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Pauciullo A, Gaspa G, Zhang Y, Liu Q, Cosenza G. CSN1S1, CSN3 and LPL: Three Validated Gene Polymorphisms Useful for More Sustainable Dairy Production in the Mediterranean River Buffalo. Animals (Basel) 2024; 14:1414. [PMID: 38791632 PMCID: PMC11117199 DOI: 10.3390/ani14101414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The search for DNA polymorphisms useful for the genetic improvement of dairy farm animals has spanned more than 40 years, yielding relevant findings in cattle for milk traits, where the best combination of alleles for dairy processing has been found in casein genes and in DGAT1. Nowadays, similar results have not yet been reached in river buffaloes, despite the availability of advanced genomic technologies and accurate phenotype records. The aim of the present study was to investigate and validate the effect of four single nucleotide polymorphisms (SNP) in the CSN1S1, CSN3, SCD and LPL genes on seven milk traits in a larger buffalo population. These SNPs have previously been reported to be associated with, or affect, dairy traits in smaller populations often belonging to one farm. A total of 800 buffaloes were genotyped. The following traits were individually recorded, monthly, throughout each whole lactation period from 2010 to 2021: daily milk yield (dMY, kg), protein yield (dPY, kg) and fat yield (dFY, kg), fat and protein contents (dFP, % and dPP, %), somatic cell count (SCC, 103 cell/mL) and urea (mg/dL). A total of 15,742 individual milk test day records (2496 lactations) were available for 680 buffalo cows, with 3.6 ± 1.7 parities (from 1 to 13) and an average of 6.1 ± 1.2 test day records per lactation. Three out four SNPs in the CSN1S1, CSN3 and LPL genes were associated with at least one of analyzed traits. In particular, the CSN1S1 (AJ005430:c.578C>T) gave favorable associations with all yield traits (dMY, p = 0.022; dPY, p = 0.014; dFY, p = 0.029) and somatic cell score (SCS, p = 0.032). The CSN3 (HQ677596: c.536C>T) was positively associated with SCS (p = 0.005) and milk urea (p = 0.04). Favorable effects on daily milk yield (dMY, p = 0.028), fat (dFP, p = 0.027) and protein (dPP, p = 0.050) percentages were observed for the LPL. Conversely, the SCD did not show any association with milk traits. This is the first example of a confirmation study carried out in the Mediterranean river buffalo for genes of economic interest in the dairy field, and it represents a very important indication for the preselection of young bulls destined for breeding programs aimed at more sustainable dairy production.
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Affiliation(s)
- Alfredo Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Turin, 10095 Grugliasco, Italy
| | - Giustino Gaspa
- Department of Agricultural, Forest and Food Sciences, University of Turin, 10095 Grugliasco, Italy
| | - Yi Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qingyou Liu
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Gianfranco Cosenza
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy
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Chen R, Liu J, Zhang Y, Cai W, Zhang X, Xu Y, Dou X, Wang Z, Han D, Wang J, Lin G, Wang L, Sun Y, Bai Z, Gu M, Wang Z. Association analysis between reproduction genes INHA, PGR, RARG with lamb and other traits of Liaoning cashmere goats. Anim Biotechnol 2023; 34:2094-2105. [PMID: 35622393 DOI: 10.1080/10495398.2022.2077212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Reproductive traits have a high economic value in goat breeding, and increasing the number of lambs produced by ewes is of great importance to improve the production efficiency of goat farming. Lambing traits in goats are low heritability traits, but their genetic basis is ultimately determined by genes. This study aimed to investigate the relationship between INHA, RARG, and PGR gene polymorphisms and production performance, such as lambing, cashmere production, milk production, and body size in Liaoning cashmere goats. A total of six single nucleotide polymorphisms (SNPs) loci were identified in these three genes, G144A and T504C on the INHA gene, A56G, G144A, G490C on the RARG gene, and G109519T on the PGR gene. For lambing and cashmere production traits, the AA genotype of G144A on the INHA gene, TT on the T504C genotype, GG genotype of G144A on the INHA gene, A56G, G144A, and T504C on RARG and G109519T on PGR gene are dominant genotypes. AATT is a dominant haplotype combination. Allele G can be used as a molecular marker for lambing, cashmere, and milk production traits in Liaoning cashmere goats. Marker-assisted selection can be used for early selection to achieve improvement of genetic traits in Liaoning cashmere goats.
