[Show abstract][Hide abstract] ABSTRACT: Recently, single nucleotide polymorphisms (SNPs) have been used to identify genes or genomic regions responsible for economic traits, including genetic diseases in domestic animals, and to examine genetic diversity of populations. In this study, we genotyped 70 chicken autosomal SNPs using DigiTag2 assay to understand the genetic structure of the Japanese native chicken breeds Satsumadori and Ingie, and the relationship of these breeds with other established breeds, Rhode Island Red (RIR), commercial broiler and layer. Five breeds, each consisting of approximately 20 chickens, were subjected to the assay, revealing the following: Average expected heterozygosities of broiler, Satsumadori, RIR, layer and Ingie were 0.265, 0.254, 0.244, 0.179 and 0.176, respectively. Phylogenetic analysis using the concatenated 70 autosomal SNP genotypes distinguished all chickens and formed clusters of chickens belonging to the respective breeds. In addition, the 2-D scatter plot of the first two principal components was consistent with the phylogenic tree. Taken together with the pairwise F(st) distances, broiler and RIR were closely positioned near each other, while Ingie was positioned far from the other breeds. Structure analysis revealed that the probable number of genetic clusters (K) was six and four with maximum likelihood and ΔK values, respectively. The clustering with maximum likelihood revealed that, in addition to the clustering of the other five breeds, the Satsumadori was subdivided into two genetic clusters. The clustering with ΔK value indicated that the broiler and Rhode Island Red were assigned to the same genetic cluster.
[Show abstract][Hide abstract] ABSTRACT: We performed quantitative trait locus (QTL) analyses for egg production traits, including age at first egg (AFE) and egg production rates (EPR) measured every 4 weeks from 22 to 62 weeks of hen age, in a population of 421 F(2) hens derived from an intercross between the Oh-Shamo (Japanese Large Game) and White Leghorn breeds of chickens. Simple interval mapping revealed a main-effect QTL for AFE on chromosome 1 and four main-effect QTL for EPR on chromosomes 1 and 11 (three on chromosome 1 and one on chromosome 11) at the genome-wide 5% levels. Among the three EPR QTL on chromosome 1, two were identified at the early stage of egg laying (26-34 weeks of hen age) and the remaining one was discovered at the late stage (54-58 weeks). The alleles at the two EPR QTL derived from the Oh-Shamo breed unexpectedly increased the trait values, irrespective of the Oh-Shamo being inferior to the White Leghorn in the trait. This suggests that the Oh-Shamo, one of the indigenous Japanese breeds, is an untapped resource that is important for further improvement of current elite commercial laying chickens. In addition, six epistatic QTL were identified on chromosomes 2, 4, 7, 8, 17 and 19, where none of the above main-effect QTL were located. This is the first example of detection of epistatic QTL affecting egg production traits. The main and epistatic QTL identified accounted for 4-8% of the phenotypic variance. The total contribution of all QTL detected for each trait to the phenotypic and genetic variances ranged from 4.1% to 16.9% and from 11.5% to 58.5%, respectively.
[Show abstract][Hide abstract] ABSTRACT: Recent studies have revealed that cytokines, including TNFα and IL-6 play key roles in the priming phase of liver regeneration. However, further knowledge of molecular events in the priming phase is needed for more comprehensively understanding the initiation of liver regeneration. In the present study, we attempted to identify additional genes involved in an early phase (2-6 h post partial hepatectomy, PH). The expression of 71 genes was shown to be up-regulated more than 3-fold in the liver at 2 h and 6 h post PH, as compared to 0 h (normal livers) using microarray analysis. Among them, Rab30 and S100a8/S100a9, were identified as novel genes up-regulated over 20-fold at 2 h post PH as compared to normal liver, and were further examined by RT-qPCR to confirm microarray results. Rab30 showed no significant up-regulation in organs other than the liver, whereas S100a8/S100a9 showed significant up-regulation in other organs, such as the lung and spleen at 6 h post PH as compared to those of sham-operated mice, indicating the existence of a different up-regulation machinery between Rab30 and S100a8/S100a9. Their expression was further investigated in the liver at various developmental stages. Rab30 was shown to be expressed only in newborn liver, whereas S100a8/S100a9 was highly expressed in embryo stages, and exhibited the highest levels in newborn liver. These findings imply that Rab30 and S100a8/S100a9 are possibly involved in the functional switch from hematopoiesis support to metabolism in the newborn stage, but might play different roles in liver development. In conclusion, Rab30 and S100a8/S100a9 were indicated to play roles in the initiation of liver regeneration as well as possibly in the functional switch of the liver in the newborn stage.
