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Kumar H, Panigrahi M, G Strillacci M, Sonejita Nayak S, Rajawat D, Ghildiyal K, Bhushan B, Dutt T. Detection of genome-wide copy number variation in Murrah buffaloes. Anim Biotechnol 2023; 34:3783-3795. [PMID: 37381739 DOI: 10.1080/10495398.2023.2227670] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Riverine Buffaloes, especially the Murrah breed because of their adaptability to harsh climatic conditions, is farmed in many countries to convert low-quality feed into valuable dairy products and meat. Here, we investigated the copy number variations (CNVs) in 296 Murrah buffalo using the Axiom® Buffalo Genotyping Array 90K (Affymetrix, Santa Clara, CA, USA). The CNVs were detected on the autosomes, using the Copy Number Analysis Module (CNAM) using the univariate analysis. 7937 CNVs were detected in 279 Buffaloes, the average length of the CNVs was 119,048.87 bp that ranged between 7800 and 4,561,030 bp. These CNVs were accounting for 10.33% of the buffalo genome, which was comparable to cattle, sheep, and goat CNV analyses. Further, CNVs were merged and 1541 CNVRs were detected using the Bedtools-mergeBed command. 485 genes were annotated within 196 CNVRs that were identified in at least 10 animals of Murrah population. Out of these, 40 CNVRs contained 59 different genes that were associated with 69 different traits. Overall, the study identified a significant number of CNVs and CNVRs in the Murrah breed of buffalo, with a wide range of lengths and frequencies across the autosomes. The identified CNVRs contained genes associated with important traits related to production and reproduction, making them potentially important targets for future breeding and genetic improvement efforts.
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Affiliation(s)
- Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Maria G Strillacci
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy
| | | | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, India
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2
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Benedek I, Altbäcker V, Zsolnai A, Nagy I, Mezőszentgyörgyi D, Molnár T. The Role of PRLR Gene Polymorphisms in Milk Production in European Wild Rabbit ( Oryctolagus cuniculus). Animals (Basel) 2023; 13:ani13040671. [PMID: 36830458 PMCID: PMC9951758 DOI: 10.3390/ani13040671] [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: 12/15/2022] [Revised: 01/28/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
One of the problematic points of rabbit breeding is that the nutritional requirements of the kits are not fully satisfied by the does' milk production from the third week of lactation onwards. The prolactin receptor gene has a significant effect on reproductive processes, and its polymorphisms have been associated with milk production in several species (cattle, goats, sheep, and buffalo). The European wild rabbit (Oryctolagus cuniculus), has a more diverse genetic background compared to domesticated lines. In the course of our study, sequencing of the 1210 bp long segment of the PRLR gene promoter region was accomplished. We detected four point mutations (SNP1-407G > A, SNP2-496G > C, SNP3-926T> and SNP4-973A > C) and one microsatellite at position 574. In our population, the four SNPs were segregated into four genotypes: AACCCCCC, GGGGTTAA, AAGGTTAC, and GGGGTCAC. Our results show that the genotype in the homozygous form is associated with higher milk production (1564.7 ± 444.7 g) compared to the other three genotypes (AACCCCCC 1399.1 ± 326.8 g; GTGACCTT 1403.8 ± 517.1 g; GGGGTCAC 1220.0 ± 666.2 g), and the short microsatellite repeat (167 bp) also coincides with significantly higher milk production (1623.8 ± 525.1 g). These results make the marker-assisted selection possible also for domesticated lines.
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Affiliation(s)
- Ildikó Benedek
- Department of Animal Breeding, Institute of Animal Breeding Sciences, Hungarian University of Agriculture and Life Sciences, 7400 Kaposvar, Hungary
- Correspondence: or (I.B.); (T.M.)
| | - Vilmos Altbäcker
- Department of Nature Conservation, Institute for Wildlife Management and Nature, Hungarian University of Agriculture and Life Sciences, 7400 Kaposvar, Hungary
| | - Attila Zsolnai
- Department of Animal Breeding, Institute of Animal Breeding Sciences, Hungarian University of Agriculture and Life Sciences, 7400 Kaposvar, Hungary
| | - István Nagy
- Department of Animal Breeding, Institute of Animal Breeding Sciences, Hungarian University of Agriculture and Life Sciences, 7400 Kaposvar, Hungary
| | - Dávid Mezőszentgyörgyi
- Department of Animal Breeding, Institute of Animal Breeding Sciences, Hungarian University of Agriculture and Life Sciences, 7400 Kaposvar, Hungary
| | - Tamás Molnár
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 7400 Kaposvar, Hungary
- Correspondence: or (I.B.); (T.M.)
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3
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El-Shorbagy HM, Abdel-Aal ES, Mohamed SA, El-Ghor AA. Association of PRLR, IGF1, and LEP genes polymorphism with milk production and litter size in Egyptian Zaraibi goat. Trop Anim Health Prod 2022; 54:321. [PMID: 36155857 PMCID: PMC9512711 DOI: 10.1007/s11250-022-03316-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/14/2022] [Indexed: 11/26/2022]
Abstract
Studying variation in genes responsible for physiological characters is important to enhance goat productive and reproductive efficiency. This study aimed to detect specific nucleotide polymorphisms in prolactin receptor (PRLR), insulin-like growth factor (IGF1), and leptin (LEP) genes and their correlation with milk production (MP) and litter size (LS) traits in Zaraibi goat. PCR-SSCP products of different patterns of each gene were sequenced and aligned to reveal two mutations (T > C) and (G > A) in 3′UTR of PRLR gene and registered on NCBI with accession numbers OM418863 for TT and OM418864 for CT, while (G > A) variation was registered as OM418861 for GG and OM418862 for AG in exon 10. TT, CT, AG, and GG genotypes were distributed in the studied animals with frequencies 0.43, 0.57, 0.65, and 0.35, respectively. While alleles C, T, A, and G frequencies were 0.28, 0.72, 0.32, and 0.68, respectively. CT and AG genotypes associated significantly (P < 0.05) with higher MP and LS, respectively. By studying the haplotypes of PRLR, C-A and T-A were associated with the highest and the lowest level of MP, respectively. For LS, T-A and C-G showed significant correlation with the highest and the lowest rate, respectively. Regarding IGF1 gene, two polymorphisms were detected; T74C at exon 4 which registered on NCBI as OM418860, and combined mutations as ins. G470, A531G, and T534C (PP genotype) at 5′ flanking region that registered as OM418859. For LEP, only one polymorphism was found in intron 2 (G281A) which submitted to NCBI as OM418855. All detected polymorphisms have shown to be involved in regulating the MP or LS as reproductive traits in goat.
