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Zhou F, Fan X, Xu X, Li Z, Qiu L, Miao Y. Molecular Characteristics and Polymorphisms of Buffalo ( Bubalus bubalis) ABCG2 Gene and Its Role in Milk Fat Synthesis. Animals (Basel) 2023; 13:3156. [PMID: 37835762 PMCID: PMC10571847 DOI: 10.3390/ani13193156] [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: 08/30/2023] [Revised: 09/24/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
The ATP-binding cassette subfamily G member 2 (ABCG2) serves crucial roles in secreting riboflavin and biotin vitamins into the milk of cattle, mice, and humans, as well as in the transportation of xenotoxic and cytostatic drugs across the plasma membrane. However, the specific role of the ABCG2 gene in water buffaloes (Bubalus bubalis), especially its effect on milk fat synthesis in buffalo mammary epithelial cells (BuMECs), remains inadequately understood. In this study, the full-length CDS of the buffalo ABCG2 gene was isolated and identified from the mammary gland in buffaloes. A bioinformatics analysis showed a high degree of similarity in the transcriptional region, motifs, and conservative domains of the buffalo ABCG2 with those observed in other Bovidae species. The functional role of buffalo ABCG2 was associated with the transportation of solutes across lipid bilayers within cell membranes. Among the 11 buffalo tissues detected, the expression levels of ABCG2 were the highest in the liver and brain, followed by the mammary gland, adipose tissue, heart, and kidney. Notably, its expression in the mammary gland was significantly higher during peak lactation than during non-lactation. The ABCG2 gene was identified with five SNPs in river buffaloes, while it was monomorphic in swamp buffaloes. Functional experiments revealed that ABCG2 increased the triglyceride (TAG) content by affecting the expression of liposynthesis-related genes in BuMECs. The results of this study underscore the pivotal role of the ABCG2 gene in influencing the milk fat synthesis in BuMECs.
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Affiliation(s)
- Fangting Zhou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (F.Z.); (X.F.); (X.X.); (Z.L.); (L.Q.)
- College of Chemistry, Biology and Environment, Yuxi Normal University, Yuxi 653100, China
| | - Xinyang Fan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (F.Z.); (X.F.); (X.X.); (Z.L.); (L.Q.)
| | - Xiaoqi Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (F.Z.); (X.F.); (X.X.); (Z.L.); (L.Q.)
| | - Zhuoran Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (F.Z.); (X.F.); (X.X.); (Z.L.); (L.Q.)
| | - Lihua Qiu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (F.Z.); (X.F.); (X.X.); (Z.L.); (L.Q.)
| | - Yongwang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (F.Z.); (X.F.); (X.X.); (Z.L.); (L.Q.)
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Bozhilova-Sakova M, Dimitrova I, Stancheva N, Ignatova M, Ivanova T. 35-bp deletion in ABCG2 gene: mini-review and report on two herds of Bulgarian dairy synthetic population sheep breed. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2107949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Milena Bozhilova-Sakova
- Department of Genetics, Breeding and Reproduction, Institute of Animal Science, Agricultural Academy, Kostinbrod, Bulgaria
| | - Ivona Dimitrova
- Agronomy Faculty, Department of Plant Protection, University of Forestry, Sofia, Bulgaria
| | - Nevyana Stancheva
- Department of Animal Science, Agricultural Academy, Agricultural Institute, Shumen, Bulgaria
| | - Maya Ignatova
- Department of Genetics, Breeding and Reproduction, Institute of Animal Science, Agricultural Academy, Kostinbrod, Bulgaria
| | - Tanya Ivanova
- Department of Genetics, Breeding and Reproduction, Institute of Animal Science, Agricultural Academy, Kostinbrod, Bulgaria