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Affiliation(s)
- Rui Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jichang Liu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yurou Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Weidong Cai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xinjiang Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanan Xu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xingtang Dou
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Zhanhong Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Di Han
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Jiaming Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Guangyu Lin
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Lingling Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Yinggang Sun
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhixian Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ming Gu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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Brzáková M, Rychtářová J, Čítek J, Sztankóová Z. A Candidate Gene Association Study for Economically Important Traits in Czech Dairy Goat Breeds. Animals (Basel) 2021; 11:ani11061796. [PMID: 34208578 PMCID: PMC8234603 DOI: 10.3390/ani11061796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/25/2022] Open
Abstract
Milk production is influenced by many factors, including genetic and environmental factors and their interactions. Animal health, especially udder health, is usually evaluated by the number of somatic cells. The present study described the effect of polymorphisms in the ACACA, BTN1A1, LPL, and SCD genes on the daily milk yield, fat, and protein percentages and somatic cell count. In this study, 590 White Shorthaired (WSH) and Brown Shorthaired (BSH) goats were included. SNP genotyping was performed by PCR-RFLP and multiplex PCR followed by SNaPshot minisequencing analysis. The linear mixed model with repeated measurement was used to identify the genetic associations between the studied genes/SNPs and chosen traits. All selected genes were polymorphic in the tested goat populations and showed significant associations with milk traits. Only BTN1A1 (SNP g.599 A > G) showed a significant association with the somatic cell score. After Bonferroni correction, a significant effect of LPL g.300G > A on daily milk yield and fat percentage, LPL g.185G > T on protein percentage, and LPL G50C, SCD EX3_15G > A, and SCD EX3_68A > G on fat percentage was found. The importance of environmental factors, such as the herd-year effect, month of milking, and lactation order on all milk performance indicators was confirmed.
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Affiliation(s)
- Michaela Brzáková
- Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, 104 00 Prague, Czech Republic;
- Correspondence: ; Tel.: +420-606-794059
| | - Jana Rychtářová
- Department of Biology of Reproduction, Institute of Animal Science, 104 00 Prague, Czech Republic;
| | - Jindřich Čítek
- Department of Genetics and Agricultural Biotechnologies, Faculty of Agriculture, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic;
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, 621 00 Brno, Czech Republic
| | - Zuzana Sztankóová
- Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, 104 00 Prague, Czech Republic;
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Gu M, Cosenza G, Gaspa G, Iannaccone M, Macciotta NPP, Chemello G, Di Stasio L, Pauciullo A. Sequencing of lipoprotein lipase gene in the Mediterranean river buffalo identified novel variants affecting gene expression. J Dairy Sci 2020; 103:6374-6382. [PMID: 32418698 DOI: 10.3168/jds.2019-17968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/13/2020] [Indexed: 01/23/2023]
Abstract
Lipoprotein lipase (LPL) is a key enzyme for lipid metabolism, playing a fundamental role in the composition of fat in adipose tissue and milk. The LPL gene has been seldom investigated in dairy ruminants and barely studied in river buffalo (Bubalus bubalis). The aim of this work was to explore the genetic diversity of LPL and its promoter and to identify functional mutations, using a combined approach based on sequencing, dual-color electrophoretic mobility shift assay, and quantitative PCR. Thirteen consensus sequences for transcription factors were found in the promoter. Eleven SNP were detected, and the attention was focused on the SNP with potential functional effects: g.-446A>G, because the presence of G created a consensus motif for the transcription factor Sp1, and g.107A>G, which was the only exonic SNP. We developed PCR-RFLP methods for genotyping the 2 SNP and calculated the allele frequencies. A strong linkage disequilibrium (D' = 1; r2 = 0.903) was found between the 2 SNP. The dual-color electrophoretic mobility shift assay demonstrated that only genotype g.-446GG allowed the binding of the Sp1 transcription factor, resulting in overexpression of the gene (~2.5 fold), as confirmed by the quantitative PCR results. Haploinsufficiency is proposed as a regulation mechanism. This study adds further knowledge on the structure of the LPL gene and its expression in river buffalo, with potential effects on milk qualitative and quantitative production.
