1
|
Pauciullo A, Gaspa G, Zhang Y, Liu Q, Cosenza G. CSN1S1, CSN3 and LPL: Three Validated Gene Polymorphisms Useful for More Sustainable Dairy Production in the Mediterranean River Buffalo. Animals (Basel) 2024; 14:1414. [PMID: 38791632 PMCID: PMC11117199 DOI: 10.3390/ani14101414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The search for DNA polymorphisms useful for the genetic improvement of dairy farm animals has spanned more than 40 years, yielding relevant findings in cattle for milk traits, where the best combination of alleles for dairy processing has been found in casein genes and in DGAT1. Nowadays, similar results have not yet been reached in river buffaloes, despite the availability of advanced genomic technologies and accurate phenotype records. The aim of the present study was to investigate and validate the effect of four single nucleotide polymorphisms (SNP) in the CSN1S1, CSN3, SCD and LPL genes on seven milk traits in a larger buffalo population. These SNPs have previously been reported to be associated with, or affect, dairy traits in smaller populations often belonging to one farm. A total of 800 buffaloes were genotyped. The following traits were individually recorded, monthly, throughout each whole lactation period from 2010 to 2021: daily milk yield (dMY, kg), protein yield (dPY, kg) and fat yield (dFY, kg), fat and protein contents (dFP, % and dPP, %), somatic cell count (SCC, 103 cell/mL) and urea (mg/dL). A total of 15,742 individual milk test day records (2496 lactations) were available for 680 buffalo cows, with 3.6 ± 1.7 parities (from 1 to 13) and an average of 6.1 ± 1.2 test day records per lactation. Three out four SNPs in the CSN1S1, CSN3 and LPL genes were associated with at least one of analyzed traits. In particular, the CSN1S1 (AJ005430:c.578C>T) gave favorable associations with all yield traits (dMY, p = 0.022; dPY, p = 0.014; dFY, p = 0.029) and somatic cell score (SCS, p = 0.032). The CSN3 (HQ677596: c.536C>T) was positively associated with SCS (p = 0.005) and milk urea (p = 0.04). Favorable effects on daily milk yield (dMY, p = 0.028), fat (dFP, p = 0.027) and protein (dPP, p = 0.050) percentages were observed for the LPL. Conversely, the SCD did not show any association with milk traits. This is the first example of a confirmation study carried out in the Mediterranean river buffalo for genes of economic interest in the dairy field, and it represents a very important indication for the preselection of young bulls destined for breeding programs aimed at more sustainable dairy production.
Collapse
Affiliation(s)
- Alfredo Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Turin, 10095 Grugliasco, Italy
| | - Giustino Gaspa
- Department of Agricultural, Forest and Food Sciences, University of Turin, 10095 Grugliasco, Italy
| | - Yi Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qingyou Liu
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Gianfranco Cosenza
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy
| |
Collapse
|
2
|
Atashi H, Chen Y, Vanderick S, Hubin X, Gengler N. Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cows. J Dairy Sci 2024; 107:3020-3031. [PMID: 38056570 DOI: 10.3168/jds.2023-23902] [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: 06/26/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
The aims of this study were to conduct a single-step genome-wide association to identify genomic regions associated with milk urea (MU) and to estimate genetic correlations between MU and milk yield (MY), milk composition (calcium content [CC], fat percentage [FP], protein percentage [PP], and casein percentage [CNP]), and cheese-making properties (CMP; coagulation time [CT], curd firmness after 30 min from rennet addition [a30], and titratable acidity [TA]). The used data have been collected from 2015 to 2020 on 78,073 first-parity (485,218 test-day records) and 48,766 second-parity (284,942 test-day records) Holstein cows distributed in 671 herds in the Walloon Region of Belgium. Data of 565,533 SNP located on 29 BTA of 6,617 animals (1,712 males) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of ∼216 kb) was calculated, and the top-3 genomic regions explaining the largest rate of the genetic variance were considered promising regions and used to identify potential candidate genes. Mean (SD) MU was 25.38 (8.02) mg/dL and 25.03 (8.06) mg/dL in the first and second lactation, respectively. Mean heritability estimates for daily MU were 0.21 and 0.23 for the first and second lactation, respectively. The genetic correlations estimated between MU and MY, milk composition, and CMP were quite low (ranged from -0.10 [CC] to 0.10 [TA] and -0.05 [CT] to 0.13 [TA] for the first and second lactations, respectively). The top-3 regions associated with MU were located from 80.61 to 80.74 Mb on BTA6, 103.26 to 103.41 Mb on BTA11, and 1.59 to 2.15 Mb on BTA14. Genes including KCNT1, MROH1, SHARPIN, TSSK5, CPSF1, HSF1, TONSL, DGAT1, SCX, and MAF1 were identified as positional candidate genes for MU. The findings of this study can be used for a better understanding of the genomic architecture underlying MU in Holstein cattle.
