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Pauciullo A, Versace C, Miretti S, Giambra IJ, Gaspa G, Letaief N, Cosenza G. Genetic variability among and within domestic Old and New World camels at the α-lactalbumin gene (LALBA) reveals new alleles and polymorphisms responsible for differential expression. J Dairy Sci 2024; 107:1068-1084. [PMID: 38122895 DOI: 10.3168/jds.2023-23813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/13/2023] [Indexed: 12/23/2023]
Abstract
α-Lactalbumin (α-LA), which is encoded by the LALBA gene, is a major whey protein that binds to Ca2+ and facilitates lactose synthesis as a regulatory subunit of the synthase enzyme complex. In addition, it has been shown to play central roles in immune modulation, cell-growth regulation, and antimicrobial activity. In this study, a multitechnical approach was used to fully characterize the LALBA gene and its variants in both coding and regulatory regions for domestic camelids (dromedary, Bactrian camel, alpaca, and llama). The gene analysis revealed a conserved structure among the camelids, but a slight difference in size (2,012 bp on average) due to intronic variations. Promoters were characterized for the transcription factor binding sites (11 found in total). Intraspecies sequence comparison showed 36 SNPs in total (2 in the dromedary, none in the Bactrian camel, 22 in the alpaca, and 12 in the llama), whereas interspecies comparison showed 86 additional polymorphic sites. Eight SNPs were identified as trans-specific polymorphisms, and 2 of them (g.112A>G and g.1229A>G) were particularly interesting in the New World camels. The first creates a new binding site for transcription factor SP1. An enhancing effect of the g.112G variant on the expression was demonstrated by 3 independent pGL3 gene reporter assays. The latter is responsible for the p.78Ile>Val AA replacement and represents novel allelic variants (named LALBA A and B). A link to protein variants has been established by isoelectric focusing (IEF), and bioinformatics analysis revealed that carriers of valine (g.1229G) have a higher glycosylation rate. Genotyping methods based on restriction fragment length polymorphism (PCR-RFLP) were set up for both SNPs. Overall, adenine was more frequent (0.54 and 0.76) at both loci. Four haplotypes were found, and the AA and GA were the most common with a frequency of 0.403 and 0.365, respectively. Conversely, a putative biological gain characterizes the haplotype GG. Therefore, opportunities for rapid directional selection can be realized if this haplotype is associated with favorable milk protein properties. This study adds knowledge at the gene and protein level for α-LA (LALBA) in camelids and importantly contributes to a relatively unexplored research area in these species.
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Affiliation(s)
- A Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy.
| | - C Versace
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy
| | - S Miretti
- Department of Veterinary Sciences, University of Torino, 10095 Grugliasco (TO), Italy
| | - I J Giambra
- Institute for Animal Breeding and Genetics, Justus Liebig University, 35390 Gießen, Germany
| | - G Gaspa
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy
| | - N Letaief
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy; Laboratory of Animal and Forage Production, National Agricultural Research Institute of Tunisia, University of Carthage, Ariana 1004, Tunisia
| | - G Cosenza
- Department of Agriculture, University of Napoli Federico II, 80055 Portici (NA), Italy
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Qu Y, Chen L, Ren X, Shari A, Yuan Y, Yu M, Xiao H, Li G. Milk proteomic analysis reveals differentially expressed proteins in high-yielding and low-yielding Guanzhong dairy goats at peak lactation. J DAIRY RES 2024; 91:31-37. [PMID: 38415394 DOI: 10.1017/s0022029924000013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The aim of this experiment was to investigate the differential proteomic characteristics of milk from high- and low-yielding Guanzhong dairy goats during the peak lactation period under the same feeding conditions. Nine Guanzhong dairy goats with high yield (H: 3.5 ± 0.17 kg/d) and nine with low yield (L:1.2 ± 0.25 kg/d) were selected for milk proteomic analysis using tandem mass tag technology. A total of 78 differentially expressed proteins were identified. Compared with L, 50 proteins including HK3, HSPB1 and ANXA2 were significantly upregulated in H milk, while 28 proteins including LALBA and XDH were significantly downregulated. Bioinformatics analysis of the differentially expressed proteins showed that galactose metabolism, purine metabolism, glycolysis/gluconeogenesis, MAPK signaling pathway, regulation of actin cytoskeleton and other pathways were closely related to milk yield. HK3, HSPB1, ANXA2, LALBA and XDH were important candidate proteins associated with the milk production characteristics of Guanzhong dairy goats. Our data provide relevant biomarkers and a theoretical basis for improving milk production in Guanzhong dairy goats.