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Affiliation(s)
- M Gu
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy; School of Life Science, Peking University, 100871 Beijing, China
| | - G Cosenza
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy
| | - G Gaspa
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy
| | - M Iannaccone
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy
| | - N P P Macciotta
- Department of Agricultural Sciences, University of Sassari, 07100, Sassari, Italy
| | - G Chemello
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy
| | - L Di Stasio
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy
| | - A Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy; National Research Council of Italy, Istituto per il Sistema Produzione Animale in Ambiente Mediterraneo, Laboratory of Animal Cytogenetic and Gene Mapping, 80147 Naples, Italy.
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SINGH KARANVEER, JAYAKUMAR S, DIXIT SP, MALIK ZS. SNPs association studies in promoter III of the acetyl coenzyme-A carboxylase-α gene (ACACA) in Munjal–A threatened sheep population of India. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i7.81481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Yan Q, Tang S, Tan Z, Zhou C, Basang Z, Ao S, Hou S. Replacement of oat grass with highland barley straw: effects on lipid profiles, FA composition and lipogenetic genes expression in Tibetan sheep. ITALIAN JOURNAL OF ANIMAL SCIENCE 2017. [DOI: 10.1080/1828051x.2017.1412274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Qiongxian Yan
- South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Research Center of Livestock & Poultry Sciences, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, China
- Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Changsha, China
| | - Shaoxun Tang
- South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Research Center of Livestock & Poultry Sciences, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, China
- Hunan Co-Innovation Center of Animal Production Safety, CICAPS, Changsha, China
| | - Zhiliang Tan
- South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Research Center of Livestock & Poultry Sciences, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, China
- Hunan Co-Innovation Center of Animal Production Safety, CICAPS, Changsha, China
| | - Chuanshe Zhou
- South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Research Center of Livestock & Poultry Sciences, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, China
- Hunan Co-Innovation Center of Animal Production Safety, CICAPS, Changsha, China
| | - Zhuzha Basang
- Department of Animal Science and Veterinary Medicine, Tibetan Autonomous Prefecture Academy of Agricultural and Animal Husbandry Science, Lhasa, Tibet
| | - Siman Ao
- Department of Animal Science and Veterinary Medicine, Tibetan Autonomous Prefecture Academy of Agricultural and Animal Husbandry Science, Lhasa, Tibet
| | - Shengzhen Hou
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, China
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Avilés C, Horcada A, Polvillo O, Membrillo A, Anaya G, Molina A, Alcalde M, Panea B. Association study between variability in the SCD gene and the fatty acid profile in perirenal and intramuscular fat deposits from Spanish goat populations. Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2016.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/904281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Goat genomics has evolved at a low pace because of a lack of molecular tools and sufficient investment. Whilst thousands and hundreds of quantitative trait loci (QTL) have been identified in cattle and sheep, respectively, about nine genome scans have been performed in goats dealing with traits as conformation, growth, fiber quality, resistance to nematodes, and milk yield and composition. In contrast, a great effort has been devoted to the characterization of candidate genes and their association with milk, meat, and reproduction phenotypes. In this regard, causal mutations have been identified in the αS1-casein gene that has a strong effect on milk composition and the PIS locus that is linked to intersexuality and polledness. In recent times, the development of massive parallel sequencing technologies has allowed to build a reference genome for goats as well as to monitor the expression of mRNAs and microRNAs in a broad array of tissues and experimental conditions. Besides, the recent design of a 52K SNP chip is expected to have a broad impact in the analysis of the genetic architecture of traits of economic interest as well as in the study of the population structure of goats at a worldwide scale.
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