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Affiliation(s)
- Haidan M El-Shorbagy
- Zoology Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
- Faculty of Biotechnology, October University for Modern Science and Arts, 6th October, Giza, Egypt
| | - Ehab S Abdel-Aal
- Sheep & Goat Research Department, Animal Production Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Shaimaa A Mohamed
- Sheep & Goat Research Department, Animal Production Research Institute, Agricultural Research Center (ARC), Giza, Egypt.
| | - Akmal A El-Ghor
- Zoology Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
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4
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Zhang X, Chen N, Chen H, Lei C, Sun T. Comparative analyses of copy number variations between swamp and river buffalo. Gene X 2022; 830:146509. [PMID: 35460806 DOI: 10.1016/j.gene.2022.146509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Domestic buffalo is an important livestock in the tropical and sub-tropical region, including two types: swamp and river buffalo. The swamp buffalo is mainly used as draft animal, while the river buffalo is raised for milk production. In this study, based on the new high-quality buffalo reference genome UOA_WB_1, we firstly investigated the copy number variants in buffalo using whole-genome Illumina sequencing. A total of 3,734 CNV regions (CNVRs) were detected in 106 buffalo population with a total length of 23,429,066 bp, corresponding to ∼ 0.88% of the water buffalo genome (UOA_WB_1). Our results revealed a clear population differentiation in CNV between swamp and river buffalo. In addition, a total of 667 highly differentiated CNVRs (covering 886 genes) were detected between river and swamp buffalo population. We detected a set of CNVR-overlapping genes associated with exercise, immunity, nerve, and milk trait which exhibited different copy numbers between swamp and river buffalo population. This study provides valuable genome variation resources for buffalo and would contribute to understanding the genetic differences between swamp and river buffalo.
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Affiliation(s)
- Xianfu Zhang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, Zhejiang 311300, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
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Abd El Fattah EM, Behour TS, Ashour AF, Amin AMS. Association analysis of prolactin and prolactin receptor genes with selected productive and reproductive traits in Egyptian buffalo. Anim Biotechnol 2022:1-9. [PMID: 35148254 DOI: 10.1080/10495398.2022.2028160] [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: 11/01/2022]
Abstract
A total of 266 records of buffalo raised in two experimental herds in Egypt were assessed to detect prolactin (PRL) and prolactin receptor (PRLR) genes' polymorphism using PCR-Single Strand Conformational Polymorphism (SSCP) and PCR-Restricted Fragment Length Polymorphism (RFLP) techniques as well as to investigate their association with calf birth weight (BW), weaning weight (WW), lactation period (LP), total milk yield (TMY), stillbirth, calving ease (CE), gestation length (GL), postpartum interval to pregnancy (PPIP), calving interval (CI), and age at first calving (AFC). Predicted breeding values were estimated and used in the association with detected genotypes. A monomorphic pattern of the studied PRL 156 bp segment was recorded and absence of its polymorphism in buffalo was corroborated. We also determined polymorphism of PRLR reflected in three loci: PRLR2, PRLR4, and PRLR9. Significant differences among PRLP9 genotypes (AA, AB, and BB) were displayed for all studied traits as well as among PRLR2 genotypes, except for CE, while PRLR4 genotypes significantly differed only in BW, WW, TMY, stillbirth, GL, and AFC. In practice, strong associations among genotypes of the PRLR gene and the traits of interest candidate this gene to be selective in Egyptian buffalo breeding for improving both productive and reproductive traits.
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Affiliation(s)
- Eman Mohamed Abd El Fattah
- Animal Reproduction Research Institute (ARRI), Agricultural Research Center, Ministry of Agriculture and Land Reclamation, Giza, Egypt
| | - Tahani Salama Behour
- Animal Reproduction Research Institute (ARRI), Agricultural Research Center, Ministry of Agriculture and Land Reclamation, Giza, Egypt
| | - Ayman Fouad Ashour
- Animal Production Research Institute (APRI), Agricultural Research Center, Ministry of Agriculture and Land Reclamation, Dokki, Giza, Egypt
| | - Amin Mohamed Said Amin
- Animal Production Research Institute (APRI), Agricultural Research Center, Ministry of Agriculture and Land Reclamation, Dokki, Giza, Egypt
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6
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Işık R, Özkan Ünal E, Soysal M. Polymorphism detection of <i>DGAT1</i> and <i>Lep</i> genes in Anatolian water buffalo (<i>Bubalus bubalis</i>) populations in Turkey. Arch Anim Breed 2022; 65:1-9. [PMID: 35024434 PMCID: PMC8738919 DOI: 10.5194/aab-65-1-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 11/29/2021] [Indexed: 11/11/2022] Open
Abstract
Acyl-CoA: diacylglycerol–acyltransferase 1 (DGAT1)
enzyme plays a key role in controlling the synthesis rate triglyceride from
diacylglycerol. Leptin (LP, OB, obese) is an important hormone that
synthesizes mostly from adipose tissue and regulates glucose metabolism and
homeostasis. DGAT1 and Lep genes are closely related to reproduction, growth, milk
yield and composition in water buffalo breeds. This study aimed to identify
genetic variation in the DGAT1 and Lep gene regions in 150 water buffalo individuals
from five different provinces of Turkey using DNA sequencing. A total of 38
nucleotide variations and indels have identified 761 bp long partial intron
2 and exon 3 and 5′ UTR regions of the Lep gene in Anatolian water buffalo
populations; 422 bp long partial exon 7–9 and exon 8 regions of DGAT1 gene were
amplified and two mutations were defined in the point of 155 and 275
nucleotide that is three genotypes for S allele and Y allele of DGAT1 gene in
intron 7 in Anatolian buffalo populations, respectively. These SNPs may have
an effect on reproduction, growth, milk yield and composition in water
buffalo populations and may prove to be useful for water buffalo breeding.
