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Guo X, Li T, Lu D, Yamada T, Li X, Bao S, Liu J, Borjigin G, Cang M, Tong B. Effects of the Expressions and Variants of the CAST Gene on the Fatty Acid Composition of the Longissimus Thoracis Muscle of Grazing Sonid Sheep. Animals (Basel) 2023; 13:ani13020195. [PMID: 36670735 PMCID: PMC9855194 DOI: 10.3390/ani13020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/20/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Fatty acid (FA) composition has an important impact on the nutrition and flavor of meat, and on consumer health, and is receiving more attention in the sheep industry. This study aimed to evaluate the relationship between the expression levels of the CAST gene and the FA composition in the longissimus thoracis (LL) muscle, to identify novel variants of CAST, and to perform association analysis with the FA composition in grazing Sonid lambs. The correlation results showed that high expression levels of CAST are correlated with better FA compositions and classes in LL. For association studies, the results showed that c.1210C>T and c.1437G>A in LD-M, and c.2097C>T mutations are associated with some compositions and classes of FA in the LL of grazing Sonid sheep. Two missense c.646G>C (G216R) and c.1210C>T (R404C) mutations were predicted to influence the Calpain_inhib domains of CAST. Thus, the correlation results and associated mutations are expected to be genetic selection markers for the FA composition and meat quality of grazing Sonid lamb muscle and provide new insights into sheep meat quality traits influenced by the ovine CAST gene.
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Affiliation(s)
- Xin Guo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Terigele Li
- Inner Mongolia Agriculture Animal Husbandry Fishery and Biology Experiment Research Centre, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Datong Lu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Takahisa Yamada
- Department of Agrobiology, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Xihe Li
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Siqin Bao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Jiasen Liu
- Institute of Animal Science, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Gerelt Borjigin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Ming Cang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
- Correspondence: (M.C.); (B.T.)
| | - Bin Tong
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
- Correspondence: (M.C.); (B.T.)
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Sustained Effects of Muscle Calpain System Genotypes on Tenderness Phenotypes of South African Beef Bulls during Ageing up to 20 Days. Animals (Basel) 2022; 12:ani12060686. [PMID: 35327083 PMCID: PMC8944438 DOI: 10.3390/ani12060686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/25/2022] [Accepted: 02/02/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary When searching for genetic markers for the selection of more tender beef, it is important to maintain minimal environmental variation from pre-slaughter, right through to the ageing process, to ensure the accuracy of the obtained phenotypes. This is because beef quality traits have a large environmental component that can greatly alter the characteristics of the meat, which would not reflect a true genetic effect. We propose that variable ageing times are especially important in determining whether markers are associated with tenderization or not. Our analyses included candidate genes for the protein degrading enzyme system for calpains, because they contribute the most to tenderization. We were able to validate these markers in South African beef cattle, where they could be useful for selection. The timing of the collection of tenderness data was critical, as only a few (6/134) genetic markers sustained their association with tenderization over ageing to 20 days. A larger tenderization effect earlier in ageing, as shown here for the capn1_187 and capn1_4751 markers, would decrease the length of ageing. This would not only increase profits, but also decrease the energy needed during the storage and refrigeration of aged beef, decreasing the carbon footprint of beef production. Abstract The most important factor that determines beef tenderness is its proteolytic activity, and the balance between calpain-1 protease activity and calpastatin inhibition is especially important, while contributions can also arise from calpain-2 and, possibly, calpain-3. The meat ageing process itself affects these processes. To determine whether genotypes in the calpain–calpastatin system can enhance tenderness through a 20-day ageing period, South African purebred beef bulls (n = 166) were genotyped using the Illumina BovineHD SNP BeadChip through a gene-based association analysis targeting the cast, capn3, capn2 and capn1 genes. The Warner–Bratzler shear force (WBSF) and myofibril fragment length (MFL) of Longissimus thoracis et lumborum (LTL) steaks were evaluated between d 3 and d 20 of ageing, with protease enzyme activity in the first 20 h post-mortem. Although several of the 134 SNPs are associated with tenderness, only seven SNP in the cast, capn2 and capn1 genes sustained genetic associations, additive to the ageing-associated increases in tenderness for at least three of the four ageing periods. While most genomic associations were relatively stable over time, some genotypes within the SNP responded differently to ageing, resulting in altered genomic effects over time. The level of ageing at which genomic associations are performed is an important factor that determines whether SNPs affect tenderness phenotypes.
