Refining the evolutionary tree of the horse Y chromosome

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity

ミトコンドリアゲノムによるキジ目の分子系統学的研究

広島大学(Hiroshima University)博士(農学)Agriculturedoctora

The complete mitochondrial genome of the Japanese rock ptarmigan (Lagopus muta japonica Clark, 1907)

The rock ptarmigan Lagopus muta is a grouse widely distributed in the arctic and subarctic regions of Eurasia and North America. The range of Japanese endemic subspecies (Japanese rock ptarmigans: L. m. japonica) is the southernmost of this species, but their origin is little known. Here, we determined the complete mitogenome of this subspecies and carried out the phylogenetic analysis. It was demonstrated that Japanese rock ptarmigans are old divergent lineage

ブタ卵子減数分裂再開時における卵丘細胞のプロジェステロン受容体遺伝子発現の経時的変化

In this study, to investigate the time dependent changes in progesterone receptor (PR) expression in cumulus cells during meiotic resumption of porcine oocytes, each amount of PR-A and PR-B mRNA was analyzed by RT-PCR with primer sets for the PR-B region and the PR-A/B common region. The results showed that the levels of both PR-A/B and PR-B mRNA were very low in cumulus cells immediately recovered from their follicles. The cultivation with FSH and LH significantly increased the level of both PR-A/B and PR-B mRNA in cumulus cell of COCs, whereas the level of PR-B mRNA significantly decreased at 12-hr cultivation. Nevertheless, the higher level of PR-A/B mRNA was maintained up to 20-hr cultivation, suggesting that PR-A was mainly expressed in cumulus cells during cultivation from 12 hr to 20 hr. When COCs were cultured for 10 hr and then further cultured with RU486 for 10 hr, the proportion of oocytes undergoing GVBD significantly decreased in a dose dependent fashion. These results suggest that the high ratios of PR-A to PR-B in cumulus cells of COCs during 12-hr to 20-hr cultivation, are required for meiotic resumption of porcine cumulus-enclosed oocytes in vitro

Complete Nucleotide Sequence of Numida meleagris (Helmeted Guineafowl) Mitochondrial Genome

Guineafowl has been classified into the order Galliformes. However, little genetic information was available to establish the phylogenetic position of the Guineafowl. In the present study we subjected the mitochondrial DNA (mtDNA) of Numida mereagris, a representative member of Guineafowl, to complete sequencing. It was revealed that the mtDNA is a circular DNA of 16,726bp with a genomic structure the same as that of Gallus gallus var. domesticus and Coturnix japonica mtDNAs, though it is 62bp smaller than G. g. domesticus mtDNA and 29bp larger than C. japonica mtDNA. Similarities of the 13 genes and two ribosomal RNAs except D-loop and transfer RNAs between N. meleagris and G. g. domesticus and between N. meleagris and C. japonica ranged from 77.0% to 88.8% and from 76.2% to 88.4%, respectively. As the sequences of NADH dehydrogenase subunit 2 and cytochrome b genes have been reported for nine species (Bambusicola thoracis, Coturnix chinensis, C. japonica, G. g. domesticus, Gallus varius, Pavo cristatus, Perdix perdix, Phasianus colchicus, Tympanchus phasianellus) in the order Galliformes, the concatenated nucleotide sequences and amino-acid sequences of these two genes were subjected to phylogenetic analysis of N. meleagris against these nine species with Ayathya americana (Anseriformes) as an outgroup using a maximum likelihood (ML) method. The ML analyses of the first/second bases of codons, the third base of codons, and the amino-acid sequence consistently demonstrated that N. meleagris did not form clades with other species in the order but stayed in a remote position in the tree

Characterization of Major Histocompatibility Complex Genes in Jungle Fowls, Genus Gallus

Chicken major histocompatibility complex (Mhc) is smaller in size and contains fewer genes than does mammal Mhc. To clarify the characters of Mhc genes in junglefowls as the ancestral species of domestic chickens, we analyzed their Mhc class I B-F and Mhc class IV B-G genes using the restriction fragment length polymorphisms (RFLPs) method in addition to comparing the B blood types of Red junglefowls and Green junglefowls. The B blood types were quite different between the two species of junglefowls. Green junglefowl had small variation of B blood types, almost Green junglefowls reacted with all of the B antisera, BABCDEGIKLMT.Using the B-G gene probe gene 8.5 in RFLPs, many bands were observed in the junglefowls. The RFLPs patterns based on B-G genes as the probes of Red junglefowls and Green junglefowls were quite different patterns within the same B blood type as determined by hemagglutination. On the contrary, the RFLPs of regions of Green junglefowls showed the same patterns regardless of chicken B blood types. We suggest that the Mhc class I B-F and Mhc class IV B-G genes might not be affected by their history of domestication from junglefowls, and artificial selection only reduced the number of B-G genes

Production and price of indigenous naked neck and full

A total of 63 farm families and 63 consumers from Gazipur and Mymensingh districts were randomly selected to assess the production and local market price of indigenous naked neck (Nana) and full feathered (nana) chickens reared under rural scavenging system. Data were collected through personal interviews using semi-structured and pre-tested interview schedules for the period of July to December, 2009. Clutch size, egg production and hatchability at set eggs were statistically similar between Nana and nana chickens. However, Nana chicken tended to be higher at 1.67% clutch length, 3.4 eggs/hen/year and 0.42% hatchability than that of nana counterpart. Nana had significantly (P<0.05) higher egg weight by 5% compared with nana chicken. Price per kg live bird was almost similar between Nana and nana chicken (P>0.05), with Nana males sold at 10.57% higher price in comparison with that of nana chicken (P<0.01). Genotype and sex independently did not influence live weight (P>0.05). Genotype and sex interacted significantly (P<0.05) for live weight. Preference for Nana chickens was 58.73% for producers and 53.96% for consumers, whereas 41.26% producers and 46.03% consumers disliked Nana chickens. The reasons for liking Nana include better appearance, larger size, exotic looks rarity, larger egg size and high vigor. Dislike for Nana chicken is based on superstition, dull and sickly appearance, lower disease resistance, generally rarity, shortage of roosters, and higher feed requirement. Therefore, indigenous chickens may show potentials for productive adaptability, and Nana chicken might be suitable for production of egg and meat in tropical climate