1
|
Topno NA, Kesarwani V, Kushwaha SK, Azam S, Kadivella M, Gandham RK, Majumdar SS. Non-Synonymous Variants in Fat QTL Genes among High- and Low-Milk-Yielding Indigenous Breeds. Animals (Basel) 2023; 13:ani13050884. [PMID: 36899741 PMCID: PMC10000039 DOI: 10.3390/ani13050884] [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: 10/13/2022] [Revised: 12/17/2022] [Accepted: 12/25/2022] [Indexed: 03/06/2023] Open
Abstract
The effect of breed on milk components-fat, protein, lactose, and water-has been observed to be significant. As fat is one of the major price-determining factors for milk, exploring the variations in fat QTLs across breeds would shed light on the variable fat content in their milk. Here, on whole-genome sequencing, 25 differentially expressed hub or bottleneck fat QTLs were explored for variations across indigenous breeds. Out of these, 20 genes were identified as having nonsynonymous substitutions. A fixed SNP pattern in high-milk-yielding breeds in comparison to low-milk-yielding breeds was identified in the genes GHR, TLR4, LPIN1, CACNA1C, ZBTB16, ITGA1, ANK1, and NTG5E and, vice versa, in the genes MFGE8, FGF2, TLR4, LPIN1, NUP98, PTK2, ZTB16, DDIT3, and NT5E. The identified SNPs were ratified by pyrosequencing to prove that key differences exist in fat QTLs between the high- and low-milk-yielding breeds.
Collapse
Affiliation(s)
- Neelam A. Topno
- DBT—National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India
- RCB—Regional Centre of Biotechnology, Delhi 121001, India
| | - Veerbhan Kesarwani
- DBT—National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India
| | | | - Sarwar Azam
- DBT—National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India
| | - Mohammad Kadivella
- DBT—National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India
| | - Ravi Kumar Gandham
- ICAR—Indian Veterinary Research Institute, Bareilly 243122, India
- Correspondence: (R.K.G.); (S.S.M.)
| | - Subeer S. Majumdar
- DBT—National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India
- Correspondence: (R.K.G.); (S.S.M.)
| |
Collapse
|
2
|
Nazar M, Abdalla IM, Chen Z, Ullah N, Liang Y, Chu S, Xu T, Mao Y, Yang Z, Lu X. Genome-Wide Association Study for Udder Conformation Traits in Chinese Holstein Cattle. Animals (Basel) 2022; 12:2542. [PMID: 36230283 PMCID: PMC9559277 DOI: 10.3390/ani12192542] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Udder conformation traits are one of the most economic traits in dairy cows, greatly affecting animal health, milk production, and producer profitability in the dairy industry. Genetic analysis of udder structure and scores have been developed in Holstein cattle. In our research, we conducted a genome-wide association study for five udder traits, including anterior udder attachment (AUA), central suspensory ligament (CSL), posterior udder attachment height (PUAH), posterior udder attachment width (PUAW), and udder depth (UD), in which the fixed and random model circulating probability unification (FarmCPU) model was applied for the association analysis. The heritability and the standard errors of these five udder traits ranged from 0.04 ± 0.00 to 0.49 ± 0.03. Phenotype data were measured from 1000 Holstein cows, and the GeneSeek Genomic Profiler (GGP) Bovine 100 K SNP chip was used to analyze genotypic data in Holstein cattle. For GWAS analysis, 984 individual cows and 84,407 single-nucleotide polymorphisms (SNPs) remained after quality control; a total of 18 SNPs were found at the GW significant threshold (p < 5.90 × 10−7). Many candidate genes were identified within 200kb upstream or downstream of the significant SNPs, which include MGST1, MGST2, MTUS1, PRKN, STXBP6, GRID2, E2F8, CDH11, FOXP1, SLF1, TMEM117, SBF2, GC, ADGRB3, and GCLC. Pathway analysis revealed that 58 Gene Ontology (GO) terms and 18 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched with adjusted p values, and these GO terms and the KEGG pathway analysis were associated with biological information, metabolism, hormonal growth, and development processes. These results could give valuable biological information for the genetic architecture of udder conformation traits in dairy Holstein cattle.