Collapse
Affiliation(s)
- H Atashi
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; Department of Animal Science, Shiraz University, 71441-13131 Shiraz, Iran.
| | - Y Chen
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - S Vanderick
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - X Hubin
- Elevéo asbl Awé Group, 5590 Ciney, Belgium
| | - N Gengler
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| |
Collapse
|
3
|
Buitenhuis AJ, Poulsen NA. Estimation of heritability for milk urea and genetic correlations with milk production traits in 3 Danish dairy breeds. J Dairy Sci 2023; 106:5562-5569. [PMID: 37331871 DOI: 10.3168/jds.2022-22798] [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: 09/20/2022] [Accepted: 02/17/2023] [Indexed: 06/20/2023]
Abstract
The aim of this study was to estimate genetic parameters for milk urea (MU) content in 3 main Danish dairy breeds. As a part of the Danish milk recording system, milk samples from cows on commercial farms were analyzed for MU concentration (mmol/L) and the percentages of fat and protein. There were 323,800 Danish Holstein, 70,634 Danish Jersey, and 27,870 Danish Red cows sampled with a total of 1,436,580, 368,251, and 133,922 test-day records per breed, respectively, included in the data set. Heritabilities for MU were low to moderate (0.22, 0.18, and 0.24 for the Holstein, Jersey, and Red breeds, respectively). The genetic correlation was close to zero between MU and milk yield in Jersey and Red, and -0.14 for Holstein. The genetic correlations between MU and fat and protein percentages, respectively, were positive for all 3 dairy breeds. Herd-test-day explained 51%, 54%, and 49% of the variation in MU in Holstein, Jersey, and Red, respectively. This indicates that MU levels in milk can be reduced by farm management. The current study shows that there are possibilities to influence MU by genetic selection as well as by farm management.
Collapse
Affiliation(s)
- A J Buitenhuis
- Center for Quantitative Genetics and Genomics, Aarhus University, DK-8000 Aarhus C, Denmark.
| | - N A Poulsen
- Department of Food Science, Aarhus University, DK-8200 Aarhus N, Denmark
| |
Collapse
|
4
|
Jahnel RE, Blunk I, Wittenburg D, Reinsch N. Relationship between milk urea content and important milk traits in Holstein cattle. Animal 2023; 17:100767. [PMID: 37141636 DOI: 10.1016/j.animal.2023.100767] [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: 06/08/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 05/06/2023] Open
Abstract
Breeding cattle with low nitrogen emissions has been proposed as a countermeasure against eutrophication due to dairy production. Milk urea content (MU) could potentially serve as a new readily measured indicator trait for nitrogen emissions by cows. Therefore, we estimated genetic parameters related to MU and its relationship with other milk traits. We analysed 4 178 735 milk samples collected between January 2008 and June 2019 from 261 866 German Holstein dairy cows during their first, second, and third lactations. Restricted maximum likelihood estimation was conducted using univariate and bivariate random regression sire models in WOMBAT. We obtained moderate average daily heritability estimates for the daily MU of 0.24 in first lactation cows, 0.23 in second lactation cows, and 0.21 in third lactation cows with average daily genetic SDs of 25.16 mg/kg, 24.93 mg/kg, and 23.75 mg/kg, respectively. Averaged over days in milk, the repeatability estimates were low at 0.41 in first, second, and third lactation cows. A strong positive genetic correlation was found between MU and milk urea yield (MUY; 0.72 on average). In addition, 305-day heritabilities were estimated as 0.50, 0.52, and 0.50 in first, second, and third lactation cows, respectively, with genetic correlations of 0.94 or higher for MU in different lactations. By contrast, the averaged estimates of the genetic correlations between MU and other milk traits were low (-0.07 to 0.15). Moderate heritability estimates clearly allow the possible selection for MU, and the near-zero estimates of genetic correlations indicate no risk of undesired correlated selection responses in other milk traits. However, a relationship still needs to be established between MU as an indicator trait and the target trait, defined as total individual nitrogen emissions.