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Affiliation(s)
- Raziye Işık
- Faculty of Agriculture, Department of Agricultural Biotechnology,
Tekirdağ Namık Kemal University, Tekirdağ 59030, Turkey
| | - Emel Özkan Ünal
- Faculty of Agriculture, Department of Animal Science, Tekirdağ
Namık Kemal University, Tekirdağ 59030, Turkey
| | - M. İhsan Soysal
- Faculty of Agriculture, Department of Animal Science, Tekirdağ
Namık Kemal University, Tekirdağ 59030, Turkey
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7
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Deng TX, Ma XY, Lu XR, Duan AQ, Shokrollahi B, Shang JH. Signatures of selection reveal candidate genes involved in production traits in Chinese crossbred buffaloes. J Dairy Sci 2021; 105:1327-1337. [PMID: 34955275 DOI: 10.3168/jds.2021-21102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/03/2021] [Indexed: 12/11/2022]
Abstract
Identification of selection signature is important for a better understanding of genetic mechanisms that affect phenotypic differentiation in livestock. However, the genome-wide selection responses have not been investigated for the production traits of Chinese crossbred buffaloes. In this study, an SNP data set of 133 buffaloes (Chinese crossbred buffalo, n = 45; Chinese local swamp buffalo, n = 88) was collected from the Dryad Digital Repository database (https://datadryad.org/stash/). Population genetics analysis showed that these buffaloes were divided into the following 2 groups: crossbred buffalo and swamp buffalo. The crossbred group had higher genetic diversity than the swamp group. Using 3 complementary statistical methods (integrated haplotype score, cross population extended haplotype homozygosity, and composite likelihood ratio), a total of 31 candidate selection regions were identified in the Chinese crossbred population. Here, within these candidate regions, 25 genes were under the putative selection. Among them, several candidate genes were reported to be associated with production traits. In addition, we identified 13 selection regions that overlapped with bovine QTLs that were mainly involved in milk production and composition traits. These results can provide useful insights regarding the selection response for production traits of Chinese crossbred buffalo, as identified candidate genes influence production performance.
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Affiliation(s)
- T X Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
| | - X Y Ma
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - X R Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - A Q Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Borhan Shokrollahi
- Department of Animal Science, Faculty of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran 5595-73919
| | - J H Shang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
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8
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Khan MZ, Ma Y, Ma J, Xiao J, Liu Y, Liu S, Khan A, Khan IM, Cao Z. Association of DGAT1 With Cattle, Buffalo, Goat, and Sheep Milk and Meat Production Traits. Front Vet Sci 2021; 8:712470. [PMID: 34485439 PMCID: PMC8415568 DOI: 10.3389/fvets.2021.712470] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
Milk fatty acids are essential for many dairy product productions, while intramuscular fat (IMF) is associated with the quality of meat. The triacylglycerols (TAGs) are the major components of IMF and milk fat. Therefore, understanding the polymorphisms and genes linked to fat synthesis is important for animal production. Identifying quantitative trait loci (QTLs) and genes associated with milk and meat production traits has been the objective of various mapping studies in the last decade. Consistently, the QTLs on chromosomes 14, 15, and 9 have been found to be associated with milk and meat production traits in cattle, goat, and buffalo and sheep, respectively. Diacylglycerol O-acyltransferase 1 (DGAT1) gene has been reported on chromosomes 14, 15, and 9 in cattle, goat, and buffalo and sheep, respectively. Being a key role in fat metabolism and TAG synthesis, the DGAT1 has obtained considerable attention especially in animal milk production. In addition to milk production, DGAT1 has also been a subject of interest in animal meat production. Several polymorphisms have been documented in DGAT1 in various animal species including cattle, buffalo, goat, and sheep for their association with milk production traits. In addition, the DGAT1 has also been studied for their role in meat production traits in cattle, sheep, and goat. However, very limited studies have been conducted in cattle for association of DGAT1 with meat production traits in cattle. Moreover, not a single study reported the association of DGAT1 with meat production traits in buffalo; thus, further studies are warranted to fulfill this huge gap. Keeping in view the important role of DGAT1 in animal production, the current review article was designed to highlight the major development and new insights on DGAT1 effect on milk and meat production traits in cattle, buffalo, sheep, and goat. Moreover, we have also highlighted the possible future contributions of DGAT1 for the studied species.
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Affiliation(s)
- Muhammad Zahoor Khan
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Faculty of Veterinary and Animal Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Yulin Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiaying Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianxin Xiao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yue Liu
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuai Liu
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Adnan Khan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ibrar Muhammad Khan
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
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El-Magd MA, Fathy A, Kahilo KA, Saleh AA, El Sheikh AI, AL-Shami S, El-Komy SM. Polymorphisms of the PRLR Gene and Their Association with Milk Production Traits in Egyptian Buffaloes. Animals (Basel) 2021; 11:ani11051237. [PMID: 33923003 PMCID: PMC8146870 DOI: 10.3390/ani11051237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary The two non-synonymous g.11685G>A and g.11773T>C SNPs of PRLR(L2) were significantly associated with milk yield, fat%, and protein%, and mRNA and protein levels of PRL and PRLR in milk somatic cells. GT-animals had the best milk performance; however, AC-animals had inferior milk production. Thus, the selection of buffaloes with GT haplotypes may enhance milk performance in Egyptian buffaloes. Abstract Prolactin (PRL) and its receptor (PRLR) were considered as potential genetic markers for milk production and quality traits in cattle. However, little information is available regarding PRLR genetic diversity and association studies with milk traits in Egyptian water buffaloes. Therefore, the present study was conducted to search for mutations in PRLR and determine their associations with milk performance in these animals. Exon3 (E3) and E10 of PRLR were screened for polymorphisms using single strand conformation polymorphism (SSCP) and sequencing in 400 buffaloes. The associations between haplotypes and milk production (fat%, protein%, lactose%, and solid%) traits as well as mRNA and protein levels of PRL and PRLR were studied. Two single nucleotide polymorphisms (SNPs) in E10 were detected: g.11685G>A (p.Ala494Thr) and g.11773T>C (p.Val523Aal). The G and T alleles were wild (ancestral) alleles, while the A and C alleles were mutant alleles. These SNPs resulted in four haplotypes; AC, AT, GC, and GT. Buffaloes with wild GT haplotypes showed significantly higher milk yield, fat% and protein%, mRNA and protein levels of PRL and PRLR in milk somatic cells than other animals. Animals carrying mutant AC haplotype had inferior milk traits and lowest levels of associated mRNAs and proteins. With these results, we could conclude that the selection of buffaloes with wild GT haplotypes for g.11685G>A and g.11773T>C SNPs of the PRLR gene might improve the milk production traits of Egyptian water buffaloes.
