Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens.

Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200-4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome of a Tibetan chicken and resequenced whole genomes of 32 additional chickens, including Tibetan chickens, village chickens, game fowl, and Red Junglefowl, and found that the Tibetan chickens could broadly be placed into two groups. Further analyses revealed that several candidate genes in the calcium-signaling pathway are possibly involved in adaptation to the hypoxia experienced by these chickens, as these genes appear to have experienced directional selection in the two Tibetan chicken populations, suggesting a potential genetic mechanism underlying high altitude adaptation in Tibetan chickens. The candidate selected genes identified in this study, and their variants, may be useful targets for clarifying our understanding of the domestication of chickens in Tibet, and might be useful in current breeding efforts to develop improved breeds for the highlands.

Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa.

Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

[Polymorphisms of inhibin α gene exon 1 in buffalo (Bubalus bubalis), gayal (Bos frontalis) and yak (Bos grunniens)].

To elucidate the genetic characteristics of the bovine Inhibin α subunit (INHA) gene, the polymorphisms in exon 1 of INHA and its bilateral sequences were assayed using PCR with direct sequencing in buffalo, gayal and yak. A comparative analysis was conducted by pooled the results in this study with the published data of INHA on some mammals including some bovine species together. A synonymous substitution c.73C>A was identified in exon 1 of INHA for buffalo, which results in identical encoding product in river and swamp buffalo. In gayal, two non-synonymous but same property substitutions in exon 1 of INHA, viz. c.62 C>T and c.187 G>A, were detected, which lead to p. P21L, p. V63M changes in INHA, respectively. In yak, nucleotide substitution c.62C> T, c.129A>G were found in exon 1 of INHA, the former still causes p. P21L substitution and the latter is synonymous. For the sequence of the 5'-flanking region of INHA examined, no SNPs were found within the species, but a substitution, c. -6T>G, was found. The nucleotide in this site in gayal, yak and cattle was c. -6G, whereas in buffalo it was c. -6T. Meanwhile, a 6-bp deletion, namely c. 262+31_262+36delTCTGAC, was found in the intron of buffalo INHA gene. For this deletion, wild types (+/+) account for main part in river buffalo while mutant types (-/-) are predominant in swamp buffalo. This deletion was not found in gayal, yak and cattle, though these all have another deletion in the intron of INHA, c. 262+78_262+79delTG. The results of sequence alignment showed that the substitutions c. 43A and c. 67G in exon 1 of INHA are specific to buffalo, whereas the substitutions c. 173A and c. 255G are exclusive to gayal, yak and cattle, and c. 24C, c. 47G, c. 174T and c. 206T are specific to goat. Furthermore, there are few differences among gayal, yak and cattle, but there relatively great differences between buffalo, goat and other bovine species regarding the sequences of INHA exon 1.

[Genetic characteristics on exon 4 of prolactin gene in 12 water buffalo populations].

The prolactin exerts obvious adjustment and control function for mammary gland development, lactation and milk protein gene expression in water buffalo. In this study the sequence features and polymorphisms of the exon 4 in prolactin gene were examined in 385 individuals which came from 12 river and swamp type buffalo populations using DNA direct sequencing and PCR-SSCP methods. The results showed that the sequence of exon 4 in prolactin gene was consists of 180 nucleotides, the fragment had high conservative character in different species. The e4. 109 C>T substitution was detected in nine swamp buffalo populations, and it was a silent mutation and was not associated with the traits of milk yield in buffalo. The PBA gene was the predominant gene in seven swamp type buffalo populations, while PBB gene was the dominant gene in Dehong and Fuzhong populations. The frequencies of PBA in swamp type buffalo was 0.400 -0.917 and the average value was 0.629+/-0.049. The polymorphism wasn't found in river buffalo, all the samples from river buffalo were holding nucleotides e4.109 C. The results indicate that there is distinct genetic differentiation between swamp and river type buffalo.

Multiple maternal origins of chickens: out of the Asian jungles.

Domestic chickens have long been important to human societies for food, religion, entertainment, and decorative uses, yet the origins and phylogeography of chickens through Eurasia remain uncertain. Here, we assessed their origins and phylogeographic history by analyzing the mitochondrial DNA hypervariable segment I (HVS-I) for 834 domestic chickens (Gallus gallus domesticus) across Eurasia as well as 66 wild red jungle fowls (Gallus gallus) from Southeast Asia and China. Phylogenetic analyses revealed nine highly divergent mtDNA clades (A-I) in which seven clades contained both the red jungle fowls and domestic chickens. There was no breed-specific clade in the chickens. The clades A, B, and E are distributed ubiquitously in Eurasia, while the other clades were restricted to South and Southeast Asia. Clade C was mainly distributed in Japan and Southeast China, while clades F and G were exclusive to Yunnan, China. The geographic distribution of clade D was closely related to the distribution of the pastime of cock fighting. Statistical tests detect population expansion within each subclade. These distinct distribution patterns and expansion signatures suggest that different clades may originate from different regions, such as Yunnan, South and Southwest China and/or surrounding areas (i.e., Vietnam, Burma, and Thailand), and the Indian subcontinent, respectively, which support the theory of multiple origins in South and Southeast Asia.