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Zhang H, Wang A, Xiao W, Mi S, Hu L, Brito LF, Guo G, Yan Q, Chen S, Wang Y. Genetic parameters and genome-wide association analyses for lifetime productivity in Chinese Holstein cattle. J Dairy Sci 2024:S0022-0302(24)00990-1. [PMID: 39004135 DOI: 10.3168/jds.2023-24632] [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: 12/30/2023] [Accepted: 06/14/2024] [Indexed: 07/16/2024]
Abstract
Lifetime productivity is a trait of great importance to dairy cattle populations as it combines information from production and longevity variables. Therefore, we investigated the genetic background of lifetime productivity in high-producing dairy cattle by integrating genomics and transcriptomics data sets. A total of 3,365,612 test-day milk yield records from 134,029 Chinese Holstein cows were used to define 6 lifetime productivity traits, including lifetime milk yield covering full lifespan and 5 cumulative milk yield traits covering partial lifespan. Genetic parameters were estimated based on univariate and bivariate linear animal models and the Restricted Maximum Likelihood (REML) method. Genome-wide association studies (GWAS) and weighted gene co-expression network analyses (WGCNA) were performed to identify candidate genes associated with lifetime productivity based on genomic data from 3,424 cows and peripheral blood RNA-seq data from 23 cows, respectively. Lifetime milk yield averaged 24,800.8 ± 14,396.6 kg (mean ± SD) across an average of 2.4 parities in Chinese Holstein population. The heritability estimates for lifetime productivity traits ranged from 0.05 (±0.01 for SE) to 0.10 (±0.02 for SE). The estimate of genetic correlation between lifetime milk yield and productive life is 0.88 (±0.3 for SE) while the genetic correlation with 305d milk yield in the first lactation was 0.49 (±0.08 for SE). Absolute values for most genetic correlation estimates between lifetime productivity and type traits were lower than 0.30. Moderate genetic correlations were found between udder related traits and lifetime productivity, such as with udder depth (0.33), rear udder attachment height (0.33), and udder system (0.34). Some single nucleotide polymorphisms and gene co-expression modules significantly associated with lifetime milk yield were identified based on GWAS and WGCNA analyses, respectively. Functional enrichment analyses of the candidate genes identified revealed important pathways related to immune system, longevity, energy utilization and metabolism, and FoxO signaling. The genes NTMT1, FNBP1, and S1PR1 were considered to be the most important candidate genes influencing lifetime productivity in Holstein cows. Overall, our findings indicate that lifetime productivity is heritable in Chinese Holstein cattle and important candidate genes were identified by integrating genomic and transcriptomic data sets.
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Affiliation(s)
- Hailiang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ao Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Weiming Xiao
- Laboratory of Dairy Cattle Genetic Improvement and Milk Quality Research in Zhejiang Province, Wenzhou, China.
| | - Siyuan Mi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lirong Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China; Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Gang Guo
- Beijing Sunlon Livestock Development Company Limited, Beijing, China
| | | | | | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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Gajaweera C, Kang DH, Lee DH, Kim YK, Park BH, Chang SS, Kim UH, Lee SH, Chung KY. Development of nutrigenomic based precision management model for Hanwoo steers. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2023; 65:596-610. [PMID: 37332286 PMCID: PMC10271920 DOI: 10.5187/jast.2023.e38] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/25/2023] [Accepted: 04/13/2023] [Indexed: 06/20/2023]
Abstract
Focusing high marble deposition, Hanwoo feedlot system uses high-energy diet over the prolonged fattening period. However, due to the individual genetic variation, around 40% of them are graded into inferior quality grades (QG), despite they utilized the same resources. Therefore, focusing on development of a nutrigenomic based precision management model, this study was to evaluated the response to the divergent selection on genetic merit for marbling score (MS), under different dietary total digestible nutrient (TDN) levels. Total of 111 calves were genotyped and initially grouped according to estimated breeding value (high and low) for marbling score (MS-EBV). Subsequently, managed under two levels of feed TDN%, over the calf period, early, middle, and final fattening periods following 2 × 2 factorial arrangement. Carcasses were evaluated for MS, Back fat thickness (BFT) and Korean beef quality grading standard. As the direct response to the selection was significant, the results confirmed the importance of initial genetic grouping of Hanwoo steers for MS-EBV. However, dietary TDN level did not show an effect (p > 0.05) on the MS. Furthermore, no genetic-by-nutrition interaction for MS (p > 0.05) was also observed. The present results showed no correlation response on BFT (p > 0.05), which indicates that the selection based on MS-EBV can be used to enhance the MS without undesirable effect on BFT. Ultimate turnover of the Hanwoo feedlot operation is primarily determined by the QGs. The present model shows that the initial grouping for MS-EBV increased the proportion of carcasses graded for higher QGs (QG1++ and QG1+) by approximately 20%. Moreover, there appear to be a potential to increase the proportion of QG 1++ animals among the high-genetic group by further increasing the dietary energy content. Overall, this precision management strategy suggests the importance of adopting an MS based initial genetic grouping system for Hanwoo steers with a subsequent divergent management based on dietary energy level.