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Single Nucleotide Polymorphisms, Gene Expression and Economic Evaluation of Parameters Associated with Mastitis Susceptibility in European Cattle Breeds. Vet Sci 2022; 9:vetsci9060294. [PMID: 35737346 PMCID: PMC9229636 DOI: 10.3390/vetsci9060294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022] Open
Abstract
The objective of this study was to explore single nucleotide polymorphisms (SNPs), gene expression and economic evaluation of parameters associated with mastitis susceptibility in Holstein and Brown Swiss dairy cows. Two hundred and forty Holstein and Brown Swiss dairy cows (120 cows of each breed) were used in this study. The investigated dairy cows in each breed were allocated into two equal-sized groups (60 cows each); mastitis tolerant and affected groups. PCR-DNA sequencing of SELL, ABCG2, SLC11A1, FEZL, SOD1, CAT, GPX1, and AhpC/TSA revealed nucleotide sequence variations in the form of SNPs associated with mastitis tolerance/susceptibility in investigated Holstein and Brown Swiss dairy cows. Levels of SELL, SLC11A1 and FEZL gene expression were significantly up-regulated in mastitic Holstein and Brown Swiss dairy cows than in tolerant ones. Meanwhile, ABCG2, SOD1, CAT, GPX1, and AhpC/TSA genes were significantly downregulated. Regarding the economic parameters, significant differences were recorded for net returns and a reduction in the percentage of net profit, as the higher values of net returns were recorded for tolerant dairy cows than mastitic ones in both breeds; moreover, the net profit was reduced by 39% and 27% in mastitic Holstein and Brown Swiss dairy cows, respectively, when compared to tolerant ones. The results herein confirmed the potential significance of investigated genes as candidates for mastitis tolerance/susceptibility in Holstein and Brown Swiss dairy cows. Mastitis also has detrimental impacts on economic efficiency in dairy farms.
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Hassan FU, Nadeem A, Javed M, Saif-ur-Rehman M, Shahzad MA, Azhar J, Shokrollahi B. Nutrigenomic Interventions to Address Metabolic Stress and Related Disorders in Transition Cows. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2295017. [PMID: 35726316 PMCID: PMC9206560 DOI: 10.1155/2022/2295017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/23/2022] [Indexed: 12/21/2022]
Abstract
For dairy cattle, the period involving a shift from late pregnancy to early lactation termed transition or periparturient is an excruciating phase. Health-related disorders are likely to happen in this time frame. Timely postpartum and metabolic adjustments to this new physical state demands correct management strategies to fulfill the cow's needs for a successful transition to this phase. Among the management strategies, one of the most researched methods for managing transition-related stress is nutritional supplementation. Dietary components directly or indirectly affect the expression of various genes that are believed to be involved in various stress-related responses during this phase. Nutrigenomics, an interdisciplinary approach that combines nutritional science with omics technologies, opens new avenues for studying the genome's complicated interactions with food. This revolutionary technique emphasizes the importance of food-gene interactions on various physiological and metabolic mechanisms. In animal sciences, nutrigenomics aims to promote the welfare of livestock animals and enhance their commercially important qualities through nutritional interventions. To this end, an increasing volume of research shows that nutritional supplementation can be effectively used to manage the metabolic stress dairy cows undergo during the transition period. These nutritional supplements, including polyunsaturated fatty acids, vitamins, dietary amino acids, and phytochemicals, have been shown to modulate energy homeostasis through different pathways, leading to addressing metabolic issues in transition cows.