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Seong HS, Kim NY, Kim DC, Hwang NH, Son DH, Shin JS, Lee JH, Chung WH, Choi JW. Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski's horse. Genes Genomics 2019; 41:621-628. [PMID: 30941726 DOI: 10.1007/s13258-019-00795-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 02/11/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds. OBJECTIVE The objective of this study was to report genomic characteristics of domestic horse populations that inhabit South Korea (Jeju, Jeju crossbred, and Thoroughbred) and a wild horse breed (Przewalski's horse). RESULTS Using the equine reference genome assembly (EquCab 2.0), more than ~ 6.5 billion sequence reads were successfully mapped, which generated an average of 40.87-fold coverage throughout the genome. Using these data, we detected a total of 12.88 million SNPs, of which 73.7% were found to be novel. All the detected SNPs were deeply annotated to retrieve SNPs in gene regions using the RefSeq and Ensemble gene sets. Approximately 27% of the total SNPs were located within genes, whereas the remaining 73% were found in intergenic regions. Using 129,776 coding SNPs, we retrieved a total of 49,171 nonsynonymous SNPs in 12,351 genes. Furthermore, we identified a total of 10,770 deleterious nonsynonymous SNPs which are predicted to affect protein structure or function. CONCLUSION We showed numerous genomic variants from domestic and wild horse breeds. These results provide a valuable resource for further studies on functions of SNP-containing genes, and can aid in determining the molecular basis underlying variation in economically important traits of horses.
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Affiliation(s)
- Ha-Seung Seong
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Nam-Young Kim
- Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 690-150, Republic of Korea
| | - Dae Cheol Kim
- Jeju Special Self-Governing Province Livestock Promotion, Jeju, Republic of Korea
| | - Nam-Hyun Hwang
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Da-Hye Son
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jong Suh Shin
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Joon-Hee Lee
- Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Won-Hyong Chung
- Division of Food Functionality Research, Research Group of Healthcare, Wanju-gun, 55365, Republic of Korea.
| | - Jung-Woo Choi
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Sun X, Wu X, Fan Y, Mao Y, Ji D, Huang B, Yang Z. Effects of polymorphisms in CAPN1 and CAST genes on meat tenderness of Chinese Simmental cattle. Arch Anim Breed 2018; 61:433-439. [PMID: 32175450 PMCID: PMC7065412 DOI: 10.5194/aab-61-433-2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022] Open
Abstract
Considerable evidence has demonstrated that the μ -calpain (CAPN1) gene and its inhibitor calpastatin (CAST) gene are major factors affecting meat quality. Marker-assisted selection (MAS) has been widely used to improve beef quality traits. Therefore, the objective of the present study was to investigate the single nucleotide polymorphisms (SNPs) of bovine CAPN1 and CAST genes using 367 animals representing the four main Chinese cattle breeds and to explore the effects of these SNPs on meat quality traits. Two SNPs within CAPN1 and one SNP in CAST were successfully identified in cattle. Genetic diversity analyses suggested that most SNPs in the four breeds exhibited a moderate genetic diversity. Moreover, associations between individual markers and meat quality traits were analyzed in Chinese Simmental cattle. The CAPN1 4558 A > G locus was found to be significantly associated with shear force value (SFV) and marbling score (BMS), and CAPN1 4684 C > T exerted a significant effect on SFV, while the CAST genotype was not significantly associated with any of the measured traits. SFV, commonly used to measure meat tenderness, represents an important quality trait as it contributes to the flavor of cooked meat. This work confirms the effect of CAPN1 on beef tenderness and lays an important foundation for future cattle breeding.
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Affiliation(s)
- Xiaomei Sun
- Key Lab of Animal Genetics, Breeding & Molecular Design of Jiangsu
Province, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product
Safety of Ministry of Education of China, Yangzhou University, Yangzhou
225002, China
| | - Xiuxiang Wu
- Department of Neurobiology, Xuzhou Medical College, Xuzhou 221004,
Jiangsu, China
| | - Yongliang Fan
- Key Lab of Animal Genetics, Breeding & Molecular Design of Jiangsu
Province, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product
Safety of Ministry of Education of China, Yangzhou University, Yangzhou
225002, China
| | - Yongjiang Mao
- Key Lab of Animal Genetics, Breeding & Molecular Design of Jiangsu
Province, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product
Safety of Ministry of Education of China, Yangzhou University, Yangzhou
225002, China
| | - Dejun Ji
- Key Lab of Animal Genetics, Breeding & Molecular Design of Jiangsu
Province, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product
Safety of Ministry of Education of China, Yangzhou University, Yangzhou
225002, China
| | - Bizhi Huang
- Academe of grassland and animal science, Kunming 650000, China
| | - Zhangping Yang
- Key Lab of Animal Genetics, Breeding & Molecular Design of Jiangsu
Province, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product
Safety of Ministry of Education of China, Yangzhou University, Yangzhou
225002, China
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Wang J, Elzo MA, Jia X, Chen S, Lai S. Calpastatin gene polymorphism is associated with rabbit meat quality traits. JOURNAL OF APPLIED ANIMAL RESEARCH 2016. [DOI: 10.1080/09712119.2016.1191498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Jie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Mauricio A. Elzo
- Department of Animal Science, University of Florida, Gainesville, FL, USA
| | - Xianbo Jia
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Shiyi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Songjia Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
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