosomes. Differences in LD, haplotype variation, and haplotype sharing between populations were largely in line with known demographic history of the commercial chicken. Despite very low levels of LD, as measured by r2 for most populations, some haploblock structure was observed, particularly in the macrochromosomes, but the haploblock sizes were typically less than 10 kb. CONCLUSION: Differences in LD between micro- and macrochromosomes were almost completely explained by differences in recombination rate. Differences in haplotype diversity and haplotype sharing between micro- and macrochromosomes were explained by differences in recombination rate and genotype variation. Haploblock structure was consistent with demography of the chicken populations, and differences in recombination rates between micro- and macrochromosomes. The limited haploblock structure and LD suggests that future whole-genome marker assays will need 100+K SNPs to exploit haplotype information. Interpretation and transferability of genetic parameters will need to take into account the size of chromosomes in chicken, and, since most birds have microchromosomes, in other avian species as well.

Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus.

BACKGROUND: The comparative analysis of genome sequences emerging for several avian species with the fully sequenced chicken genome enables the genome-wide investigation of selective processes in functionally important chicken genes. In particular, because of pathogenic challenges it is expected that genes involved in the chicken immune system are subject to particularly strong adaptive pressure. Signatures of selection detected by inter-species comparison may then be investigated at the population level in global chicken populations to highlight potentially relevant functional polymorphisms. RESULTS: Comparative evolutionary analysis of chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genes identified interleukin 4 receptor alpha-chain (IL-4Ralpha), a key cytokine receptor as a candidate with a significant excess of substitutions at nonsynonymous sites, suggestive of adaptive evolution. Resequencing and detailed population genetic analysis of this gene in diverse village chickens from Asia and Africa, commercial broilers, and in outgroup species red jungle fowl (JF), grey JF, Ceylon JF, green JF, grey francolin and bamboo partridge, suggested elevated and balanced diversity across all populations at this gene, acting to preserve different high-frequency alleles at two nonsynonymous sites. CONCLUSION: Haplotype networks indicate that red JF is the primary contributor of diversity at chicken IL-4Ralpha: the signature of variation observed here may be due to the effects of domestication, admixture and introgression, which produce high diversity. However, this gene is a key cytokine-binding receptor in the immune system, so balancing selection related to the host response to pathogens cannot be excluded.

Contrasting evolution of diversity at two disease-associated chicken genes.

There have been significant evolutionary pressures on the chicken during both its speciation and its subsequent domestication by man. Infectious diseases are expected to have exerted strong selective pressures during these processes. Consequently, it is likely that genes associated with disease susceptibility or resistance have been subject to some form of selection. Two genes involved in the immune response (interferon-gamma and interleukin 1-beta) were selected for sequencing in diverse chicken populations from Pakistan, Sri Lanka, Bangladesh, Kenya, Senegal, Burkina Faso and Botswana, as well as six outgroup samples (grey, green, red and Ceylon jungle fowl and grey francolin and bamboo partridge). Haplotype frequencies, tests of neutrality, summary statistics, coalescent simulations and phylogenetic analysis by maximum likelihood were used to determine the population genetic characteristics of the genes. Networks indicate that these chicken genes are most closely related to the red jungle fowl. Interferon-gamma had lower diversity and considerable coding sequence conservation, which is consistent with its function as a key inflammatory cytokine of the immune response. In contrast, the pleiotropic cytokine interleukin 1-beta had higher diversity and showed signals of balancing selection moderated by recombination, yielding high numbers of diverse alleles, possibly reflecting broader functionality and potential roles in more diseases in different environments.

Mitochondrial DNA sequence and haplotype variation analysis in the chicken (Gallus gallus).

Although it is known to be useful for certain genotype:phenotype assignments, our knowledge of the nature and extent of variation in the entire chicken (Gallus gallus) mitochondrial genome (mtGenome) is limited. Here, we used experimental and in silico tools to identify nucleotide variants in the mtGenome, including the coding and non-coding (D-loop) regions. The distribution of the experimentally identified mitochondrial DNA variants in meat- (broilers) and egg-type (White Leghorn) chickens was also assessed. A total of 113 single-nucleotide polymorphisms (SNPs) were identified. The in silico analysis revealed a total of 91 SNPs, with 70 in the coding region and 21 in the non-coding region. Of the 41 experimentally identified SNPs, 27 were in the D-loop. Together, the experimentally identified SNPs in the non-coding region formed 11 haplotypes, whereas the 14 SNPs in the coding region formed 6. Though, 9 of the D-loop region haplotypes were observed only in broilers, 3 of the 6 haplotypes from the coding region occurred at a significantly higher frequency in broilers. To our knowledge, this investigation represents the first whole-mtGenome scan for variation and an evaluation, though limited in sample size, of the haplotype distribution in meat- and egg-type populations, using the SNPs and haplotypes identified.