泰国多品种奶牛群体精液生产性状的五组重叠和非重叠滑动窗口比较。
A comparison of five sets of overlapping and non-overlapping sliding windows for semen production traits in the Thai multibreed dairy population.
作者信息
Sarakul Mattaneeya, Elzo Mauricio A, Koonawootrittriron Skorn, Suwanasopee Thanathip, Jattawa Danai, Laodim Thawee
机构信息
Department of Animal Science, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand.
Department of Animal Sciences, University of Florida, Gainesville, FL 32611-0910, USA.
出版信息
Anim Biosci. 2024 Mar;37(3):428-436. doi: 10.5713/ab.23.0230. Epub 2023 Nov 1.
OBJECTIVE
This study compared five distinct sets of biological pathways and associated genes related to semen volume (VOL), number of sperm (NS), and sperm motility (MOT) in the Thai multibreed dairy population.
METHODS
The phenotypic data included 13,533 VOL records, 12,773 NS records, and 12,660 MOT records from 131 bulls. The genotypic data consisted of 76,519 imputed and actual single nucleotide polymorphisms (SNPs) from 72 animals. The SNP additive genetic variances for VOL, NS, and MOT were estimated for SNP windows of one SNP (SW1), ten SNP (SW10), 30 SNP (SW30), 50 SNP (SW50), and 100 SNP (SW100) using a single-step genomic best linear unbiased prediction approach. The fixed effects in the model were contemporary group, ejaculate order, bull age, ambient temperature, and heterosis. The random effects accounted for animal additive genetic effects, permanent environment effects, and residual. The SNPs explaining at least 0.001% of the additive genetic variance in SW1, 0.01% in SW10, 0.03% in SW30, 0.05% in SW50, and 0.1% in SW100 were selected for gene identification through the NCBI database. The pathway analysis utilized genes associated with the identified SNP windows.
RESULTS
Comparison of overlapping and non-overlapping SNP windows revealed notable differences among the identified pathways and genes associated with the studied traits. Overlapping windows consistently yielded a larger number of shared biological pathways and genes than non-overlapping windows. In particular, overlapping SW30 and SW50 identified the largest number of shared pathways and genes in the Thai multibreed dairy population.
CONCLUSION
This study yielded valuable insights into the genetic architecture of VOL, NS, and MOT. It also highlighted the importance of assessing overlapping and non-overlapping SNP windows of various sizes for their effectiveness to identify shared pathways and genes influencing multiple traits.
目的
本研究比较了泰国多品种奶牛群体中与精液量（VOL）、精子数量（NS）和精子活力（MOT）相关的五组不同的生物途径及相关基因。
方法
表型数据包括来自131头公牛的13533条VOL记录、12773条NS记录和12660条MOT记录。基因型数据由来自72头动物的76519个估算和实际单核苷酸多态性（SNP）组成。使用单步基因组最佳线性无偏预测方法，对一个SNP（SW1）、十个SNP（SW10）、30个SNP（SW30）、50个SNP（SW50）和100个SNP（SW100）的SNP窗口估计VOL、NS和MOT的SNP加性遗传方差。模型中的固定效应为同期组、射精顺序、公牛年龄、环境温度和杂种优势。随机效应包括动物加性遗传效应、永久环境效应和残差。通过NCBI数据库选择在SW1中解释至少0.001%的加性遗传方差、在SW10中解释0.01%、在SW30中解释0.03%、在SW50中解释0.05%和在SW100中解释0.1%的SNP进行基因鉴定。通路分析利用与鉴定出的SNP窗口相关的基因。
结果
重叠和非重叠SNP窗口的比较揭示了与所研究性状相关的已鉴定途径和基因之间的显著差异。与非重叠窗口相比，重叠窗口始终产生更多数量的共享生物途径和基因。特别是，重叠的SW30和SW50在泰国多品种奶牛群体中鉴定出的共享途径和基因数量最多。
结论
本研究对VOL、NS和MOT的遗传结构提供了有价值的见解。它还强调了评估不同大小的重叠和非重叠SNP窗口对于识别影响多个性状的共享途径和基因的有效性的重要性。
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