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Affiliation(s)
- Mohammed A. El-Magd
- Department of Anatomy & Embryology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
- Correspondence:
| | - Aziza Fathy
- Department of Biochemistry, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt; (A.F.); (K.A.K.)
| | - Khaled A. Kahilo
- Department of Biochemistry, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt; (A.F.); (K.A.K.)
| | - Ayman A. Saleh
- Department of Animal Wealth Development, Veterinary Genetics & Genetic Engineering, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Ahmed I. El Sheikh
- Department of Public Health, Faculty of Veterinary Medicine, King Faisal University, Alahssa 31982, Saudi Arabia; (A.I.E.S.); (S.A.-S.)
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Alexandria University, Alexandria 21561, Egypt
| | - Salah AL-Shami
- Department of Public Health, Faculty of Veterinary Medicine, King Faisal University, Alahssa 31982, Saudi Arabia; (A.I.E.S.); (S.A.-S.)
| | - Shymaa M. El-Komy
- Department of Animal Production, Faculty of Agriculture, Tanta University, Tanta 31527, Egypt;
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Genetic Association of PPARGC1A Gene Single Nucleotide Polymorphism with Milk Production Traits in Italian Mediterranean Buffalo. BIOMED RESEARCH INTERNATIONAL 2021; 2021:3653157. [PMID: 33829059 PMCID: PMC8004361 DOI: 10.1155/2021/3653157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 11/29/2022]
Abstract
PPARGC1A gene plays an important role in the activation of various important hormone receptors and transcriptional factors involved in the regulation of adaptive thermogenesis, gluconeogenesis, fiber-type switching in skeletal muscle, mitochondrial biogenesis, and adipogenesis, regulating the reproduction and proposed as a candidate gene for milk-related traits in cattle. This study identified polymorphisms in the PPARGC1A gene in Italian Mediterranean buffaloes and their associations to milk production and quality traits (lactation length, peak milk yield, fat and protein yield, and percentage). As a result, a total of seven SNPs (g.-78A>G, g.224651G>C, g.286986G>A, g.304050G>A, g.325647G>A, g.325817T>C, and g.325997G>A) were identified by DNA pooled sequencing. Analysis of productivity traits within the genotyped animals revealed that the g.286986G>A located at intron 4 was associated with milk production traits, but the g.325817T>C had no association with milk production. Polymorphisms in g.-78A>G was associated with peak milk yield and milk yield, while g.304050G>A and g.325997 G>A were associated with both milk yield and protein percentage. Our findings suggest that polymorphisms in the buffalo PPARGC1A gene are associated with milk production traits and can be used as a candidate gene for milk traits and marker-assisted selection in the buffalo breeding program.
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11
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Krovvidi S, Metta M. Evaluation of non-synonym mutation in DGAT1 K232A as a marker for milk production traits in Ongole cattle and Murrah buffalo from Southern India. Trop Anim Health Prod 2021; 53:118. [PMID: 33439326 DOI: 10.1007/s11250-021-02560-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/05/2021] [Indexed: 11/25/2022]
Abstract
Various candidate genes have been reported to affect milk yield and composition in dairy cattle. A non-synonymous mutation in the DGAT1 gene, i.e., K232A was reported to have a strong association with milk yield and milk composition of Bos taurus. A study has been undertaken on 502 unrelated individuals belonging to indigenous Ongole cattle, crossbred cattle, and Murrah buffaloes from the Indian sub-continent with the objective to determine the polymorphism of the K232A locus and their association with milk yield and composition. Typing DGAT1 K232A allelic variation by PCR-RFLP using CfrI restriction enzyme revealed three genotypes in crossbred cattle. Genotype KK was more prevalent (0.60) in Jersey crossbred, whereas in Holstein Friesian crossbred it was KA genotype (0.48). In Ongole cattle and Murrah buffaloes, the locus did not exhibit polymorphism. The least-square mean of milk yields pooled over lactations across the DGAT1 variants was significantly (P < 0.05) higher among the homozygous (AA) genotypes, both in Jersey crossbred and HF crossbred cattle after adjusting for the effects of farm, parity, and season. The fat, SNF, and protein content values of AA genotypes were less than the KK genotypes in both the genetic groups (P > 0.05). The fixation of the DGAT1K allele at the locus in Bos indicus cattle and Bubalus bubalis in the present study did not support its use as a reliable universal marker for milk production and composition traits.
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Affiliation(s)
- Sudhakar Krovvidi
- Department of Animal Genetics and Breeding, NTR College of Veterinary Science (Sri Venkateswara Veterinary University), Gannavaram, Andhra Pradesh, 521 102, India.
| | - Muralidhar Metta
- Department of Animal Genetics and Breeding, NTR College of Veterinary Science (Sri Venkateswara Veterinary University), Gannavaram, Andhra Pradesh, 521 102, India
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12
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El-Komy SM, Saleh AA, Abd El-Aziz RM, El-Magd MA. Association of GH polymorphisms with growth traits in buffaloes. Domest Anim Endocrinol 2021; 74:106541. [PMID: 32916521 DOI: 10.1016/j.domaniend.2020.106541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 07/28/2020] [Accepted: 08/11/2020] [Indexed: 10/23/2022]
Abstract
Members of the somatotrophic axis, especially GH and IGF1, are essential for growth. The association between GH polymorphisms and growth traits was numerously studied in cattle; however, no data are available for such association studies in buffalo. Therefore, this study was conducted to screen for polymorphisms in the GH gene and to study their putative association with growth traits in 200 Egyptian buffaloes. Polymerase chain reaction single-strand conformation polymorphism and sequencing were applied to look for polymorphisms in 3 loci spanning all exons and introns of buffalo GH. The C (MspI+) >T (MspI-) SNP in intron3, which is well known in cattle, was not detected in the examined buffaloes. However, 2 missense mutations were detected in exon5: one previously detected p.Leu153Val SNP, with very low frequencies for the mutant (Val) allele and one novel p.Asn174His SNP. At weaning age, the p.Leu153Val SNP was significantly associated with weaning body weight and gain with the positive effect of the wild allele (Leu) and higher GH serum, mRNA, and protein levels in animals with Leu/Asn and Leu/His haplotypes. At yearling age, the 2 SNPs associated with yearling weight and gain with positive effect for the mutant (Val and His) alleles with increased GH, and IGF1 serum, mRNA, and protein and GHR mRNA and protein levels in animals with Val/Asn haplotype. Therefore, the selection of Egyptian buffaloes with the Val/Asn haplotype could improve the growth traits of Egyptian buffaloes at yearling age which is the target age for perfect growing.
