1
|
Hirano T, Nishimura S, Hara H, Sugimoto Y, Hanzawa K. Mapping of Calf Death in Japanese Black Cattle. Anim Biotechnol 2017; 28:242-247. [PMID: 28103142 DOI: 10.1080/10495398.2016.1267643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Weak calf syndrome (WCS) is a major cause of calf death in Japanese Black cattle. Among IARS disorders, the isoleucyl-tRNA synthetase c.235G>C mutation has been identified as one of the causes of WCS. However, calf deaths differing from those attributed to IARS disorder has been occurring. To identify other genes potentially responsible for these calf deaths, we constructed three populations of three bulls (Bull-1, -2 and -3) that did not carry the IARS mutation, and dead calves (18, 28, and 31 calves) and healthy cattle (18, 15, and 10 cattle) sired by these bulls. The populations were genotyped using the BovineSNP50 BeadChip, but homozygosity mapping did not detect any associated genomic regions with calf death. Linkage analysis performed using each population as a paternal half-sib family of Bull-1, Bull-2, and Bull-3 revealed that, in the Bull-1 population, calf death was mapped to the 8.94 Mb-14.53 Mb and 29.82 Mb-33.77 Mb regions of BTA29. The findings suggested that the incidence of calf death in calves sired by Bull-1 was a hereditary disease exhibiting a dominant, not recessive, inheritance pattern.
Collapse
Affiliation(s)
- Takashi Hirano
- a Faculty of Agriculture, Tokyo University of Agriculture, Funako , Atsugi , Kanagawa , Japan
| | - Shota Nishimura
- b Shirakawa Institute of Animal Genetics, Odakura, Nishigo, Nishi-shirakawa , Fukushima , Japan
| | - Hiromi Hara
- a Faculty of Agriculture, Tokyo University of Agriculture, Funako , Atsugi , Kanagawa , Japan
| | - Yoshikazu Sugimoto
- b Shirakawa Institute of Animal Genetics, Odakura, Nishigo, Nishi-shirakawa , Fukushima , Japan
| | - Kei Hanzawa
- a Faculty of Agriculture, Tokyo University of Agriculture, Funako , Atsugi , Kanagawa , Japan
| |
Collapse
|
2
|
Hirano T, Kobayashi N, Matsuhashi T, Watanabe D, Watanabe T, Takasuga A, Sugimoto M, Sugimoto Y. Mapping and exome sequencing identifies a mutation in the IARS gene as the cause of hereditary perinatal weak calf syndrome. PLoS One 2013; 8:e64036. [PMID: 23700453 PMCID: PMC3660308 DOI: 10.1371/journal.pone.0064036] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 04/08/2013] [Indexed: 11/29/2022] Open
Abstract
We identified an IARS (isoleucyl-tRNA synthetase) c.235G>C (p.Val79Leu) substitution as the causative mutation for neonatal weakness with intrauterine growth retardation (perinatal weak calf syndrome). In Japanese Black cattle, the syndrome was frequently found in calves sired by Bull A. Hence, we employed homozygosity mapping and linkage analysis. In order to identify the perinatal weak calf syndrome locus in a 4.04-Mb region of BTA 8, we analysed a paternal half-sibling family with a BovineSNP50 BeadChip and microsatellites. In this critical region, we performed exome sequencing to identify a causative mutation. Three variants were detected as possible candidates for causative mutations that were predicted to disrupt the protein function, including a G>C (p.Val79Leu) mutation in IARS c.235. The IARS c.235G>C mutation was not a homozygous risk allele in the 36 healthy offspring of Bull A. Moreover, the IARS Val79 residue and its flanking regions were evolutionarily and highly conserved. The IARS mutant (Leu79) had decreased aminoacylation activity. Additionally, the homozygous mutation was not found in any of 1526 healthy cattle. Therefore, we concluded that the IARS c.235G>C mutation was the cause of hereditary perinatal weak calf syndrome.
Collapse
Affiliation(s)
- Takashi Hirano
- Shirakawa Institute of Animal Genetics, Fukushima, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
3
|
Honda T, Sasazaki S, Oyama K, Mukai F, Nomura T. Sampling method for estimating neutral allele frequency in a pedigreed population. J Anim Breed Genet 2012; 129:226-33. [PMID: 22583327 DOI: 10.1111/j.1439-0388.2011.00968.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The estimated allele frequency at neutral DNA marker loci is a fundamental parameter for establishing a conservation scheme for a set of livestock breeds. In this study, we propose a novel 'minimum distance (MD) method' for estimating neutral allele frequencies, which minimizes the error by the use of pedigree information. Using computer simulation and actual microsatellite data for a pedigreed cattle population, the performance of the proposed method was compared with that of conventional random sampling (RND). MD manifests a promising superiority to RND, irrespective of the sample size and the depth of pedigree. It is theoretically demonstrated that the error of the estimates depends on both the sample size and the distance of founder allele frequencies between the sampled and the non-sampled individuals. MD samples individuals so as to minimize the latter source of estimation error.