Collapse
Affiliation(s)
- Mudasir Nazar
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | | | - Zhi Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Numan Ullah
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yan Liang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shuangfeng Chu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tianle Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Yongjiang Mao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
3
|
Genome-Wide SNP Analysis for Milk Performance Traits in Indigenous Sheep: A Case Study in the Egyptian Barki Sheep. Animals (Basel) 2021; 11:ani11061671. [PMID: 34205212 PMCID: PMC8228706 DOI: 10.3390/ani11061671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary The Barki sheep is one of the three main breeds in Egypt, which is spread mainly throughout the northwestern coastal zone, which has harsh conditions. Considering the harsh, semi-arid habitat of this breed, milk performance traits such as milk yield and milk composition have a very important role in the feeding of newborn lambs and affect their growth during the early stage of life. In this study, rare milk performance data and genomic information of Barki sheep were used to uncover diversified genomic regions that could explain the variability of milk yield and milk quality traits in the studied population of Barki ewes. Genome-wide analysis identified genomic regions harboring interesting candidate genes such as SLC5A8, NUB1, TBC1D1, KLF3 and ABHD5 for milk yield and PPARA and FBLN1 genes for milk quality traits. The findings offer valuable information for obtaining a better understanding of the genetics of milk performance traits and contribute to the genetic improvement of these traits in Barki sheep. Abstract Sheep milk yield and milk composition traits play an important role in supplying newborn lambs with essential components such as amino acids, energy, vitamins and immune antibodies and are also of interest in terms of the nutritional value of the milk for human consumption. The aim of this study was to identify genomic regions and candidate genes for milk yield and milk composition traits through genome-wide SNP analyses between high and low performing ewes of the Egyptian Barki sheep breed, which is well adapted to the harsh conditions of North-East Africa. Therefore, out of a herd of 111 ewes of the Egyptian Barki sheep breed (IBD = 0.08), ewes representing extremes in milk yield and milk quality traits (n = 25 for each group of animals) were genotyped using the Illumina OvineSNP50 V2 BeadChip. The fixation index (FST) for each SNP was calculated between the diversified groups. FST values were Z-transformed and used to identify putative SNPs for further analysis (Z(FST) > 10). Genome-wide SNP analysis revealed genomic regions covering promising candidate genes related to milk performance traits such as SLC5A8, NUB1, TBC1D1, KLF3 and ABHD5 for milk yield and PPARA and FBLN1 genes for milk quality trait. The results of this study may contribute to the genetic improvement of milk performance traits in Barki sheep breed and to the general understanding of the genetic contribution to variability in milk yield and quality traits.
Collapse
|
4
|
Li C, Cai W, Liu S, Zhou C, Cao M, Yin H, Sun D, Zhang S, Loor JJ. Association of UDP-galactose-4-epimerase with milk protein concentration in the Chinese Holstein population. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1725-1731. [PMID: 32106650 PMCID: PMC7649079 DOI: 10.5713/ajas.19.0549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 02/14/2020] [Indexed: 01/20/2023]
Abstract
Objective An initial RNA-Sequencing study revealed that UDP-galactose-4-epimerase (GALE) was one of the most promising candidates for milk protein concentration in Chinese Holstein cattle. This enzyme catalyzes the interconversion of UDP-galactose and UDP-glucose, an important step in galactose catabolism. To further validate the genetic effect of GALE on milk protein traits, genetic variations were identified, and genotypes-phenotypes associations were performed. Methods The entire coding region and the 5′-regulatory region (5′-UTR) of GALE were re-sequenced using pooled DNA of 17 unrelated sires. Association studies for five milk production traits were performed using a mixed linear animal model with a population encompassing 1,027 Chinese Holstein cows. Results A total of three variants in GALE were identified, including two novel variants (g.2114 A>G and g.2037 G>A) in the 5′-UTR and one previously reported variant (g.3836 G>C) in an intron. All three single nucleotide polymorphisms (SNPs) were associated with milk yield (p<0.0001), fat yield (p = 0.0006 to <0.0001), protein yield (p = 0.0232 to <0.0001) and protein percentage (p<0.0001), while no significant associations were detected between the SNPs and fat percentage. A strong linkage disequilibrium (D’ = 0.96 to 1.00) was observed among all three SNPs, and a 5 Kb haplotype block involving three main haplotypes with GAG, AGC, and AGG was formed. The results of haplotype association analyses were consistent with the results of single locus association analysis (p<0.0001). The phenotypic variance ratio above 3.00% was observed for milk protein yield that was explained by SNP-g.3836G >C. Conclusion Overall, our findings provided new insights into the polymorphic variations in bovine GALE gene and their associations with milk protein concentration. The data indicate their potential uses for marker-assisted breeding or genetic selection schemes.