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Affiliation(s)
- Faiz-ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Asif Nadeem
- Department of Biotechnology, Virtual University of Pakistan, Lahore, Pakistan
| | - Maryam Javed
- Institute of Biochemistry & Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | | | | | - Jahanzaib Azhar
- Department of Biotechnology, Virtual University of Pakistan, Lahore, Pakistan
| | - Borhan Shokrollahi
- Department of Animal Science, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
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Anamika, Magotra A, Bangar YC, Malik BS, Garg AR. Evaluation of candidate genotype of GH gene associated with growth, production and reproduction traits in Dairy Cows. Reprod Domest Anim 2022; 57:711-721. [PMID: 35258127 DOI: 10.1111/rda.14110] [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: 12/29/2021] [Accepted: 03/04/2022] [Indexed: 11/29/2022]
Abstract
Growth hormone (GH) is a major regulator of postnatal growth and metabolism in mammals and plays a critical role in growth, production and fertility in cattle. The present study was conducted in dairy cattle to find the association of g.48769565 C>T mutation with growth, production and reproduction traits in Sahiwal and Hardhenu cattle. PCR-RFLP was performed to genotype g.48769565 C>T mutation using the MspI restriction enzyme in our resource cattle population. In Hardhenu cattle, the frequencies of C and T alleles were 0.59 and 0.41 respectively while genotypic frequencies were 0.06, 0.36 and 0.58 for CC,CT and TT respectively. The frequencies of the C and T allele were 0.24 and 0.76 respectively in Sahiwal cattle and it was observed that highest frequency was forTT genotype (0.58) and lowest for CC genotype (0.06). Chi-square analysis showed that g.48769565C>T SNP loci did not meet with the Hardy-Weinberg equilibrium (p< 0.01) in Sahiwal cattle. From the least-squares analysis, it was observed that CC genotype was significantly associated with total Milk Yield (TMY), 300 days milk yield (300D MY), lactation length (LL), Dry period (DP) and Artificial insemination (AI)/conception (p<0.05). We also observed a significant association (p<0.05) of genotype CT with 3-month calves body weight. Cows with TT genotype revealed comparatively revealed favourable service period (SP) and calving interval (CI) in both Hardhenu and Sahiwal. These observed differences in their allelic and genotypic frequencies in association with the traitsunderlying production and fertility can be utilized for genetic improvement in dairy cattle.
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Affiliation(s)
- Anamika
- Department of Animal Genetics and Breeding, LalaLajpatRai University of Veterinary and Animal Sciences (LUVAS), Hisar, 125004, Haryana, India
| | - Ankit Magotra
- Department of Animal Genetics and Breeding, LalaLajpatRai University of Veterinary and Animal Sciences (LUVAS), Hisar, 125004, Haryana, India
| | - Yogesh C Bangar
- Department of Animal Genetics and Breeding, LalaLajpatRai University of Veterinary and Animal Sciences (LUVAS), Hisar, 125004, Haryana, India
| | - B S Malik
- Department of Animal Genetics and Breeding, LalaLajpatRai University of Veterinary and Animal Sciences (LUVAS), Hisar, 125004, Haryana, India
| | - Asha Rani Garg
- Department of Animal Genetics and Breeding, LalaLajpatRai University of Veterinary and Animal Sciences (LUVAS), Hisar, 125004, Haryana, India
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Buaban S, Lengnudum K, Boonkum W, Phakdeedindan P. Genome-wide association study on milk production and somatic cell score for Thai dairy cattle using weighted single-step approach with random regression test-day model. J Dairy Sci 2021; 105:468-494. [PMID: 34756438 DOI: 10.3168/jds.2020-19826] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 08/24/2021] [Indexed: 12/26/2022]
Abstract
Genome-wide association studies are a powerful tool to identify genomic regions and variants associated with phenotypes. However, only limited mutual confirmation from different studies is available. The objectives of this study were to identify genomic regions as well as genes and pathways associated with the first-lactation milk, fat, protein, and total solid yields; fat, protein, and total solid percentage; and somatic cell score (SCS) in a Thai dairy cattle population. Effects of SNPs were estimated by a weighted single-step GWAS, which back-solved the genomic breeding values predicted using single-step genomic BLUP (ssGBLUP) fitting a single-trait random regression test-day model. Genomic regions that explained at least 0.5% of the total genetic variance were selected for further analyses of candidate genes. Despite the small number of genotyped animals, genomic predictions led to an improvement in the accuracy over the traditional BLUP. Genomic predictions using weighted ssGBLUP were slightly better than the ssGBLUP. The genomic regions associated with milk production traits contained 210 candidate genes on 19 chromosomes [Bos taurus autosome (BTA) 1 to 7, 9, 11 to 16, 20 to 21, 26 to 27 and 29], whereas 21 candidate genes on 3 chromosomes (BTA 11, 16, and 21) were associated with SCS. Many genomic regions explained a small fraction of the genetic variance, indicating polygenic inheritance of the studied traits. Several candidate genes coincided with previous reports for milk production traits in Holstein cattle, especially a large region of genes on BTA14. We identified 141 and 5 novel genes related to milk production and SCS, respectively. These novel genes were also found to be functionally related to heat tolerance (e.g., SLC45A2, IRAG1, and LOC101902172), longevity (e.g., SYT10 and LOC101903327), and fertility (e.g., PAG1). These findings may be attributed to indirect selection in our population. Identified biological networks including intracellular cell transportation and protein catabolism implicate milk production, whereas the immunological pathways such as lymphocyte activation are closely related to SCS. Further studies are required to validate our findings before exploiting them in genomic selection.