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Affiliation(s)
- Chandima Gajaweera
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
- Department of Animal Science, Faculty of Agriculture, University of Ruhuna, Matara 81100, Sri Lanka
| | - Dong Hun Kang
- Department of Livestock, Korea National University of Agriculture and Fisheries, Jeonju 54874, Korea
| | - Doo Ho Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Yeong-Kuk Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Bo Hye Park
- Department of Livestock, Korea National University of Agriculture and Fisheries, Jeonju 54874, Korea
| | - Sun Sik Chang
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang 25340, Korea
| | - Ui Hyung Kim
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang 25340, Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Ki Yong Chung
- Department of Livestock, Korea National University of Agriculture and Fisheries, Jeonju 54874, Korea
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Association of SNPs in AKIRIN2, TTN, EDG1 and MYBPC1 genes with growth and carcass traits in Qinchuan cattle. ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2021-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Growth and carcass traits are the main breeding objectives in beef cattle. The aim of this study was to confirm genetic effects of the c.*188G>A SNP of AKIRIN2, the g.231054C>T SNP of TTN, the g.1471620G>T SNP of EDG1 and the g.70014208A>G SNP of MYBPC1 on growth and carcass traits in Chinese Qinchuan (QC) cattle, as well as to compare the frequencies of the well-characterized alleles of these SNPs among six Chinese cattle populations, three Japanese cattle populations, two European cattle populations and one Korean cattle population. In this study, a total of 665 cattle samples were genotyped using MassARRAY and PCR-RFLP. Association analysis explored effects of four SNPs on growth and carcass traits including body length, wither height, hip height, hip width, rump length, chest depth, chest circumference, back fat thickness, ultrasound longissimus muscle area and ultrasound longissimus muscle depth in QC (P<0.05 to P<0.001). The well-characterized A (c.*188G>A), T (g.231054C>T) and T (g.1471620G>T) alleles in Japanese Black cattle were significantly higher than Chinese cattle breeds, on the contrary, the G allele (g.70014208A>G) was markedly higher in Chinese cattle breeds than other cattle breeds. These results suggest that the four SNPs might be useful as a molecular marker for growth-related traits in Chinese QC cattle.
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Kawaguchi F, Tsuchimura M, Oyama K, Matsuhashi T, Maruyama S, Mannen H, Sasazaki S. Effect of DNA markers on the fertility traits of Japanese Black cattle for improving beef quantity and quality. Arch Anim Breed 2020; 63:9-17. [PMID: 32166108 PMCID: PMC7053510 DOI: 10.5194/aab-63-9-2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/22/2019] [Indexed: 11/12/2022] Open
Abstract
Carcass traits have been efficiently improved by recent selection using DNA
markers in beef cattle. Additionally, DNA markers might have an effect on other
traits such as fertility traits; therefore attention should also be paid
to such pleiotropic effects. However, the effects of the markers on both
carcass and fertility traits have never been evaluated in the same
population, since they are generally measured in different populations. The
objective in the current study was to discuss effectiveness of DNA markers
developed for carcass traits through investigation of their effects on
carcass and fertility traits in a population. We genotyped six markers SCD
V293A, FASN g.841G>C, PLAG1 g.49066C>G, NCAPG I442M, DGAT1 K232A, and
EDG1 g.1471620G>T in a Japanese Black cattle population (n=515). To
investigate their effects on carcass and fertility traits, we performed
statistical analysis (ANOVA and the Tukey–Kramer honestly significant difference (HSD) test). In the results,
three of six markers, SCD V293A, NCAPG I442M, and EGD1 g.1471620G>T, were
significantly associated with both carcass and fertility traits.
Remarkably, the same allele for each marker had positive effects on both
traits, suggesting that we would be able to simultaneously improve them
using these markers in this population. However, previous studies reported
that the effects of DNA markers could differ among populations. Therefore,
it is necessary to confirm the effect of the marker in each population
before it is used for improvement.
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Affiliation(s)
- Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Miyako Tsuchimura
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Kenji Oyama
- Food Resources Education & Research Center, Kobe University, Kasai, 657-2103, Japan
| | - Tamako Matsuhashi
- Institute of Advanced Technology, Kindai University, Kinokawa, 649-6493, Japan.,Gifu Prefectural Livestock Research Institute, Takayama, 506-0101, Japan
| | - Shin Maruyama
- Gifu Prefectural Livestock Research Institute, Takayama, 506-0101, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
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Tsuda K, Kawahara-Miki R, Sano S, Imai M, Noguchi T, Inayoshi Y, Kono T. Abundant sequence divergence in the native Japanese cattle Mishima-Ushi (Bos taurus) detected using whole-genome sequencing. Genomics 2013; 102:372-8. [PMID: 23938316 DOI: 10.1016/j.ygeno.2013.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/06/2013] [Accepted: 08/02/2013] [Indexed: 12/30/2022]
Abstract
The native Japanese cattle Mishima-Ushi, a designated national natural treasure, are bred on a remote island, which has resulted in the conservation of their genealogy. We examined the genetic characteristics of 8 Mishima-Ushi individuals by using single nucleotide polymorphisms (SNPs), insertions, and deletions obtained by whole-genome sequencing. Mapping analysis with various criteria showed that predicted heterozygous SNPs were more prevalent than predicted homozygous SNPs in the exonic region, especially non-synonymous SNPs. From the identified 6.54 million polymorphisms, we found 400 non-synonymous SNPs in 313 genes specific to each of the 8 Mishima-Ushi individuals. Additionally, 3,170,833 polymorphisms were found between the 8 Mishima-Ushi individuals. Phylogenetic analysis confirmed that the Mishima-Ushi population diverged from another strain of Japanese cattle. This study provides a framework for further genetic studies of Mishima-Ushi and research on the function of SNP-containing genes as well as understanding the genetic relationship between the domestic and native Japanese cattle breeds.
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Affiliation(s)
- Kaoru Tsuda
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
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