International Journal of Molecular Medicine 02/2011; 27(4):567-74. · 1.96 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We determined the complete nucleotide sequence of the mitochondrial genome of the semidomestic red deer (Cervus elaphus) of New Zealand. The genome was 16,357 bp long and contained 13 protein-coding genes, 12SrRNA, 16SrRNA, 22 tRNAs and a D-loop as found in other mammals. Database homology searches showed that the mitochondrial DNA (mtDNA) sequence from the New Zealand semidomestic deer was similar to partial mtDNA sequences from the European, Norwegian (C. e. atlanticus) and Spanish red deer (C. e. hispanicus). Phylogenetic analysis of the mitochondrial protein-coding regions revealed two well-defined monophyletic clades in subfamilies Cervinae and Muntiacinae. However, red deer and Sika deer were not found to be close relatives. The analysis did identify the red deer as a sister taxon of a Samber/Sika deer clade, although it was more closely related to the Samber than the Sika group.
[Show abstract][Hide abstract] ABSTRACT: The Onagadori is a distinguished chicken breed that is characterized by an extremely long tail in the male. In this breed, three different plumage colour varieties have been developed (black-breasted white, black-breasted red and white) in which the black-breasted white is believed to be the original colour of the Onagadori, based on historical records. To establish a conservation strategy, 176 birds were genotyped for autosomal microsatellites. Significant genetic distinctness was found between the original (black-breasted white) and two derivative varieties (F(ST) = 0.091 and 0.093). At the same time, a Bayesian model-based clustering revealed that the majority of individuals belonging to the black-breasted red and white varieties had an extremely low proportion of the genome shared with the original type (black-breasted white). This suggests that derivative varieties were created by crossing with other breeds, with low introgression of the original-type genome. We propose that the three plumage colour varieties should be treated as separate genetic units in a conservation programme.
[Show abstract][Hide abstract] ABSTRACT: Calcitonin (CT) has been shown to have various functions including osteoclast activity and calcium and phosphorus metabolism in mammals. In the present study, we measured the amounts of CT mRNA in the mouse brain, liver, kidney, heart and testis at various development stages, 14 days post-coitum (dpc), 17-dpc, newborn, 1 week and 8 weeks (adult), using real-time PCR. In the brain and kidney, the amount of CT mRNA decreased with development. In the testis, elevated amounts were observed at 17-dpc and 8 weeks. In the liver, the amount increased from the 14 dpc embryo to newborn stage and then decreased. In the heart, elevated amounts were observed at 17-dpc. Additionally, the CT antisense transcript was determined using a modified RT-PCR and nucleotide sequencing in the present study. Organs with high mRNA expressions were examined for localization of transcripts using in situ hybridization. The CT sense and antisense transcripts in the 14 dpc brain were mainly localized in the mesencephalon. In the pre- and postnatal stages, sense and antisense transcripts were shown to exist rather uniformly in the kidney, heart, liver and testis. In the 17-dpc rib and thyroid lobe and the adult ovary, the sense and antisense transcripts were found to be densely localized.
Journal of Veterinary Medical Science 06/2009; 71(5):561-8. · 0.88 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Bovine neosporosis, caused by Neospora caninum is a leading cause of abortion in cattle. We postulated that neosporosis could lead to fetal death and mummification. Fifteen mummified fetuses were tested by polymerase chain reaction (PCR) for the mutation in the bovine SLC35A3 gene that causes complex vertebral malformation (CVM) and the pNC-5 gene which identifies N. caninum infection. DNA was extracted from the mummified fetuses and the sex of the mummies was determined by PCR. The CVM mutation was not detected in the mummified fetuses, but 4 fetuses were positive for N. caninum infection. The ages of the mummies with N. caninum infection were 100, 113, 123, and 131 days. Twelve of the 15 mummified fetuses were male. To our knowledge, this is the first detection of N. caninum as a possible cause of bovine fetal mummification.