Collapse
Affiliation(s)
- Takeshi Honda
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Hyogo, Japan.
| | | | | | | | | |
Collapse
|
4
|
Hirano T, Matsuhashi T, Kobayashi N, Watanabe T, Sugimoto Y. Identification of an FBN1 mutation in bovine Marfan syndrome-like disease. Anim Genet 2011; 43:11-7. [PMID: 22221020 DOI: 10.1111/j.1365-2052.2011.02209.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mutations in the gene encoding fibrillin-1 (FBN1), a component of the extracellular microfibril, cause Marfan syndrome (MFS). Frequent observation of cattle with a normal withers height, but lower body weight than age-matched normal cattle, was recently reported among cattle sired by phenotypically normal Bull A, in Japanese Black cattle. These cattle also showed other characteristic features similar to the clinical phenotype of human MFS, such as a long phalanx proximalis, oval face and crystalline lens cloudiness. We first screened a paternal half-sib family comprising 36 affected and 10 normal offspring of Bull A using the BovineSNP50 BeadChip (illumina). Twenty-two microsatellite markers mapped to a significant region on BTA10 were subsequently genotyped on the family. The bovine Marfan syndrome-like disease (MFSL) was mapped onto BTA10. As FBN1 is located in the significant region, FBN1 was sequenced in Bull A, and three affected and one normal cattle. A G>A mutation at the intron64 splicing accepter site (c.8227-1G>A) was detected in 31 of 36 affected animals (84.7%). The c.8227-1G>A polymorphism was not found in 20 normal offspring of Bull A or in 93 normal cattle unrelated to Bull A. The mutation caused a 1-base shift of the intron64 splicing accepter site to the 3' direction, and a 1-base deletion in processed mRNA. This 1-base deletion creates a premature termination codon, and a 125-amino acid shorter Fibrillin-1 protein is produced from the mutant mRNA. We therefore conclude that the c.8227-1G>A mutation is causative for MFSL. Furthermore, it was suggested that Bull A exhibited germline mosaicism for the mutation, and that the frequency of the mutant sperm was 14.9%.
Collapse
Affiliation(s)
- T Hirano
- Shirakawa Institute of Animal Genetics, Odakura, Nishigo, Nishi-Shirakawa, Fukushima, Japan.
| | | | | | | | | |
Collapse
|
5
|
Shiga K, Umeki H, Shimura H, Fujita T, Watanabe S, Nagai T. Growth and fertility of bulls cloned from the somatic cells of an aged and infertile bull. Theriogenology 2005; 64:334-43. [PMID: 15955357 DOI: 10.1016/j.theriogenology.2004.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Indexed: 11/20/2022]
Abstract
In the present study, somatic cell cloning technology was used to produce eight newborn calves from an aged, infertile bull. Average birth weight of these calves was significantly higher than that of calves produced using AI. Four of the cloned calves died during the peripartum period; the remaining four (Clones A-D) survived and were used in this study. Two of the surviving calves (Clones C and D) were castrated; growth rates of the intact and castrated clones were similar to those of intact and castrated bulls, respectively, that had been derived by AI. Both uncastrated bulls (Clones A and B) began to produce normal semen at approximately 12 months of age. Semen produced by these clones, and their nuclear donor, was subsequently used for IVF; the proportion of IVM-IVF oocytes developing to the blastocyst stage was 23.4% (50/214), 28.4% (52/183) and 30.9% (63/204), respectively. Conception rates for AI were 54.5% (12/22) and 62.7% (64/102) for semen derived from Clone A and from the nuclear donor, respectively. The length of pregnancy and birth weight of the calves derived from semen collected from clones were similar to those of calves obtained by conventional AI using semen from their nuclear donor. Therefore, sires cloned from the somatic cells of an aged and infertile bull had normal fertility.