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Affiliation(s)
- S M El-Komy
- Department of Animal Production, Faculty of Agriculture, Tanta University, Tanta, Egypt
| | - A A Saleh
- Department of Animal Wealth Development, Veterinary Genetics & Genetic Engineering, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - R M Abd El-Aziz
- Department of Physiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - M A El-Magd
- Department of Anatomy & Embryology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt.
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13
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El-Komy SM, Saleh AA, Abdel-Hamid TM, El-Magd MA. Association of GHR Polymorphisms with Milk Production in Buffaloes. Animals (Basel) 2020; 10:ani10071203. [PMID: 32679878 PMCID: PMC7401641 DOI: 10.3390/ani10071203] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/03/2020] [Accepted: 07/08/2020] [Indexed: 01/09/2023] Open
Abstract
Simple Summary The present study reported two missense mutations in the buffalo GHR gene: A novel (c.380G>A) and (c.836T>A) which was described in previous studies. These two single nucleotide polymorphisms (SNPs) were found to be associated with milk yield, fat %, protein %, and 305 day-milk, fat and protein yield, with higher performance for AA haplotype animals. Therefore, selection of buffaloes with AA haplotype would more likely improve milk production traits. Consequently, this would allow breeders to take more precise selection decisions, leading to significantly higher productivity and profitability within the Egyptian buffalo herds. Abstract For its role in the mediation of growth hormone (GH) galactopoietic effect, growth hormone receptor (GHR) was considered a functional candidate gene for milk performance in cattle. However, its genetic variation and potential effect have not been investigated in Egyptian buffaloes. This study aimed to screen GHR for polymorphisms and study their associations with milk traits in Egyptian buffaloes. Polymerase chain reaction, single-strand conformation polymorphism, and sequencing were used to identify mutations in 4 exons (E4–E6 and E8) of the GHR gene in 400 Egyptian buffaloes. No polymorphisms were found in E4, while 2 SNPs (c.380G>A/p.Arg127Lys and c.387C>T/p.Gly129) in E5, one silent mutation (c.435A>G/p.Pro145) in E6, and another missense mutation (c.836T>A/p.Phe279Tyr) in E8 were detected. The c.380G>A SNP in the extracellular domain was associated with milk yield, fat %, protein %, and 305-day milk, fat and protein yield, with higher levels in animals carrying the mutant A allele. The c.836T>A SNP in the transmembrane domain was associated with milk yield, fat %, protein %, and 305-day milk, fat and protein yield, with higher milk yield and lower fat %, protein %, fat and protein yield in the mutant A allele-animals. Interestingly, animals with the two mutant AA alleles produced higher milk yield, fat %, protein %, fat and protein yield, accompanied with upregulated expressions of GHR, GH, insulin-like growth factor 1 (IGF1), prolactin (PRL), prolactin receptor (PRLR), β-casein (encoded by CSN2 gene), and diacylglycerol acyltransferase-1 (DGAT1) genes and proteins in milk somatic cells. Therefore, selection of Egyptian buffaloes with mutant AA haplotypes for the novel c.380G>A SNP and the well-known c.836T>A SNP could improve milk yield and quality in buffaloes.
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Affiliation(s)
- Shymaa M. El-Komy
- Department of Animal Production, Faculty of Agriculture, Tanta University, Tanta 31527, Egypt;
| | - Ayman A. Saleh
- Department of Animal Wealth Development, Veterinary Genetics & Genetic Engineering, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Tamer M. Abdel-Hamid
- Department of Animal Wealth Development, Animal Breeding and Production, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Mohammed A. El-Magd
- Department of Anatomy & Embryology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
- Correspondence:
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14
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Liu J, Wang Z, Li J, Li H, Yang L. Genome-wide identification of Diacylglycerol Acyltransferases (DGAT) family genes influencing Milk production in Buffalo. BMC Genet 2020; 21:26. [PMID: 32138658 PMCID: PMC7059399 DOI: 10.1186/s12863-020-0832-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/25/2020] [Indexed: 12/24/2022] Open
Abstract
Background The diacylglycerol acyltransferases (DGAT) are a vital group of enzymes in catalyzing triacylglycerol biosynthesis. DGAT genes like DGAT1 and DGAT2, have been identified as two functional candidate genes affecting milk production traits, especially for fat content in milk. Buffalo milk is famous for its excellent quality, which is rich in fat and protein content. Therefore, this study aimed to characterize DGAT family genes in buffalo and to find candidate markers or DGAT genes influencing lactation performance. Results We performed a genome-wide study and identified eight DGAT genes in buffalo. All the DGAT genes classified into two distinct clades (DGAT1 and DGAT2 subfamily) based on their phylogenetic relationships and structural features. Chromosome localization displayed eight buffalo DGAT genes distributed on five chromosomes. Collinearity analysis revealed that the DGAT family genes were extensive homologous between buffalo and cattle. Afterward, we discovered genetic variants loci within the genomic regions that DGAT genes located in buffalo. Seven haplotype blocks were constructed and were associated with buffalo milk production traits. Single marker association analyses revealed four most significant single nucleotide polymorphisms (SNPs) mainly affecting milk protein percentage or milk fat yield in buffalo. Genes functional analysis indicated that these DGAT family genes could influence lactation performance in the mammal through regulating lipid metabolism. Conclusion In the present study, we performed a comprehensive analysis for the DGAT family genes in buffalo, which including identification, structural characterization, phylogenetic classification, chromosomal distribution, collinearity analysis, association analysis, and functional analysis. These findings provide useful information for an in-depth study to determine the role of DGAT family gens play in the regulation of milk production and milk quality improvement in buffalo.
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Affiliation(s)
- Jiajia Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan, China.,School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Zhiquan Wang
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, Canada
| | - Jun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan, China.,Department of Immunology, Zunyi Medical College, Zunyi, China
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, China.
| | - Liguo Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan, China.
