Integrating Genomic Selection and a Genome-Wide Association Study to Improve Days Open in Thai Dairy Holstein Cattle: A Comprehensive Genetic Analysis
Days open (DO) is a critical economic and reproductive trait that is commonly employed in genetic selection. Making improvements using conventional genetic techniques is exceedingly challenging. Therefore, new techniques are required to improve the accuracy of genetic selection using genomic data. T...
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2024-12-01
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| author | Akhmad Fathoni Wuttigrai Boonkum Vibuntita Chankitisakul Sayan Buaban Monchai Duangjinda |
| author_facet | Akhmad Fathoni Wuttigrai Boonkum Vibuntita Chankitisakul Sayan Buaban Monchai Duangjinda |
| author_sort | Akhmad Fathoni |
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| description | Days open (DO) is a critical economic and reproductive trait that is commonly employed in genetic selection. Making improvements using conventional genetic techniques is exceedingly challenging. Therefore, new techniques are required to improve the accuracy of genetic selection using genomic data. This study examined the genetic approaches of traditional AIREML and single-step genomic AIREML (ssGAIREML) to assess genetic parameters and the accuracy of estimated breeding values while also investigating SNP regions associated with DO and identifying candidate genes through a genome-wide association study (GWAS). The dataset included 59415 DO records from 36368 Thai–Holstein crossbred cows and 882 genotyped animals. The cows were classified according to their Holstein genetic proportion (breed group, BG) as follows: BG1 (>93.7% Holstein genetics), BG2 (87.5% to 93.6% Holstein genetics), and BG3 (<87.5% Holstein genetics). AIREML was utilized to estimate genetic parameters and variance components. The results of this study reveal that the average DO values for BG1, BG2, and BG3 were 97.64, 97.25, and 96.23 days, respectively. The heritability values were estimated to be 0.02 and 0.03 for the traditional AIREML and ssGAIREML approaches, respectively. Depending on the dataset, the ssGAIREML method produced more accurate estimated breeding values than the traditional AIREML method, ranging from 40.5 to 45.6%. The highest values were found in the top 20% of the dam dataset. For the GWAS, we found 12 potential candidate genes (<i>DYRK1A</i>, <i>CALCR</i>, <i>MIR489</i>, <i>MIR653</i>, <i>SLC36A1</i>, <i>GNA14</i>, <i>GNAQ</i>, <i>TRNAC-GCA</i>, <i>XYLB</i>, <i>ACVR2B</i>, <i>SLC22A14</i>, and <i>EXOC2</i>) that are believed to have a significant influence on days open. In summary, the ssGAIREML method has the potential to enhance the accuracy and heritability of reproductive values compared to those obtained using conventional AIREML. Consequently, it is a viable alternative for transitioning from conventional methodologies to the ssGAIREML method in the breeding program for dairy cattle in Thailand. Moreover, the 12 identified potential candidate genes can be utilized in future studies to select markers for days open in regard to dairy cattle. |
| format | Article |
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| institution | Kabale University |
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| spelling | doaj-art-7500aff22f0847dd90a2f4a10954ca5a2025-01-10T13:13:53ZengMDPI AGAnimals2076-26152024-12-011514310.3390/ani15010043Integrating Genomic Selection and a Genome-Wide Association Study to Improve Days Open in Thai Dairy Holstein Cattle: A Comprehensive Genetic AnalysisAkhmad Fathoni0Wuttigrai Boonkum1Vibuntita Chankitisakul2Sayan Buaban3Monchai Duangjinda4Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDepartment of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDepartment of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDepartment of Livestock Development, Bureau of Animal Husbandry and Genetic Improvement, Pathum Thani 12000, ThailandDepartment of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDays open (DO) is a critical economic and reproductive trait that is commonly employed in genetic selection. Making improvements using conventional genetic techniques is exceedingly challenging. Therefore, new techniques are required to improve the accuracy of genetic selection using genomic data. This study examined the genetic approaches of traditional AIREML and single-step genomic AIREML (ssGAIREML) to assess genetic parameters and the accuracy of estimated breeding values while also investigating SNP regions associated with DO and identifying candidate genes through a genome-wide association study (GWAS). The dataset included 59415 DO records from 36368 Thai–Holstein crossbred cows and 882 genotyped animals. The cows were classified according to their Holstein genetic proportion (breed group, BG) as follows: BG1 (>93.7% Holstein genetics), BG2 (87.5% to 93.6% Holstein genetics), and BG3 (<87.5% Holstein genetics). AIREML was utilized to estimate genetic parameters and variance components. The results of this study reveal that the average DO values for BG1, BG2, and BG3 were 97.64, 97.25, and 96.23 days, respectively. The heritability values were estimated to be 0.02 and 0.03 for the traditional AIREML and ssGAIREML approaches, respectively. Depending on the dataset, the ssGAIREML method produced more accurate estimated breeding values than the traditional AIREML method, ranging from 40.5 to 45.6%. The highest values were found in the top 20% of the dam dataset. For the GWAS, we found 12 potential candidate genes (<i>DYRK1A</i>, <i>CALCR</i>, <i>MIR489</i>, <i>MIR653</i>, <i>SLC36A1</i>, <i>GNA14</i>, <i>GNAQ</i>, <i>TRNAC-GCA</i>, <i>XYLB</i>, <i>ACVR2B</i>, <i>SLC22A14</i>, and <i>EXOC2</i>) that are believed to have a significant influence on days open. In summary, the ssGAIREML method has the potential to enhance the accuracy and heritability of reproductive values compared to those obtained using conventional AIREML. Consequently, it is a viable alternative for transitioning from conventional methodologies to the ssGAIREML method in the breeding program for dairy cattle in Thailand. Moreover, the 12 identified potential candidate genes can be utilized in future studies to select markers for days open in regard to dairy cattle.https://www.mdpi.com/2076-2615/15/1/43genomic selectiondays openThai–Holstein crossbreedsssGAIREML |
| spellingShingle | Akhmad Fathoni Wuttigrai Boonkum Vibuntita Chankitisakul Sayan Buaban Monchai Duangjinda Integrating Genomic Selection and a Genome-Wide Association Study to Improve Days Open in Thai Dairy Holstein Cattle: A Comprehensive Genetic Analysis Animals genomic selection days open Thai–Holstein crossbreeds ssGAIREML |
| title | Integrating Genomic Selection and a Genome-Wide Association Study to Improve Days Open in Thai Dairy Holstein Cattle: A Comprehensive Genetic Analysis |
| title_full | Integrating Genomic Selection and a Genome-Wide Association Study to Improve Days Open in Thai Dairy Holstein Cattle: A Comprehensive Genetic Analysis |
| title_fullStr | Integrating Genomic Selection and a Genome-Wide Association Study to Improve Days Open in Thai Dairy Holstein Cattle: A Comprehensive Genetic Analysis |
| title_full_unstemmed | Integrating Genomic Selection and a Genome-Wide Association Study to Improve Days Open in Thai Dairy Holstein Cattle: A Comprehensive Genetic Analysis |
| title_short | Integrating Genomic Selection and a Genome-Wide Association Study to Improve Days Open in Thai Dairy Holstein Cattle: A Comprehensive Genetic Analysis |
| title_sort | integrating genomic selection and a genome wide association study to improve days open in thai dairy holstein cattle a comprehensive genetic analysis |
| topic | genomic selection days open Thai–Holstein crossbreeds ssGAIREML |
| url | https://www.mdpi.com/2076-2615/15/1/43 |
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