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Affiliation(s)
- Yingxin Qu
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Lu Chen
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xinyang Ren
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Akang Shari
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Yuxin Yuan
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Mengqi Yu
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Haoqi Xiao
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Guang Li
- Technology Innovation Laboratory of Dairy Sheep Industry, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
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Xu C, Xie J, Ji F, Peng W, Song Y, Diao X, Wu H. Supplementation of dietary semen vaccariae extracts to lactating sow diets: effects on the production performance, milk components, and gene expression related to mammogenesis. Front Vet Sci 2023; 10:1284552. [PMID: 38026663 PMCID: PMC10666067 DOI: 10.3389/fvets.2023.1284552] [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: 08/28/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
This study aimed to investigate the effects of dietary semen vaccariae extracts (SVE) on the production performance, colostrum components, and relative gene expression related to mammogenesis of lactating sows. 48 pregnant sows were selected and randomly allocated into four groups, with six replicates and two sows per replicate. The first group was the control (CON), while the other groups received the same diet further supplemented with 1.5, 3.0 and 4.5 g SVE per kg (SV1, SV2 and SV3, respectively). Compared with the control group, (1) the average daily gain was increased (p < 0.05) in SV1, SV2, and SV3 during the 11-21 days and 1-21 days of lactation; (2) the serum insulin-like growth factor-1, insulin, prolactin, and estrogen contents in SV1, SV2, and SV3 were increased (p < 0.05) on the 1st and 21st day of lactation; (3) The plasma Lysine, Threonine, and Tryptophan concentrations were also higher (p < 0.05) in SV1, SV2, and SV3 on the 1st and 21st day of lactation; (4) The milk Lysine, Methionine, Threonine, and Tryptophan concentrations were higher (p < 0.05) in SV1, SV2, and SV3 on the 1st and 21st day of lactation; (5) The milk lactose ratio and milk protein content were increased (p < 0.05) in the groups treated with semen vaccariae on the 1st day of lactation, while the milkfat ratio and milk protein content were increased (p < 0.05) in SV2 and SV3 on the 21st day of lactation; (6) the immunoglobulin M, A, and G contents were increased (p < 0.05) in the groups treated with the semen vaccariae on the first day of lactation; and (7) the relative PRLR, STAT5a, FcRn, CSN2, and LALBA expressions were higher (p < 0.05) in the groups treated with the semen vaccariae on the 1st and 21st day of lactation. In this study, the optimum dosage was 3.0 g/kg semen vaccariae, which increased the average daily gain of piglets, total lactation yield, and serum hormone levels, improved the amino acid levels in plasma, and facilitated the milk quality, up-regulated the relative gene expressions in the mammogenesis.