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15
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Du C, Deng T, Zhou Y, Ye T, Zhou Z, Zhang S, Shao B, Wei P, Sun H, Khan FA, Yang L, Hua G. Systematic analyses for candidate genes of milk production traits in water buffalo (Bubalus Bubalis). Anim Genet 2019; 50:207-216. [PMID: 30937948 DOI: 10.1111/age.12739] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2018] [Indexed: 11/28/2022]
Abstract
Water buffalo (Bubalus bubalis) is of great economic importance as a provider of milk and meat in many countries. However, the milk yield of buffalo is much lower than that of Holstein cows. Selection of candidate genes related to milk production traits can be applied to improve buffalo milk performance. A systematic review of studies of these candidate genes will be greatly beneficial for researchers to timely and efficiently understand the research development of molecular markers for buffalo milk production traits. Here, we identified and classified the candidate genes associated with buffalo milk production traits. A total of 517 candidate genes have been identified as being associated with milk performance in different buffalo breeds. Nineteen candidate genes containing 47 mutation sites have been identified using the candidate gene approach. In addition, 499 candidate genes have been identified in six genome-wide association studies (GWASes) including two studies performed with the bovine SNP chip and four studies with the buffalo SNP chip. Genes CTNND2 (catenin delta 2), APOB (apolipoprotein B), FHIT (fragile histidine triad) and ESRRG (estrogen related receptor gamma) were identified in at least two GWASes. These four genes, especially APOB, deserve further study to explore regulatory roles in buffalo milk production. With growth in the number of buffalo genomic studies, more candidate genes associated with buffalo milk production traits will be identified. Therefore, future studies, such as those investigating gene location and functional analyses, are necessary to facilitate the exploitation of genetic potential and the improvement of buffalo milk performance.
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Affiliation(s)
- C Du
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - T Deng
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
| | - Y Zhou
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - T Ye
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Z Zhou
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - S Zhang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - B Shao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - P Wei
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - H Sun
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - F A Khan
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Ministry of Health, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430070, China
| | - L Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, 430070, China
| | - G Hua
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, 430070, China
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16
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Cosenza G, Iannaccone M, Auzino B, Macciotta NPP, Kovitvadhi A, Nicolae I, Pauciullo A. Remarkable genetic diversity detected at river buffalo prolactin receptor (PRLR) gene and association studies with milk fatty acid composition. Anim Genet 2018; 49:159-168. [PMID: 29569734 DOI: 10.1111/age.12645] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2018] [Indexed: 12/11/2022]
Abstract
Prolactin is an anterior pituitary peptide hormone involved in many different endocrine activities and is essential for reproductive performance. This action is mediated by its receptor, the prolactin receptor, encoded by the PRLR gene. In this study, we sequenced and characterized the Mediterranean river buffalo PRLR gene (from exon 3 to 10), and we found remarkable genetic diversity. In particular, we found 24 intronic polymorphisms and 13 exonic SNPs, seven of which were non-synonymous. Furthermore, the polymorphisms identified in the 3'-UTR were investigated to establish their possible influence on microRNA binding sites. Considering all the amino acid changes and the observed allelic combinations, it is possible to deduce at least six different translations of the buffalo prolactin receptor and, consequently, the presence at the PRLR gene of at least six alleles. Furthermore, we identified a deletion of a CACTACC heptamer between nucleotides 1102 and 1103 of exon 10 (3'-UTR), and we developed an allele-specific PCR to identify the carriers of this genetic marker. Finally, the SNP g.11188A>G, detected in exon 10 and responsible for the amino acid replacement p.His328Arg, was genotyped in 308 Italian Mediterranean river buffaloes, and an association study with milk fat traits was carried out. The statistical analysis showed a tendency that approached significance for the AA genotype with higher contents of odd branched-chain fatty acids. Thus, our results suggest that the PRLR gene is a good candidate for gene association studies with qualitative traits related to buffalo milk production.
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Affiliation(s)
- G Cosenza
- Department of Agricultural Sciences, University of Naples "Federico II", 80055, Portici, NA, Italy
| | - M Iannaccone
- Department of Agricultural Sciences, University of Naples "Federico II", 80055, Portici, NA, Italy
| | - B Auzino
- Department of Veterinary Sciences, University of Pisa, 56124, Pisa, Italy
| | - N P P Macciotta
- Department of Agricultural Sciences, University of Sassari, 07100, Sassari, Italy
| | - A Kovitvadhi
- Department of Physiology, Kasetsart University, 10900, Bangkok, Thailand
| | - I Nicolae
- Research and Development Institute for Bovine Breeding, 077015, Balotesti, Bucharest, Romania
| | - A Pauciullo
- Department of Agricultural, Forest and Food Science, University of Torino, 10095, Grugliasco, TO, Italy
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17
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Liu JJ, Liang AX, Campanile G, Plastow G, Zhang C, Wang Z, Salzano A, Gasparrini B, Cassandro M, Yang LG. Genome-wide association studies to identify quantitative trait loci affecting milk production traits in water buffalo. J Dairy Sci 2017; 101:433-444. [PMID: 29128211 DOI: 10.3168/jds.2017-13246] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 09/13/2017] [Indexed: 01/03/2023]
Abstract
Water buffalo is the second largest resource of milk supply around the world, and it is well known for its distinctive milk quality in terms of fat, protein, lactose, vitamin, and mineral contents. Understanding the genetic architecture of milk production traits is important for future improvement by the buffalo breeding industry. The advance of genome-wide association studies (GWAS) provides an opportunity to identify potential genetic variants affecting important economical traits. In the present study, GWAS was performed for 489 buffaloes with 1,424 lactation records using the 90K Affymetrix Buffalo SNP Array (Affymetrix/Thermo Fisher Scientific, Santa Clara, CA). Collectively, 4 candidate single nucleotide polymorphisms (SNP) in 2 genomic regions were found to associate with buffalo milk production traits. One region affecting milk fat and protein percentage was located on the equivalent of Bos taurus autosome (BTA)3, spanning 43.3 to 43.8 Mb, which harbored the most likely candidate genes MFSD14A, SLC35A3, and PALMD. The other region on the equivalent of BTA14 at 66.5 to 67.0 Mb contained candidate genes RGS22 and VPS13B and influenced buffalo total milk yield, fat yield, and protein yield. Interestingly, both of the regions were reported to have quantitative trait loci affecting milk performance in dairy cattle. Furthermore, we suggest that buffaloes with the C allele at AX-85148558 and AX-85073877 loci and the G allele at AX-85106096 locus can be selected to improve milk fat yield in this buffalo-breeding program. Meanwhile, the G allele at AX-85063131 locus can be used as the favorable allele for improving milk protein percentage. Genomic prediction showed that the reliability of genomic estimated breeding values (GEBV) of 6 milk production traits ranged from 0.06 to 0.22, and the correlation between estimated breeding values and GEBV ranged from 0.23 to 0.35. These findings provide useful information to understand the genetic basis of buffalo milk properties and may play a role in accelerating buffalo breeding programs using genomic approaches.
