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17 pages, 1585 KiB  
Article
Integrating Genomic Selection and a Genome-Wide Association Study to Improve Days Open in Thai Dairy Holstein Cattle: A Comprehensive Genetic Analysis
by Akhmad Fathoni, Wuttigrai Boonkum, Vibuntita Chankitisakul, Sayan Buaban and Monchai Duangjinda
Animals 2025, 15(1), 43; https://doi.org/10.3390/ani15010043 (registering DOI) - 27 Dec 2024
Viewed by 145
Abstract
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 [...] Read more.
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 (DYRK1A, CALCR, MIR489, MIR653, SLC36A1, GNA14, GNAQ, TRNAC-GCA, XYLB, ACVR2B, SLC22A14, and EXOC2) 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. Full article
(This article belongs to the Collection Advances in Cattle Breeding, Genetics and Genomics)
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Figure 1

Figure 1
<p>Comparison of the mean values of days open (T, standard error) separated by breed group and parity. The superscripts <sup>a–c</sup> indicate statistically significant differences (<span class="html-italic">p</span> &lt; 0.05) within each breed group.</p>
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<p>The SNP effect from GEBVs for the days open of Thai–Holstein crossbred cattle.</p>
Full article ">Figure 3
<p>Manhattan plots of the additive genetic variance explained by windows of five adjacent SNPs for DO of Thai–Holstein crossbred cattle. The different colors in the image represent different chromosome names.</p>
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<p>Manhattan plot of GWAS for the days open of Thai–Holstein crossbred cattle. The y-axis depicts the −log10 value of the reported <span class="html-italic">p</span>-values for genome-wide SNPs, while the x-axis represents their placements on each chromosome. The horizontal line represents the threshold level, which is suggestive at a significance level of −log10 of 5 × 10<sup>−8</sup>.</p>
Full article ">
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