Collapse
Affiliation(s)
- Kazuho Shiga
- Oita Prefectural Institute of Animal Industry, Kuju Naoiri, Oita 878-0201, Japan
| | | | | | | | | | | |
Collapse
|
6
|
Hanotte O, Ronin Y, Agaba M, Nilsson P, Gelhaus A, Horstmann R, Sugimoto Y, Kemp S, Gibson J, Korol A, Soller M, Teale A. Mapping of quantitative trait loci controlling trypanotolerance in a cross of tolerant West African N'Dama and susceptible East African Boran cattle. Proc Natl Acad Sci U S A 2003; 100:7443-8. [PMID: 12805560 PMCID: PMC164605 DOI: 10.1073/pnas.1232392100] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2002] [Indexed: 11/18/2022] Open
Abstract
Trypanosomosis, or sleeping sickness, is a major disease constraint on livestock productivity in sub-Saharan Africa. To identify quantitative trait loci (QTL) controlling resistance to trypanosomosis in cattle, an experimental cross was made between trypanotolerant African N'Dama (Bos taurus) and trypanosusceptible improved Kenya Boran (Bos indicus) cattle. Sixteen phenotypic traits were defined describing anemia, body weight, and parasitemia. One hundred seventy-seven F2 animals and their parents and grandparents were genotyped at 477 molecular marker loci covering all 29 cattle autosomes. Total genome coverage was 82%. Putative QTL were mapped to 18 autosomes at a genomewise false discovery rate of <0.20. The results are consistent with a single QTL on 17 chromosomes and two QTL on BTA16. Individual QTL effects ranged from approximately 6% to 20% of the phenotypic variance of the trait. Excluding chromosomes with ambiguous or nontrypanotolerance effects, the allele for resistance to trypanosomosis originated from the N'Dama parent at nine QTL and from the Kenya Boran at five QTL, and at four QTL there is evidence of an overdominant mode of inheritance. These results suggest that selection for trypanotolerance within an F2 cross between N'Dama and Boran cattle could produce a synthetic breed with higher trypanotolerance levels than currently exist in the parental breeds.
Collapse
Affiliation(s)
- O Hanotte
- International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Sugimoto M, Ihara N, Bennett GL, Sugimoto Y. Eleven previously unreported dinucleotide microsatellite loci on bovine chromosome 19. Anim Genet 2003; 34:236-7. [PMID: 12755831 DOI: 10.1046/j.1365-2052.2003.01002.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- M Sugimoto
- National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan
| | | | | | | |
Collapse
|
8
|
Takeda H, Takami M, Oguni T, Tsuji T, Yoneda K, Sato H, Ihara N, Itoh T, Kata SR, Mishina Y, Womack JE, Moritomo Y, Sugimoto Y, Kunieda T. Positional cloning of the gene LIMBIN responsible for bovine chondrodysplastic dwarfism. Proc Natl Acad Sci U S A 2002; 99:10549-54. [PMID: 12136126 PMCID: PMC124971 DOI: 10.1073/pnas.152337899] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chondrodysplastic dwarfism in Japanese brown cattle is an autosomal recessive disorder characterized by short limbs. Previously, we mapped the locus responsible for the disease on the distal end of bovine chromosome 6. Here, we narrowed the critical region to approximately 2 cM by using linkage analysis, constructed a BAC and YAC contig covering this region, and identified a gene, LIMBIN (LBN), that possessed disease-specific mutations in the affected calves. One mutation was a single nucleotide substitution leading to an activation of a cryptic splicing donor site and the other was a one-base deletion resulting in a frameshift mutation. Strong expression of the Lbn gene was observed in limb buds of developing mouse embryos and in proliferating chondrocytes and bone-forming osteoblasts in long bones. These findings indicate that LBN is responsible for bovine chondrodysplastic dwarfism and has a critical role in a skeletal development.
Collapse
Affiliation(s)
- Haruko Takeda
- Shirakawa Institute of Animal Genetics, Nishi-shirakawa, Fukushima 961-8061, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Watanabe T, Ihara N, Itoh T, Fujita T, Sugimoto Y. Deletion mutation in Drosophila ma-l homologous, putative molybdopterin cofactor sulfurase gene is associated with bovine xanthinuria type II. J Biol Chem 2000; 275:21789-92. [PMID: 10801779 DOI: 10.1074/jbc.c000230200] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Defective xanthine dehydrogenase (XDH) activity in humans results in xanthinuria and xanthine calculus accumulation in kidneys. Bovine xanthinuria was demonstrated in a local herd and characterized as xanthinuria type II, similar to the Drosophila ma-l mutations, which lose activities of molybdoenzymes, XDH, and aldehyde oxidase, although sulfite oxidase activity is preserved. Linkage analysis located the disease locus at the centromeric region of bovine chromosome 24, where a ma-l homologous, putative molybdopterin cofactor sulfurase gene (MCSU) has been physically mapped. We found that a deletion mutation at tyrosine 257 in MCSU is tightly associated with bovine xanthinuria type II.