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Affiliation(s)
- J J Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan, Hubei, China 430070; Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, Hubei, China 430070
| | - A X Liang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan, Hubei, China 430070; Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, Hubei, China 430070
| | - G Campanile
- Department of Veterinary Medicine and Animal Productions, University of Naples "Federico II", Naples, Italy 80137
| | - G Plastow
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada T6G 2C8
| | - C Zhang
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada T6G 2C8
| | - Z Wang
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada T6G 2C8
| | - A Salzano
- Department of Veterinary Medicine and Animal Productions, University of Naples "Federico II", Naples, Italy 80137
| | - B Gasparrini
- Department of Veterinary Medicine and Animal Productions, University of Naples "Federico II", Naples, Italy 80137
| | - M Cassandro
- Department of Agronomy, Food, Natural Resources, Animal, and Environment, University of Padova, Agripolis, Legnaro, Italy 35020
| | - L G Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan, Hubei, China 430070; Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, Hubei, China 430070.
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18
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Kumar R, Mishra SK, Kumar A, Srivastava S, Lathwal S, Bhatia AK, Kataria RS, Niranjan SK. Exploring polymorphism of prolactin gene and its possible association with repeat breeding in buffaloes. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Gu M, Cosenza G, Nicolae I, Bota A, Guo Y, Di Stasio L, Pauciullo A. Transcript analysis at DGAT1 reveals different mRNA profiles in river buffaloes with extreme phenotypes for milk fat. J Dairy Sci 2017; 100:8265-8276. [PMID: 28780112 DOI: 10.3168/jds.2017-12771] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/13/2017] [Indexed: 11/19/2022]
Abstract
Buffalo DGAT1 (diacylglycerol O-acyltransferase 1) was mainly investigated for the characterization of the gene itself and for the identification of the K232A polymorphism, similar to what has been accomplished in cattle, although no information has been reported so far at the mRNA level. The importance of DGAT1 for lipid metabolism led us to investigate the transcript profiles of lactating buffaloes characterized as high (9.13 ± 0.23) and low (7.94 ± 0.29) for milk fat percentage, and to explore the genetic diversity at the RNA and DNA level. A total of 336 positive clones for the DGAT1 cDNA were analyzed by PCR and chosen for sequencing according to the differences in length. The clone assembling revealed a very complex mRNA pattern with a total of 21 transcripts differently represented in the 2 groups of animals. Apart from the correct transcript (17 exons long), the skipping of exon 12 is the most significant in terms of distribution of clones with 11.6% difference between the 2 groups, whereas a totally different mRNA profile was found in approximately 12% of clones. The sequencing of genomic DNA allowed the identification of 10 polymorphic sites at the intron level, which clarify, at least partially, the genetic events behind the production of complex mRNA. Genetic diversity was found also at the exon level. The single nucleotide polymorphism c.1053C>T represents the first example of polymorphism in a coding region for the DGAT1 in the Italian Mediterranean breed. To establish whether this polymorphism is present in other buffalo breeds, a quick method based on PCR-RFLP was set up for allelic discrimination in the Italian Mediterranean and the Romanian Murrah (200 animals in total). The alleles were equally represented in the overall population, whereas the analysis of the 2 breeds showed different frequencies, likely indicating diverse genetic structure of the 2 breeds. The T allele might be considered as the ancestral condition of the DGAT1 gene, being present in the great part of the sequenced species. These data add knowledge at the transcript and genetic levels for the buffalo DGAT1 and open the opportunity for further investigation of other genes involved in milk fat metabolism for the river buffalo, including the future possibility of selecting alleles with quantitative or qualitative favorable effects (or both).
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Affiliation(s)
- M Gu
- Department of Agricultural, Forest and Food Science, University of Torino, 10095 Grugliasco (TO), Italy; College of Animal Science and Technology, Beijing University of Agriculture, 102206 Beijing, China
| | - G Cosenza
- Department of Agricultural Sciences, University of Naples "Federico II", 80055 Portici (NA), Italy
| | - I Nicolae
- Research and Development Institute for Bovine Breeding, Balotesti, 077015 Bucharest, Romania
| | - A Bota
- Research and Development Station for Buffalo Breeding, 507195 Şercaia, Romania
| | - Y Guo
- College of Animal Science and Technology, Beijing University of Agriculture, 102206 Beijing, China
| | - L Di Stasio
- Department of Agricultural, Forest and Food Science, University of Torino, 10095 Grugliasco (TO), Italy
| | - A Pauciullo
- Department of Agricultural, Forest and Food Science, University of Torino, 10095 Grugliasco (TO), Italy.
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20
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Cai X, Liu Q, Zhang X, Ren Y, Lei X, Li S, Chen Q, Deng K, Wang P, Zhang H, Shi D. Identification and analysis of the expression of microRNA from lactating and nonlactating mammary glands of the Chinese swamp buffalo. J Dairy Sci 2017; 100:1971-1986. [PMID: 28109598 DOI: 10.3168/jds.2016-11461] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 11/20/2016] [Indexed: 11/19/2022]
Abstract
To study the role of microRNA (miR) in the lactation physiology of water buffalo, 2 multiparous dairy buffaloes (including an 8-yr-old buffalo that had been lactating for 3 mo, as well as a 10-yr-old nonlactating, nonpregnant buffalo) were used for miR library construction. The profile of differentially expressed miR in lactating and nonlactating mammary gland tissues of these water buffalo were investigated using Illumina-Solexa high-throughput sequencing technology (Illumina, San Diego, CA). The data identified 259 miR families, 359 mature miR, 363 pre-miR, 230 novel buffalo miR, and 5 buffalo-specific miR that were expressed in mammary tissues. Some highly significantly differentially expressed miR were explored, including bbu-miR-497, bbu-miR-30a-5p, bbu-miR-148a, bbu-miR-29a, bbu-miR-125a, bbu-miR-125b, and bbu-miR-103. The expression patterns of 18 miR were confirmed by quantitative real-time PCR in both tissues, and the expression of bbu miR-103 and novel miR-57 constituted the largest differences between lactating and nonlactating tissues. Further functional analysis indicated that the overexpression or suppression of miR-103 in buffalo mammary epithelial cells downregulated or upregulated the expression of pantothenate kinase 3, and also significantly increased the transcription factor steroid regulatory element binding protein, followed by the acceleration of de novo synthesis of fatty acids by upregulation of acetyl coenzyme A carboxylase α expression. The expression levels of 34 predicted target genes of novel-miR-57 in lactating and nonlactating mammary gland tissues were all analyzed by quantitative real-time PCR. Finally, only the expression of docking protein 4 could be upregulated or downregulated selectively by bbu-novel-miR-57 in buffalo mammary epithelial cells and the Bcap-37 cell line. This study provides an overview of the miR expression profile of water buffalo and the interaction between some key miR and their target genes, which may improve understanding of the important roles of miR in buffalo milk fat synthesis.