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Affiliation(s)
- S Buaban
- Bureau of Animal Husbandry and Genetic Improvement, Department of Livestock Development, Pathum Thani 12000, Thailand
| | - K Lengnudum
- Bureau of Biotechnology in Livestock Production, Department of Livestock Development, Pathum Thani 12000, Thailand
| | - W Boonkum
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - P Phakdeedindan
- Department of Animal Husbandry, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand.
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Islam S, Reddy UK, Natarajan P, Abburi VL, Bajwa AA, Imran M, Zahoor MY, Abdullah M, Bukhari AM, Iqbal S, Ashraf K, Nadeem A, Rehman H, Rashid I, Shehzad W. Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight. PLoS One 2020; 15:e0242500. [PMID: 33232358 PMCID: PMC7685427 DOI: 10.1371/journal.pone.0242500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 11/03/2020] [Indexed: 11/20/2022] Open
Abstract
The domestic Nili-Ravi water buffalo (Bubalus bubalis) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.
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Affiliation(s)
- Saher Islam
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Purushothaman Natarajan
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Venkata Lakshmi Abburi
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Amna Arshad Bajwa
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Imran
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Yasir Zahoor
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Abdullah
- Department of Livestock Production, University of Veterinary and Animal Sciences, Pattoki, Pakistan
| | - Aamir Mehmood Bukhari
- Semen Production Unit, Qadirabad, District Sahiwal, Pakistan
- Livestock and Dairy Development Department, Government of the Punjab, Lahore, Pakistan
| | - Sajid Iqbal
- Semen Production Unit, Qadirabad, District Sahiwal, Pakistan
- Livestock and Dairy Development Department, Government of the Punjab, Lahore, Pakistan
| | - Kamran Ashraf
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Asif Nadeem
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Habibur Rehman
- Department of Physiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Imran Rashid
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Wasim Shehzad
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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Ma S, Liu H, Sun W, Mustafa A, Xi Y, Pu F, Li Y, Han C, Bai L, Hua H. Molecular evolution of the ATP-binding cassette subfamily G member 2 gene subfamily and its paralogs in birds. BMC Evol Biol 2020; 20:85. [PMID: 32664916 PMCID: PMC7362505 DOI: 10.1186/s12862-020-01654-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Background ATP-binding cassette (ABC) transporters are involved in the active transportation of various endogenous or exogenous substances. Two ABCG2 gene subfamily members have been identified in birds. A detailed comparative study of the ABCG2 and ABCG2-like genes aid our understanding of their evolutionary history at the molecular level and provide a theoretical reference for studying the specific functions of ABCG2 and ABCG2-like genes in birds. Results We first identified 77 ABCG2/ABCG2-like gene sequences in the genomes of 41 birds. Further analysis showed that both the nucleic acid and amino acid sequences of ABCG2 and ABCG2-like genes were highly conserved and exhibited high homology in birds. However, significant differences in the N-terminal structure were found between the ABCG2 and ABCG2-like amino acid sequences. A selective pressure analysis showed that the ABCG2 and ABCG2-like genes were affected by purifying selection during the process of bird evolution. Conclusions We believe that multiple members of the ABCG2 gene subfamily exist on chromosome 4 in the ancestors of birds. Over the long course of evolution, only the ABCG2 gene was retained on chromosome 4 in birds. The ABCG2-like gene on chromosome 6 might have originated from chromosome replication or fusion. The structural differences between the N terminus of ABCG2 protein and those of ABCG2-like proteins might lead to functional differences between the corresponding genes.