Collapse
Affiliation(s)
- T Watanabe
- Shirakawa Institute of Animal Genetics, Odakura, Nishigo, Nishi-shirakawa, Fukushima 961-8061, Japan
| | | | | | | | | |
Collapse
|
10
|
Hirano T, Kobayashi N, Itoh T, Takasuga A, Nakamaru T, Hirotsune S, Sugimoto Y. Null mutation of PCLN-1/Claudin-16 results in bovine chronic interstitial nephritis. Genome Res 2000; 10:659-63. [PMID: 10810088 PMCID: PMC310863 DOI: 10.1101/gr.10.5.659] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Inherited chronic renal diseases are associated with failures in glomerular filtration and tubular resorption. Such failures invariably result from defects in selective filtration and absorption in surface renal epithelium. Recently, we described an autosomal recessive chronic interstitial nephritis with diffuse zonal fibrosis (CINF) in cattle. Bovine CINF, characterized by increased blood urea nitrogen, creatinine, and urinary proteins, leads to lethality before puberty, usually within the first 6 months or year of life. Here, we demonstrate that the first four exons of PCLN-1/Claudin-16 (CL-16), which encodes a member of the claudin family of tight junction proteins, were deleted in CINF-affected cattle. CL-16 was expressed preferentially in kidneys of normal cattle, but transcripts were totally absent in affected offspring. This observation suggests that the lack of CL-16 protein contributes to the dysfunction of paracellular renal transport systems.
Collapse
Affiliation(s)
- T Hirano
- Shirakawa Institute of Animal Genetics, Odakura, Nishigo, Nishi-shirakawa, Fukushima 961-8061, Japan
| | | | | | | | | | | | | |
Collapse
|
11
|
van Hooft WF, Hanotte O, Wenink PW, Groen AF, Sugimoto Y, Prins HH, Teale A. Applicability of bovine microsatellite markers for population genetic studies on African buffalo (Syncerus caffer). Anim Genet 1999; 30:214-20. [PMID: 10442986 DOI: 10.1046/j.1365-2052.1999.00453.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The applicability of bovine autosomal microsatellite markers for population genetic studies on African buffalo was investigated. A total of 168 microsatellite markers were tested for PCR amplification on a test panel of seven African buffalo. Amplification was observed for 139 markers (83%), and 101 markers were studied further with 91 (90%) being polymorphic. The mean number of alleles per marker was 5.0 (SE = 0.2) and the mean heterozygosity per marker was 0.61 (SE = 0.03). Considering the overall high level of polymorphism, it was concluded that most bovine microsatellite markers are applicable in African buffalo.
Collapse
Affiliation(s)
- W F van Hooft
- Wageningen Agricultural University, Department of Environmental Sciences, Wageningen, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
12
|
Yang YP, Rexroad CE, Schläpfer J, Womack JE. An integrated radiation hybrid map of bovine chromosome 19 and ordered comparative mapping with human chromosome 17. Genomics 1998; 48:93-9. [PMID: 9503021 DOI: 10.1006/geno.1997.5143] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We recently constructed a 5000-rad cattle whole-genome radiation hybrid panel with the primary objective of integrating linkage maps of microsatellites with evolutionarily conserved genes into one ordered map. This study utilized the panel to construct a radiation hybrid (RH) map of bovine chromosome 19 (BTA19). Twelve microsatellites from different cattle linkage maps, 15 coding genes, and 2 expressed sequence tags were placed on the BTA19 RH map, with 16 of the markers ordered with odds of at least 1000:1. When the BTA19 RH map was compared with human chromosome 17 cytogenetic and RH maps, rearrangements in linear order were revealed for homologous genes on these two chromosomes that are totally conserved at the level of synteny mapping. Radiation hybrids, which have to date been used almost exclusively in mapping the human genome, are a potentially powerful resource for constructing maps for other species and for ordered comparative mapping between species.
Collapse
Affiliation(s)
- Y P Yang
- Department of Veterinary Pathobiology, Texas A&M University, College Station 77843-4467, USA
| | | | | | | |
Collapse
|
13
|
Martín-Burriel I, Elduque C, Osta R, Laurent P, Barendse W, Zaragoza P. SINEVA polymorphism and mapping of the bovine pregnancy-associated glycoprotein 1 gene. Mamm Genome 1998; 9:179-80. [PMID: 9457691 DOI: 10.1007/s003359900720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- I Martín-Burriel
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Spain
| | | | | | | | | | | |
Collapse
|