Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cows
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],...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-05-01
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| Series: | Journal of Dairy Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0022030223008251 |
| _version_ | 1797201240508071936 |
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| author | H. Atashi Y. Chen S. Vanderick X. Hubin N. Gengler |
| author_facet | H. Atashi Y. Chen S. Vanderick X. Hubin N. Gengler |
| author_sort | H. Atashi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-24T07:44:24Z |
| format | Article |
| id | doaj.art-3b7f8b12b46c407c99f3310761b76eaf |
| institution | Directory Open Access Journal |
| issn | 0022-0302 |
| language | English |
| last_indexed | 2024-04-24T07:44:24Z |
| publishDate | 2024-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Dairy Science |
| spelling | doaj.art-3b7f8b12b46c407c99f3310761b76eaf2024-04-19T04:16:12ZengElsevierJournal of Dairy Science0022-03022024-05-01107530203031Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cowsH. Atashi0Y. Chen1S. Vanderick2X. Hubin3N. Gengler4TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; Department of Animal Science, Shiraz University, 71441-13131 Shiraz, Iran; Corresponding authorTERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, BelgiumTERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, BelgiumElevéo asbl Awé Group, 5590 Ciney, BelgiumTERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, BelgiumABSTRACT: 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.http://www.sciencedirect.com/science/article/pii/S0022030223008251milk ureagenomic associationHolstein |
| spellingShingle | H. Atashi Y. Chen S. Vanderick X. Hubin N. Gengler Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cows Journal of Dairy Science milk urea genomic association Holstein |
| title | Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cows |
| title_full | Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cows |
| title_fullStr | Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cows |
| title_full_unstemmed | Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cows |
| title_short | Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cows |
| title_sort | single step genome wide association analyses for milk urea concentration in walloon holstein cows |
| topic | milk urea genomic association Holstein |
| url | http://www.sciencedirect.com/science/article/pii/S0022030223008251 |
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