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Affiliation(s)
- Xiaoyan Cai
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004; Guangxi Institute of Animal Science, Nanning, China, 530001
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004.
| | - Xiaoxi Zhang
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Yanping Ren
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Xiaocan Lei
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Sheng Li
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Qiuping Chen
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Kai Deng
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Ping Wang
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Haihang Zhang
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004.
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21
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Lee S, Kelleher SL. Biological underpinnings of breastfeeding challenges: the role of genetics, diet, and environment on lactation physiology. Am J Physiol Endocrinol Metab 2016; 311:E405-22. [PMID: 27354238 PMCID: PMC5005964 DOI: 10.1152/ajpendo.00495.2015] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 06/22/2016] [Indexed: 02/06/2023]
Abstract
Lactation is a dynamic process that has evolved to produce a complex biological fluid that provides nutritive and nonnutritive factors to the nursing offspring. It has long been assumed that once lactation is successfully initiated, the primary factor regulating milk production is infant demand. Thus, most interventions have focused on improving breastfeeding education and early lactation support. However, in addition to infant demand, increasing evidence from studies conducted in experimental animal models, production animals, and breastfeeding women suggests that a diverse array of maternal factors may also affect milk production and composition. In this review, we provide an overview of our current understanding of the role of maternal genetics and modifiable factors, such as diet and environmental exposures, on reproductive endocrinology, lactation physiology, and the ability to successfully produce milk. To identify factors that may affect lactation in women, we highlight some information gleaned from studies in experimental animal models and production animals. Finally, we highlight the gaps in current knowledge and provide commentary on future research opportunities aimed at improving lactation outcomes in breastfeeding women to improve the health of mothers and their infants.
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Affiliation(s)
- Sooyeon Lee
- Departments of Cellular and Molecular Physiology
| | - Shannon L Kelleher
- Departments of Cellular and Molecular Physiology, Pharmacology, and Surgery, Pennsylvania State Hershey College of Medicine, Hershey, Pennsylvania; and Department of Nutritional Sciences, The Pennsylvania State University, University Park, Pennsylvania
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22
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Menon R, Patel AB, Joshi C. Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing. PeerJ 2016; 4:e2147. [PMID: 27441113 PMCID: PMC4941740 DOI: 10.7717/peerj.2147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 05/27/2016] [Indexed: 12/17/2022] Open
Abstract
River buffalo (Bubalus bubalis) milk plays an important role in economy and nutritious diet in several developing countries. However, reliable milk-yield genomic markers and their functional insights remain unexposed. Here, we have used a target capture sequencing approach in three economically important buffalo breeds namely: Banni, Jafrabadi and Mehsani, belonging to either high or low milk-yield group. Blood samples were collected from the milk-yield/breed balanced group of 12 buffaloes, and whole exome sequencing was performed using Roche 454 GS-FLX Titanium sequencer. Using an innovative approach namely, MultiCom; we have identified high-quality SNPs specific for high and low-milk yield buffaloes. Almost 70% of the reported genes in QTL regions of milk-yield and milk-fat in cattle were present among the buffalo milk-yield gene candidates. Functional analysis highlighted transcriptional regulation category in the low milk-yield group, and several new pathways in the two groups. Further, the discovered SNP candidates may account for more than half of mammary transcriptome changes in high versus low-milk yielding cattle. Thus, starting from the design of a reliable strategy, we identified reliable genomic markers specific for high and low-milk yield buffalo breeds and addressed possible downstream effects.
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Affiliation(s)
- Ramesh Menon
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
| | - Anand B Patel
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
| | - Chaitanya Joshi
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
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23
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Feng W, Chen S, Do D, Liu Q, Deng Y, Lei X, Luo C, Huang B, Shi D. Isolation and Identification of Prepubertal Buffalo (Bubalus bubalis) Spermatogonial Stem Cells. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 29:1407-15. [PMID: 26954139 PMCID: PMC5003965 DOI: 10.5713/ajas.15.0592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/30/2015] [Accepted: 11/14/2015] [Indexed: 12/13/2022]
Abstract
Isolation and culture of spermatogonial stem cells (SSCs) are attractive for production of genetic modified offspring. In the present study, buffalo spermatogonial stem-like cells were isolated, cultured and expression pattern of different germ cell marker genes were determined. To recover spermatogonia, testes from age 3 to 7 months of buffalo were decapsulated, and seminiferous tubules were enzymatically dissociated. Two types of cells, immature sertoli cell and type A spermatogonia were observed in buffalo testes in this stage. Germ cell marker genes, OCT3/4 (Pou5f1), THY-1, c-kit, PGP9.5 (UCHL-1) and Dolichos biflorus agglutinin, were determined to be expressed both in mRNA and protein level by reverse transcription polymerase chain reaction and immunostaining in buffalo testes and buffalo spermatogonial stem-like cells, respectively. In the following, when the isolated buffalo buffalo spermatogonial stem-like cells were cultured in the medium supplemented 2.5% fetal bovine serum and 40 ng/mL glial cell-derived neurotrophic factor medium, SSCs proliferation efficiency and colony number were significantly improved than those of other groups (p<0.05). These findings may help in isolation and establishing long term in vitro culture system for buffalo spermatogonial stem-like cells, and accelerating the generation of genetic modified buffaloes.
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Affiliation(s)
- Wanyou Feng
- State Key Laboratory of Conservation and Untilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Shibei Chen
- State Key Laboratory of Conservation and Untilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China.,Center of Reproduction of Nanxishan Hospital, Guilin 541002, China
| | - Dagiang Do
- State Key Laboratory of Conservation and Untilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China.,Bacgiang Agriculture and Forestry University, Bacgiang 220000 Vietnam
| | - Qinyou Liu
- State Key Laboratory of Conservation and Untilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Yanfei Deng
- State Key Laboratory of Conservation and Untilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Xiaocan Lei
- State Key Laboratory of Conservation and Untilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Chan Luo
- State Key Laboratory of Conservation and Untilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Ben Huang
- State Key Laboratory of Conservation and Untilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Deshun Shi
- State Key Laboratory of Conservation and Untilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
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