Collapse
Affiliation(s)
- Cong Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wentao Cai
- 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, Beijing 100193, China
| | - Shuli Liu
- 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, Beijing 100193, China
| | - Chenghao Zhou
- 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, Beijing 100193, China
| | - Mingyue Cao
- 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, Beijing 100193, China
| | - Hongwei Yin
- 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, Beijing 100193, China
| | - Dongxiao Sun
- 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, Beijing 100193, China
| | - Shengli Zhang
- 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, Beijing 100193, China
| | - Juan J Loor
- Mammalian NutriPhysioGenomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA
| |
Collapse
|
5
|
Jiang J, Liu L, Gao Y, Shi L, Li Y, Liang W, Sun D. Determination of genetic associations between indels in 11 candidate genes and milk composition traits in Chinese Holstein population. BMC Genet 2019; 20:48. [PMID: 31138106 PMCID: PMC6537361 DOI: 10.1186/s12863-019-0751-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/20/2019] [Indexed: 01/20/2023] Open
Abstract
Background We have previously identified 11 promising candidate genes for milk composition traits by resequencing the whole genomes of 8 Holstein bulls with extremely high and low estimated breeding values for milk protein and fat percentages (high and low groups), including FCGR2B, CENPE, RETSAT, ACSBG2, NFKB2, TBC1D1, NLK, MAP3K1, SLC30A2, ANGPT1 and UGDH those contained 25 indels between high and low groups. In this study, the purpose was to further examine whether these candidates have significant genetic effects on milk protein and fat traits. Results With PCR product sequencing, 13 indels identified by whole genome resequencing were successfully genotyped. With association analysis in 769 Chinese Holstein cows, we found that the indel in FCGR2B was significantly associated with milk yield, protein yield and protein percentage (P = 0.0041 to 0.0297); five indels in CENPE and one indel in MAP3K1 were markedly relevant to milk yield, fat yield and protein yield (P < 0.0001 to 0.0073); polymorphism in RETSAT was evidently associated with milk yield, fat yield, protein yield and protein percentage (P = 0.0001 to 0.0237); variant in ACSBG2 affected fat yield and protein percentage (P = 0.0088 and 0.0052); one indel in TBC1D1 was with respect to fat percentage and protein percentage (P = 0.0224 and 0.0209). Significant associations were shown between indels in NLK and protein yield and protein percentage (P = 0.0012 to 0.0257); variant in UGDH was related to the milk yield (P = 0.0312). The two exonic indels in FCGR2B and CENPE were predicted to change the mRNA and protein secondary structures, and resulted in the corresponding protein dysfunction. Conclusion Our findings presented here provide the first evidence for the associations of eight functional genes with milk yield and composition traits in dairy cattle. Electronic supplementary material The online version of this article (10.1186/s12863-019-0751-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jianping Jiang
- 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.,College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Lin Liu
- Beijing Dairy Cattle Center, Beijing, 100085, China
| | - Yahui Gao
- 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
| | - Lijun Shi
- 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
- 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.,Beijing Dairy Cattle Center, Beijing, 100085, China
| | - Weijun Liang
- 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.