The Canadian veterinary journal. La revue veterinaire canadienne 05/2009; 50(4):389-92. · 0.77 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To provide a gene-based comparative map and to examine a porcine genome assembly using bacterial artificial chromosome-based sequence, we have attempted to assign 128 genes localized on human chromosome 14q (HSA14q) to a porcine 7000-rad radiation hybrid (IMpRH) map. This study, together with earlier studies, has demonstrated the following. (i) 126 genes were incorporated into two SSC7 RH linkage groups by CarthaGene analysis. (ii) In the remaining two genes, TOX4 linked to TCRA located in SSC7 by two-point analysis, whereas SIP1 showed no significant linkage with any gene/marker registered in the IMpRH Web Server. (iii) In the two groups, the gene clusters located from 19.9 to 36.5 Mb on HSA14q11.2-q13.3 and from 64.0 to 104.3 Mb on HSA14q23-q32.33 respectively were assigned to SSC7q21-q26. (iv) Comparison of the gene order between the present RH map and the latest porcine sequence assembly revealed some inconsistencies, and a redundant arrangement of 16 genes in the sequence assembly.
[Show abstract][Hide abstract] ABSTRACT: The present review work aims at determining the potential usefulness of indigenous naked neck (INN) chicken (D. Nana) for poultry production in a hot-humid climate. INN chicken has good heat dissipation mechanism and well adaptive to harsh tropical environment and nutrition, and is highly resistant to disease and superior to indigenous full-feathered and exotic egg-type or exotic naked neck counterparts in terms of growth rate, egg production, egg quality and meat yield traits. It can produce double the standard number of eggs under improved nutrition and management conditions. Crossbreds of INN with exotic chicken can perform even better than that of exotic chicken in respect of productive and reproductive traits. Consumers prefer the meat and eggs of INN chickens for reasons of pigmentation, leanness, taste, firmness, and they are also used in special dishes. INN chicken prices are typically higher compared with those of products from exotic stocks. There are a very few published papers on the molecular aspects of INN chickens, although this is essential to determine genetic distance or relationship within or between INN chicken and indigenous full-feathered (IFF) varieties (D. nana) for future breeding plans. Therefore INN strains may be a promising and worthy genetic resource for the development of a breed or strain through selective or crossbreeding program suited to Bangladesh and in other countries where similar environments and socio-economic conditions exist. Thus, the present review provides genetic and performance information on INN chickens which may be useful for further improvement of tropical breeds.
[Show abstract][Hide abstract] ABSTRACT: The reason why cows carrying the mutation of complex vertebral malformation (CVM) show poor reproductive capability although they carry only one mutant allele is still not fully understood. Monitoring the progesterone profiles during oestrous cycle and early pregnancy in carrier cows might help explain their lowered reproductive capability. Progesterone concentration was measured in 19 CVM carrier cows and 21 control cows during oestrous cycle and early pregnancy. Milk samples were collected from all cows starting on the day of artificial insemination until day 45 post-AI. Progesterone was measured in skim milk using enzyme-linked immunosorbent assay (ELISA). Progesterone concentration was significantly reduced on day 7 (p < 0.05) and day 9 (p < 0.01) post-insemination in conceived CVM carrier cows when compared with that in control conceived cows. The mean progesterone concentration during early pregnancy was significantly lower (p < 0.05) in conceived cows with CVM than that of control cows in the same period. However, the mean progesterone concentration did not differ significantly (p = 0.072) in CVM cows that showed fertilization failure or embryonic death than that of control cows. Additionally, of 13 conceived control cows, eight cows (61.5%) showed normal luteal function. In contrast, of nine conceived CVM cows, only four cows (44.4%) showed normal luteal function. The conception rate was 47.4% in CVM carrier cows and 61.9% in control cows, but this difference did not reach significance. In conclusion, progesterone concentration might be lowered during early pregnancy in conceived CVM cows compared with that in control cows.
Reproduction in Domestic Animals 02/2009; 45(4):729-33. · 1.39 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The calcitonin gene-related peptides (CGRP), alphaCGRP and betaCGRP, have been implicated to play various roles in primates and rodent. However, since the expression information has been limited, in the present study, we measured the amount of gene expression in mouse brain, liver, kidney, heart, and testis at embryonic day (E) 14, E17, postnatal day (P) 1, P7, and adult using real-time PCR, and determined the precise localization of alphaCGRP and betaCGRP sense/antisense transcripts in tissues using in situ hybridization. The sense transcripts of alphaCGRP and betaCGRP were found mainly in brain, and their amount profiles were similar in the course of development: one expression peak was observed at E17 and the other at P7. The amounts of alphaCGRP transcripts were greater than those of betaCGRP transcripts in the range between 3.6 and 31 times. In the E17 and P7 brains, the localization pattern of alphaCGRP sense transcripts was similar with that of alphaCGRP antisense transcripts. Fewer transcripts were found in neuroblasts of E17 corpus callosum, and neuroblasts of P7 corpus callosum, olfactory bulb, plexus chorioideus, and ventriculus lateralis than in other brain areas. The localization pattern of betaCGRP sense and antisense transcripts was similar to that for alphaCGRP except that the betaCGRP antisense transcripts showed spot-like localizations. Additionally, the alphaCGRP sense transcript, and betaCGRP sense and antisense transcripts were found in parafollicular cells (C cells) of E17 thyroid lobe. These findings together indicate that alphaCGRP and betaCGRP have their own roles in the ontogenic process.
