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Kinukawa M, Ito M, Uemoto Y, Ogino A, Haruta S, Kurogi K, Watanabe T, Sasaki S, Naniwa Y, Uchiyama K, Togashi K. A potent allele marker related to low bull conception rate in Japanese Black bulls. Animal 2023; 17:100804. [PMID: 37141635 DOI: 10.1016/j.animal.2023.100804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Over the years, there has been considerable variation in the bull conception rate (BCR) of Japanese Black cattle; moreover, several Japanese Black bulls with a low BCR of ≤10% have been identified. However, the alleles responsible for the low BCR are not determined yet. Therefore, in this study, we aimed to identify single-nucleotide polymorphisms (SNPs) for predicting low BCR. To this end, the genome of Japanese Black bulls was comprehensively examined by a genome-wide association study with whole-exome sequencing (WES), and the effect of the identified marker regions on BCR was determined. The WES analysis of six sub-fertile bulls with a BCR of ≤10% and 73 normal bulls with a BCR of ≥40% identified a homozygous genotype for low BCR in Bos taurus autosome 5 in the region between 116.2 and 117.9 Mb. The g.116408653G > A SNP in this region had the most significant effect on the BCR (P-value = 1.0 × 10-23), and the GG (55.4 ± 11.2%) and AG (54.4 ± 9.4%) genotypes in the SNP had a higher phenotype than the AA (9.5 ± 6.1%) genotype for the BCR. The mixed model analysis revealed that g.116408653G > A was related to approximately 43% of the total genetic variance. In conclusion, the AA genotype of g.116408653G > A is a useful index for identifying sub-fertile Japanese Black bulls. Some positive and negative effects of SNP on the BCR were presumed to identify the causative mutations, which can help evaluate bull fertility.
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Affiliation(s)
- M Kinukawa
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan.
| | - M Ito
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Y Uemoto
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan
| | - A Ogino
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - S Haruta
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - K Kurogi
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - T Watanabe
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - S Sasaki
- Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Y Naniwa
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - K Uchiyama
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - K Togashi
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
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Sasaki S, Haga Y, Wakaguri H, Abe K, Suzuki Y. De Novo Genome Assembly of Japanese Black Cattle as Model of an Economically Relevant Animal. Methods Mol Biol 2023; 2632:41-55. [PMID: 36781720 DOI: 10.1007/978-1-0716-2996-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
A genetic analysis of Japanese Black cattle using short reads and guided by the reference genome from Western breeds would miss the structural variation and/or other unique characteristics of Japanese Black cattle. To overcome this difficulty, a de novo genome assembly independent from the reference genome is required. This chapter describes the technical developments, with respect to both experimental and bioinformatics procedures, including the use of short and long reads, required for de novo genome assembly of Japanese Black cattle.
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Affiliation(s)
- Shinji Sasaki
- University of the Ryukyus, Faculty of Agriculture, Okinawa, Japan.,United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Yasuhiko Haga
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hiroyuki Wakaguri
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kazumi Abe
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
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Ogawa S, Taniguchi Y, Watanabe T, Iwaisaki H. Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle. Genes (Basel) 2022; 14:24. [PMID: 36672767 PMCID: PMC9859149 DOI: 10.3390/genes14010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
We fitted statistical models, which assumed single-nucleotide polymorphism (SNP) marker effects differing across the fattened steers marketed into different prefectures, to the records for cold carcass weight (CW) and marbling score (MS) of 1036, 733, and 279 Japanese Black fattened steers marketed into Tottori, Hiroshima, and Hyogo prefectures in Japan, respectively. Genotype data on 33,059 SNPs was used. Five models that assume only common SNP effects to all the steers (model 1), common effects plus SNP effects differing between the steers marketed into Hyogo prefecture and others (model 2), only the SNP effects differing between Hyogo steers and others (model 3), common effects plus SNP effects specific to each prefecture (model 4), and only the effects specific to each prefecture (model 5) were exploited. For both traits, slightly lower values of residual variance than that of model 1 were estimated when fitting all other models. Estimated genetic correlation among the prefectures in models 2 and 4 ranged to 0.53 to 0.71, all <0.8. These results might support that the SNP effects differ among the prefectures to some degree, although we discussed the necessity of careful consideration to interpret the current results.
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Affiliation(s)
- Shinichiro Ogawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, Tsukuba 305-0901, Japan
| | - Yukio Taniguchi
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Toshio Watanabe
- National Livestock Breeding Center, Fukushima 961-8511, Japan
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi 371-0121, Japan
| | - Hiroaki Iwaisaki
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Sado Island Center for Ecological Sustainability, Niigata University, Niigata 952-0103, Japan
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Amaral TF, de Grazia JGV, Martinhao LAG, De Col F, Siqueira LGB, Viana JHM, Hansen PJ. Actions of CSF2 and DKK1 on bovine embryo development and pregnancy outcomes are affected by composition of embryo culture medium. Sci Rep 2022; 12:7503. [PMID: 35525843 PMCID: PMC9079070 DOI: 10.1038/s41598-022-11447-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/25/2022] [Indexed: 12/29/2022] Open
Abstract
Procedures for in vitro embryo production in cattle have not been optimized. In the current experiment, we utilized a 3 × 3 factorial design to test whether the proportion of embryos becoming blastocysts in culture and the pregnancy rate after embryo transfer are affected by type of serum in the medium [no serum; 3% (v/v) KnockOut Serum Replacement (SR); 3% (v/v) fetal bovine serum (FBS)] and addition of specific embryokines [vehicle; 10 ng/mL colony stimulating factor 2 (CSF2); 100 ng/mL dickkopf related protein 1 (DKK1)] at day 5 of culture. Embryos were produced using abattoir-derived ovaries and Y-sorted semen from two Angus sires. The percent of putative zygotes and cleaved embryos becoming blastocysts was improved by SR and FBS. Pregnancy rate at day 30 was determined for 1426 Nelore recipients and calving rate for 266 recipients. In the absence of CSF2 or DKK1, pregnancy rates were lower for embryos cultured with SR or FBS. CSF2 and DKK1 reduced pregnancy rate for embryos cultured without serum but had no detrimental effect in the SR or FBS groups. Indeed, CSF2 blocked the negative effect of FBS on pregnancy rate. Data on birth weights were available for 67 bull calves. There were no effects of treatment. The sire used to produce embryos had significant and large effects on development to the blastocyst stage, pregnancy rate at day 30, calving rate and pregnancy loss between day 30 and calving. Results indicate that (1) SR and FBS can improve embryonic development in vitro while also compromising competence of embryos to survive after transfer, (2) actions of CSF2 and DKK1 depend upon other characteristics of the embryo production system, and (3) sire can have a large effect on embryonic development before and after transfer.
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Affiliation(s)
- Thiago F Amaral
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Research Program, and Genetics Institute, University of Florida, Gainesville, FL, 32611-0910, USA
- Zoetis, Kalamazoo, MI, 49007, USA
| | | | - Luany Alves Galvao Martinhao
- FIVX Apoyar Biotech LTDA, Juiz de Fora, MG, Brazil
- Biological Science Institute, University of Brasilia, Brasilia, DF, Brazil
| | | | | | | | - Peter J Hansen
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Research Program, and Genetics Institute, University of Florida, Gainesville, FL, 32611-0910, USA.
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