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Affiliation(s)
- Shengchao Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China.
| | - Wenqiang Sun
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Ahsan Mustafa
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, P.R. China
| | - Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Fajun Pu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Yanying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Lili Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - He Hua
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
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Li C, Sun D, Zhang S, Yang S, Alim MA, Zhang Q, Li Y, Liu L. Genetic effects of FASN, PPARGC1A, ABCG2 and IGF1 revealing the association with milk fatty acids in a Chinese Holstein cattle population based on a post genome-wide association study. BMC Genet 2016; 17:110. [PMID: 27468856 PMCID: PMC4963957 DOI: 10.1186/s12863-016-0418-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/20/2016] [Indexed: 02/01/2023] Open
Abstract
Background A previous genome-wide association study deduced that one (ARS-BFGL-NGS-39328), two (Hapmap26001-BTC-038813 and Hapmap31284-BTC-039204), two (Hapmap26001-BTC-038813 and BTB-00246150), and one (Hapmap50366-BTA-46960) genome-wide significant single nucleotide polymorphisms (SNPs) associated with milk fatty acids were close to or within the fatty acid synthase (FASN), peroxisome proliferator-activated receptor gamma, coactivator 1 alpha (PPARGC1A), ATP-binding cassette, sub-family G, member 2 (ABCG2) and insulin-like growth factor 1 (IGF1) genes. To further confirm the linkage and reveal the genetic effects of these four candidate genes on milk fatty acid composition, genetic polymorphisms were identified and genotype-phenotype associations were performed in a Chinese Holstein cattle population. Results Nine SNPs were identified in FASN, among which SNP rs41919985 was predicted to result in an amino acid substitution from threonine (ACC) to alanine (GCC), five SNPs (rs136947640, rs134340637, rs41919992, rs41919984 and rs41919986) were synonymous mutations, and the remaining three (rs41919999, rs132865003 and rs133498277) were found in FASN introns. Only one SNP each was identified for PPARGC1A, ABCG2 and IGF1. Association studies revealed that FASN, PPARGC1A, ABCG2 and IGF1 were mainly associated with medium-chain saturated fatty acids and long-chain unsaturated fatty acids, especially FASN for C10:0, C12:0 and C14:0. Strong linkage disequilibrium was observed among ARS-BFGL-NGS-39328 and rs132865003 and rs134340637 in FASN (D´ > 0.9), and among Hapmap26001-BTC-038813 and Hapmap31284-BTC-039204 and rs109579682 in PPARGC1A (D´ > 0.9). Subsequently, haplotype-based analysis revealed significant associations of the haplotypes encompassing eight FASN SNPs (rs41919999, rs132865003, rs134340637, rs41919992, rs133498277, rs41919984, rs41919985 and rs41919986) with C10:0, C12:0, C14:0, C18:1n9c, saturated fatty acids (SFA) and unsaturated fatty acids (UFA) (P = 0.0204 to P < 0.0001). Conclusion Our study confirmed the linkage between the significant SNPs in our previous genome-wide association study and variants in FASN and PPARGC1A. SNPs within FASN, PPARGC1A, ABCG2 and IGF1 showed significant genetic effects on milk fatty acid composition in dairy cattle, indicating their potential functions in milk fatty acids synthesis and metabolism. The findings presented here provide evidence for the selection of dairy cows with healthier milk fatty acid composition by marker-assisted breeding or genomic selection schemes, as well as furthering our understanding of technological processing aspects of cows’ milk. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0418-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cong Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Dongxiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Shengli Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Shaohua Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - M A Alim
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Qin Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Yanhua Li
- Beijing Dairy Cattle Center, Beijing, 100085, China
| | - Lin Liu
- Beijing Dairy Cattle Center, Beijing, 100085, China
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