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Affiliation(s)
- Chaohua Xu
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jiajun Xie
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Fengjie Ji
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Weiqi Peng
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Yuzhuo Song
- Department of Animal Husbandry and Veterinary Medicine, Shijiazhuang Information Engineering Vocational College, Shijiazhuang, China
| | - Xinping Diao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hongzhi Wu
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
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Ahmad SF, Chandrababu Shailaja C, Vaishnav S, Kumar A, Gaur GK, Janga SC, Ahmad SM, Malla WA, Dutt T. Read-depth based approach on whole genome resequencing data reveals important insights into the copy number variation (CNV) map of major global buffalo breeds. BMC Genomics 2023; 24:616. [PMID: 37845620 PMCID: PMC10580622 DOI: 10.1186/s12864-023-09720-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/05/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Elucidating genome-wide structural variants including copy number variations (CNVs) have gained increased significance in recent times owing to their contribution to genetic diversity and association with important pathophysiological states. The present study aimed to elucidate the high-resolution CNV map of six different global buffalo breeds using whole genome resequencing data at two coverages (10X and 30X). Post-quality control, the sequence reads were aligned to the latest draft release of the Bubaline genome. The genome-wide CNVs were elucidated using a read-depth approach in CNVnator with different bin sizes. Adjacent CNVs were concatenated into copy number variation regions (CNVRs) in different breeds and their genomic coverage was elucidated. RESULTS Overall, the average size of CNVR was lower at 30X coverage, providing finer details. Most of the CNVRs were either deletion or duplication type while the occurrence of mixed events was lesser in number on a comparative basis in all breeds. The average CNVR size was lower at 30X coverage (0.201 Mb) as compared to 10X (0.013 Mb) with the finest variants in Banni buffaloes. The maximum number of CNVs was observed in Murrah (2627) and Pandharpuri (25,688) at 10X and 30X coverages, respectively. Whereas the minimum number of CNVs were scored in Surti at both coverages (2092 and 17,373). On the other hand, the highest and lowest number of CNVRs were scored in Jaffarabadi (833 and 10,179 events) and Surti (783 and 7553 events) at both coverages. Deletion events overnumbered duplications in all breeds at both coverages. Gene profiling of common overlapped genes and longest CNVRs provided important insights into the evolutionary history of these breeds and indicate the genomic regions under selection in respective breeds. CONCLUSION The present study is the first of its kind to elucidate the high-resolution CNV map in major buffalo populations using a read-depth approach on whole genome resequencing data. The results revealed important insights into the divergence of major global buffalo breeds along the evolutionary timescale.
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Affiliation(s)
- Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
| | - Celus Chandrababu Shailaja
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Sakshi Vaishnav
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Amit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Gyanendra Kumar Gaur
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Sarath Chandra Janga
- Luddy School of Informatics, Computing & Engineering, Indiana University Indianapolis (IUI), Indianapolis, 46202, USA
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and AH, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu & Kashmir, 190006, India.
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Triveni Dutt
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
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Yang L, Han J, Deng T, Li F, Han X, Xia H, Quan F, Hua G, Yang L, Zhou Y. Comparative analyses of copy number variations between swamp buffaloes and river buffaloes. Anim Genet 2023; 54:199-206. [PMID: 36683294 DOI: 10.1111/age.13288] [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: 11/24/2022] [Revised: 11/24/2022] [Accepted: 12/12/2022] [Indexed: 01/24/2023]
Abstract
As an important source of genomic variation, copy number variation (CNV) contributes to environmental adaptation in worldwide buffaloes. Despite this importance, CNV divergence between swamp buffaloes and river buffaloes has not been studied previously. Here, we report 21 152 CNV regions (CNVRs) in 141 buffaloes of 20 breeds detected through multiple CNV calling strategies. Only 248 CNVRs were shared between river buffalo and swamp buffalo, reflecting great variation of CNVRs between the two subspecies. Population structure analysis based on CNVs successfully separated the two buffalo subspecies. We further assessed CNV divergence by calculating FST for genome-wide CNVs. Totally, we identified 110 significantly divergent CNV segments and 44 putatively selected genes between river buffaloes and swamp buffaloes. In particular, LALBA, a key gene controlling milk production in cattle, presented a highly differentiated CNV in the promoter region, which makes it a strong functional candidate gene for differences between swamp buffaloes and river buffaloes in traits related to milk production. Our study provides useful information of CNVs in buffaloes, which may help explain the genetic differences between the two subspecies.
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Affiliation(s)
- Lv Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiazheng Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Fan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaotao Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fanfan Quan
- Livestock and Poultry Breeding Center of Hubei Province, Wuhan, China
| | - Guohua Hua
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
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