Ahmad Sheikh Firdous, Singh Akansha, Gangwar Munish, Kumar Subodh, Dutt Triveni, Kumar Amit
ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
Gene. 2023 May 30;867:147365. doi: 10.1016/j.gene.2023.147365. Epub 2023 Mar 12.
Haplotype-based association analysis promises to reveal important information regarding the effect of genetic variants on economic traits of interest. The present study aimed to evaluate the haplotype structure of Vrindavani cattle and explore the association of haplotypes with (re)production traits of economic interest. Genotyping array data of medium density (Bovine50KSNP BeadChip) on 96 randomly selected Vrindavani cows was used in the present study. Genotypes were called in GenomeStudio program while quality control was undertaken in PLINK using standard thresholds. The phenotypic traits used in the present study included age at first calving, dry days, lactation length, peak yield, total lactation milk yield, inter-calving period and service period. The haplotype structure of Vrindavani population was assessed, using a sliding window of 20 SNP with a shift of 5 SNPs at a time, in terms of the size of haplotype blocks regarding their length (in Kb) and frequency in chromosome-wise fashion. Haplotype blocks were assessed for possible association with important production and reproduction traits across three lactation cycles in Vrindavani cattle population. The first ten principal components were included in the model for haplotype-based association analysis to correct for stratification effects of assessed individuals. Multiple haplotypes were found to be associated with age at first calving, total lactation milk yield, peak yield, dry days, inter-calving period and service period. Various candidate genes were found to overlap haplotypes that were significantly associated with age at first calving (CDH18, MARCHF11, MYO10, FBXL7), total lactation milk yield (TGF, PDE1A, and COL8A1), peak yield (PPARGC1A, RCAN1, KCNE1, SMIM34 and MRPS6), dry days (CPNE4, ACAD11 and MRAS), inter-calving period (ABCG5, ABCG8 and COX7A2L) and service period (FOXL2 and PIK3CB). The putative candidate genes overlapping the significantly associated haplotypes revealed important pathways affecting the production and reproduction performance of animals. The identified genes and pathways may serve as good candidate markers to select animals for improved production and reproduction performance in future generations.
基于单倍型的关联分析有望揭示有关遗传变异对感兴趣的经济性状影响的重要信息。本研究旨在评估弗林达瓦尼牛的单倍型结构，并探索单倍型与具有经济价值的（再）生产性状之间的关联。本研究使用了对96头随机选择的弗林达瓦尼奶牛进行中密度基因分型阵列数据（牛50K SNP芯片）。在GenomeStudio程序中进行基因分型，同时在PLINK中使用标准阈值进行质量控制。本研究中使用的表型性状包括初产年龄、干奶期、泌乳期长度、产奶峰值、全泌乳期产奶量、产犊间隔和配种期。通过使用20个SNP的滑动窗口，每次移动5个SNP，以染色体方式根据单倍型块的长度（以Kb为单位）和频率来评估弗林达瓦尼群体的单倍型结构。评估了单倍型块与弗林达瓦尼牛群体三个泌乳周期中重要生产和繁殖性状的可能关联。在基于单倍型的关联分析模型中纳入了前十个主成分，以校正被评估个体的分层效应。发现多个单倍型与初产年龄、全泌乳期产奶量、产奶峰值、干奶期、产犊间隔和配种期相关。发现各种候选基因与与初产年龄（CDH18、MARCHF11、MYO10、FBXL7）、全泌乳期产奶量（TGF、PDE1A和COL8A1）、产奶峰值（PPARGC1A、RCAN1、KCNE1、SMIM34和MRPS6）、干奶期（CPNE4、ACAD11和MRAS）、产犊间隔（ABCG5、ABCG8和COX7A2L）和配种期（FOXL2和PIK3CB）显著相关的单倍型重叠。与显著相关单倍型重叠的推定候选基因揭示了影响动物生产和繁殖性能的重要途径。所鉴定的基因和途径可能作为良好的候选标记，用于选择后代中生产和繁殖性能得到改善的动物。
