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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. 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. 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.

This study was conducted to assess the variations of milk coagulation properties (MCP) among two native cattle types, e.g., Thamankaduwa White (TW), Lankan cattle (LC) and two improved cattle breeds, e.g., Friesian (FR) and Jersey (JS), in relation to distinctive milk protein compositions. MCP traits, including rennet coagulation time (RCT), curd firmness, meltability and yield, were measured. The milk protein profile of each breed/type was analyzed using capillary zone electrophoresis. Significant differences (p < 0.05) were observed among two native and improved cattle breeds/types in relation to RCT. Friesian and TW milk had the longest and shortest (p < 0.05) RCT, respectively. There was no significant difference in firmness among the four breeds/types. The highest (p < 0.05) coagulum yield was recorded for TW milk, followed by LC, JS and FR. TW milk had the highest (p < 0.05) meltability values. As revealed by the protein profiles, κ-casein concentration was significantly higher in TW milk compared to the other three breeds/types. None of the other milk protein fractions showed significant differences among the four breeds/types. The overall results indicate the superior MCP of TW milk, emphasizing the value of native breeds which could be exploited in the development of niche dairy products while supporting the conservation effort of the native cattle gene pool.

To identify the genetic determinants of domestication and productivity of Asian water buffaloes (Bubalus bubalis), 470 genomes of domesticated river and swamp buffaloes along with their putative ancestors, the wild water buffaloes (Bubalus arnee) are sequenced and integrated. The swamp buffaloes inherit the morphology of the wild buffaloes. In contrast, most river buffaloes are unique in their morphology, but their genomes cluster with the wild buffaloes. The levels of genomic diversity in Italian river and Indonesian swamp buffaloes decrease at opposite extremes of their distribution range. Purifying selection prevented the accumulation of harmful loss‐of‐function variants in the Indonesian buffaloes. Genes that evolved rapidly (e.g., GKAP1) following differential selections in the river and swamp buffaloes are involved in their reproduction. Genes related to milk production (e.g., CSN2) and coat color (e.g., MC1R) underwent strong selections in the dairy river buffaloes via soft and hard selective sweeps, respectively. The selective sweeps and single‐cell RNA‐seq data revealed the luminal cells as the key cell type in response to artificial selection for milk production of the dairy buffaloes. These findings show how artificial selection has been driving the evolutionary divergence and genetic differentiation in morphology and productivity of Asian water buffaloes. This study unveils the comprehensive genomic landscape of Asian water buffaloes, highlighting how selections drive the evolutionary divergence and genetic differentiation in morphology and productivity of the domesticated buffaloes. Insights into selective sweeps reveal key genes linked to coat color and milk production, offering a deeper understanding of the biological processes behind the breed improvement of Asian water buffaloes.

The study attempted to use an indicator approach to identify food, nutrition and health vulnerability in existing agriculture systems in the hilly areas in south Asia and to identify the best adaptation strategies to ensure food security. The farming system units (FSUs) were selected randomly from sites at elevation ≥ 300 m amsl, slope ≥ 30%, and representing ≥ 30% of the agrarian population. A questionnaire survey helped recognize different farming systems and their components. Adaptation strategies to reduce food-nutrition-health vulnerability (FNHV) of 424 FSUs in Sri Lanka (Hatton and Welimada), Bangladesh (Chittagong), and Nepal (Jhikhu Khola) were assessed by the FNHV index (FNHVi) calculated using 18 climate-sensitive parameters. The spatial distribution of FNHVi (0 = least to 1 = very-highly vulnerable) was mapped for each site, and a composite index compared FNHVs among sites. The FNHVi ranged from 0.13 to 0.68 and was not dependent on the altitude of FSUs. Chittagong was the most vulnerable, with a composite FNHV of 0.51, followed by Welimada (0.42), Hatton (0.39), and Jhikhu Khola (0.35). The contribution of the selected parameters to FNHV varied among different sites and households within a location. Good adaptation strategies such as crop diversification, mixed cropping, incorporation of organic fertilizers with mineral fertilizers, integrated crop and animal husbandry, and production of food for own consumption coupled with land ownership, diversified income sources, availability of storage facilities, and adoption of proper sanitary conditions have helped build climate-resilience in the mountain ecosystems of south Asia.

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-4Rα), 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-4Rα: 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.

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.

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-γ and interleukin 1-β) 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-γ 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-β 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.

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.

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world’s most numerous domestic animal.