Brain & development 01/2009; 31(9):682-93. · 1.74 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Factor XI deficiency was detected in Holstein cows and mummified foetuses in Japan; however, no report is available about the occurrence of Factor XI deficiency in Holstein semen in Japan. Five hundred cows in twelve dairy farms in Hiroshima Prefecture, Japan were under the study. Genomic DNA was extracted from the cows using a commercial DNA kits and screened to Factor XI mutation. Based on the information of the carrier cows found in the cattle population, four Holstein bulls were analysed for Factor XI mutation. DNA was extracted from bull's semen using phenol chloroform method. Extracted genomic DNA of the bull's semen was typed for Factor XI using specific polymerase chain reaction (PCR) primers. The resultant PCR was sequenced using big dye terminator sequencing method. The pedigree of the bulls was investigated. Furthermore, the inheritance of Factor XI mutation to next generation was estimated. Out of the 500 cows, five were heterozygous to Factor XI. Moreover, out of the four bulls, one was found to carry the mutation of Factor XI; it was also a complex vertebral malformation (CVM) carrier. In DNA sequencing, the insertion mutation of 76 bp of poly-adenine that characterizes the Factor XI deficiency was detected in the carrier bull as well as the carrier cows. Pedigree analysis of the carrier bull revealed that his father and mother ID were 2247419A and 14189172A, respectively, that originated from USA Holstein. Out of six daughter cows born to the carrier bull, one cow (16.6%) inherited Factor XI mutation, while three of them (50.0%) inherited CVM mutation. Autosomal recessive genes that affect cow's reproduction have a particular concern to dairy industry. To our knowledge this is the first report of Factor XI mutation in Holstein semen in Japan.
Reproduction in Domestic Animals 10/2008; 44(5):792-6. · 1.39 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Mhc is a highly conserved gene region especially interesting to geneticists because of the rapid evolution of gene families found within it. High levels of Mhc genetic diversity often exist within populations. The chicken Mhc is the focus of considerable interest because of the strong, reproducible infectious disease associations found with particular Mhc-B haplotypes. Sequence data for Mhc-B haplotypes have been lacking thereby hampering efforts to systematically resolve which genes within the Mhc-B region contribute to well-defined Mhc-B-associated disease responses. To better understand the genetic factors that generate and maintain genomic diversity in the Mhc-B region, we determined the complete genomic sequence for 14 Mhc-B haplotypes across a region of 59 kb that encompasses 14 gene loci ranging from BG1 to BF2. We compared the sequences using alignment, phylogenetic, and genome profiling methods. We identified gene structural changes, synonymous and non-synonymous polymorphisms, insertions and deletions, and allelic gene rearrangements or exchanges that contribute to haplotype diversity. Mhc-B haplotype diversity appears to be generated by a number of mutational events. We found evidence that some Mhc-B haplotypes are derived by whole- and partial-allelic gene conversion and homologous reciprocal recombination, in addition to nucleotide mutations. These data provide a framework for further analyses of disease associations found among these 14 haplotypes and additional haplotypes segregating and evolving in wild and domesticated populations of chickens.
The Journal of Immunology 10/2008; 181(5):3393-9. · 5.52 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In the current study, we carried out assignment tests applying the Bayesian and distance-based methods, using 20 microsatellite genotypes in four chicken lines. The Bayesian method showed slightly higher performance of assignment than the distance-based method. In the assignment using the Bayesian method, >or=90% accuracy of assignment was attained by using only two of the most heterozygous markers, whereas in the case of the least heterozygous markers, six were needed to reach the same level of accuracy. In the assignment of the most closely related line pair (F(ST) = 0.1736), at least 12 markers selected by random ordering and at least 15 individuals per line were needed to stably obtain high accuracy of assignment (>or=97%), whereas using only six random markers achieved 97-100% of accuracy between the two most distinct lines (F(ST) = 0.3651) without reference to the sample size per line.