Collapse
Affiliation(s)
- R E Jahnel
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - I Blunk
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - D Wittenburg
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - N Reinsch
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| |
Collapse
|
5
|
Ma L, Luo H, Brito LF, Chang Y, Chen Z, Lou W, Zhang F, Wang L, Guo G, Wang Y. Estimation of genetic parameters and single-step genome-wide association studies for milk urea nitrogen in Holstein cattle. J Dairy Sci 2022; 106:352-363. [DOI: 10.3168/jds.2022-21857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022]
|
6
|
Chen Y, Atashi H, Grelet C, Vanderick S, Hu H, Gengler N. Defining a nitrogen efficiency index in Holstein cows and assessing its potential effect on the breeding program of bulls. J Dairy Sci 2022; 105:7575-7587. [PMID: 35931481 DOI: 10.3168/jds.2021-21681] [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: 12/09/2021] [Accepted: 05/11/2022] [Indexed: 11/19/2022]
Abstract
The purposes of this study were (1) to explore the relationship between 3 milk mid-infrared predicted features including nitrogen intake (NINT), milk true protein N (MTPN), and milk urea-N yield (MUNY); (2) to integrate these 3 features into an N efficiency index (NEI) and analyses approximate genetic correlations between the NEI and 37 traits (indices) of interest; and (3) to assess the potential effect of including the NEI into breeding programs of bulls. The edited data were 1,043,171 test-day records on 342,847 cows in 1,931 herds and 143,595 test-day records on 53,660 cows in 766 herds used for estimating breeding values (EBV) and variance components, respectively. The used records were within 5 to 50 d in milk. The records were grouped into primiparous and multiparous. The genetic parameters for the included mid-infrared features and EBV of the animals included in the pedigree were estimated using a multiple-trait repeatability animal model. Then, the EBV of the NINT, MTPN, MUNY were integrated into the NEI using a selection index assuming weights based on the N partitioning. The approximate genetic correlations between the NEI and 37 traits of interest were estimated using the EBV of the selected bulls. The bulls born from 2011 to 2014 with NEI were selected and the NEI distribution of these bulls having EBV for the 8 selected traits (indices) was checked. The heritability and repeatability estimates for NINT, MTPN, and MUNY ranged from 0.09 to 0.13, and 0.37 to 0.65, respectively. The genetic and phenotypic correlations between NINT, MTPN, and MUNY ranged from -0.31 to 0.87, and -0.02 to 0.42, respectively. The NEI ranged from -13.13 to 12.55 kg/d. In total, 736 bulls with reliability ≥0.50 for all included traits (NEI and 37 traits) and at least 10 daughters distributed in at least 10 herds were selected to investigate genetic aspects of the NEI. The NEI had positive genetic correlations with production yield traits (0.08-0.46), and negative genetic correlations with the investigated functional traits and indices (-0.71 to -0.07), except for the production economic index and functional type economic index. The daughters of bulls with higher NEI had lower NINT and MUNY, and higher MTPN. Furthermore, 26% of the bulls (n = 50) with NEI born between 2011 to 2014 had higher NEI and global economic index than the average in the selected bulls. Finally, the developed NEI has the advantage of large-scale prediction and therefore has the potential for routine application in dairy cattle breeding in the future.
Collapse
Affiliation(s)
- Y Chen
- TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech (ULiège-GxABT), 5030 Gembloux, Belgium
| | - H Atashi
- TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech (ULiège-GxABT), 5030 Gembloux, Belgium; Department of Animal Science, Shiraz University, 71441-65186 Shiraz, Iran
| | - C Grelet
- Walloon Agricultural Research Center (CRA-W), 5030 Gembloux, Belgium
| | - S Vanderick
- TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech (ULiège-GxABT), 5030 Gembloux, Belgium
| | - H Hu
- TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech (ULiège-GxABT), 5030 Gembloux, Belgium
| | - N Gengler
- TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech (ULiège-GxABT), 5030 Gembloux, Belgium.
| |
Collapse
|