| |
Collapse
|
6
|
Jiang J, Gao Y, Hou Y, Li W, Zhang S, Zhang Q, Sun D. Whole-Genome Resequencing of Holstein Bulls for Indel Discovery and Identification of Genes Associated with Milk Composition Traits in Dairy Cattle. PLoS One 2016; 11:e0168946. [PMID: 28030618 PMCID: PMC5193355 DOI: 10.1371/journal.pone.0168946] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/08/2016] [Indexed: 11/18/2022] Open
Abstract
The use of whole-genome resequencing to obtain more information on genetic variation could produce a range of benefits for the dairy cattle industry, especially with regard to increasing milk production and improving milk composition. In this study, we sequenced the genomes of eight Holstein bulls from four half- or full-sib families, with high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage at an average effective depth of 10×, using Illumina sequencing. Over 0.9 million nonredundant short insertions and deletions (indels) [1–49 base pairs (bp)] were obtained. Among them, 3,625 indels that were polymorphic between the high and low groups of bulls were revealed and subjected to further analysis. The vast majority (76.67%) of these indels were novel. Follow-up validation assays confirmed that most (70%) of the randomly selected indels represented true variations. The indels that were polymorphic between the two groups were annotated based on the cattle genome sequence assembly (UMD3.1.69); as a result, nearly 1,137 of them were found to be located within 767 annotated genes, only 5 (0.138%) of which were located in exons. Then, by integrated analysis of the 767 genes with known quantitative trait loci (QTL); significant single-nucleotide polymorphisms (SNPs) previously identified by genome-wide association studies (GWASs) to be associated with bovine milk protein and fat traits; and the well-known pathways involved in protein, fat synthesis, and metabolism, we identified a total of 11 promising candidate genes potentially affecting milk composition traits. These were FCGR2B, CENPE, RETSAT, ACSBG2, NFKB2, TBC1D1, NLK, MAP3K1, SLC30A2, ANGPT1 and UGDH. Our findings provide a basis for further study and reveal key genes for milk composition traits in dairy cattle.
Collapse
Affiliation(s)
- Jianping Jiang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Yahui Gao
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Yali Hou
- Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Wenhui Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Shengli Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Qin Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Dongxiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
- * E-mail:
| |
Collapse
|
7
|
RNA-Seq reveals 10 novel promising candidate genes affecting milk protein concentration in the Chinese Holstein population. Sci Rep 2016; 6:26813. [PMID: 27254118 PMCID: PMC4890585 DOI: 10.1038/srep26813] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/09/2016] [Indexed: 01/19/2023] Open
Abstract
Paired-end RNA sequencing (RNA-Seq) was used to explore the bovine transcriptome from the mammary tissue of 12 Chinese Holstein cows with 6 extremely high and 6 low phenotypic values for milk protein percentage. We defined the differentially expressed transcripts between the two comparison groups, extremely high and low milk protein percentage during the peak lactation (HP vs LP) and during the non-lactating period (HD vs LD), respectively. Within the differentially expressed genes (DEGs), we detected 157 at peak lactation and 497 in the non-lactating period with a highly significant correlation with milk protein concentration. Integrated interpretation of differential gene expression indicated that SERPINA1, CLU, CNTFR, ERBB2, NEDD4L, ANG, GALE, HSPA8, LPAR6 and CD14 are the most promising candidate genes affecting milk protein concentration. Similarly, LTF, FCGR3A, MEGF10, RRM2 and UBE2C are the most promising candidates that in the non-lactating period could help the mammary tissue prevent issues with inflammation and udder disorders. Putative genes will be valuable resources for designing better breeding strategies to optimize the content of milk protein and also to provide new insights into regulation of lactogenesis.
Collapse
|