Document Type : Research Paper
Authors
1 Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak,, Iran
2 ,Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
Abstract
Introduction: Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. The aim of this study was to identify candidate genes and genomic region related to litter size trait in Murcia-Granadina goats using the selective sweep methods.
Material and Methods: In this study, data from 643 Murcia-Granadina goat genotyped using Caprine 50 K BeadChip were used. Quality control measures were performed in Plink by setting animal call rate of 0.90, SNP call rate of 0.90 and SNPs with minor allele frequencies (MAF) lower than 0.01. To identify the signatures of selection, two statistical methods of FST and hapFLK were used. Candidate genes were identified by SNPs located at 1% upper range of FST and hapFLK. Finally, GeneCards and UniProtKB databases were also used to interpret the function of the obtained genes.
Results and Discussion: Using FST approach, we identified nine genomic regions on chromosomes 4, 5, 6, 8, 12, 13, 14, 15, and 22 chromosomes. The identified candidate genes associated with litter size trait in these genomic regions included KMT2E, CAMK2D, CTNNAL, DACH1, DNMT3B, STK3. Some of the genes located in identified regions under selection were associated with the oocyte growth, development and differentiation of ovarian follicles, fertility and growth and development of granulosa cells, which can be directly and indirectly related to the trait of the litter size. Also, survey on extracted QTLs was shown that these QTLs in cow orthologous associated sperm count and calf size. The results of hapFLK statistics in this research led to the identification of four genomic regions on chromosomes 1, 2, 5, and 11. The identified candidate genes associated with the litter size trait in these genomic regions included EDA2R, KCNH7 and CNOT11. It was determined that they had different functions in folliculogenesis and spermatogenesis. Also, survey on extracted QTLs was shown in cow orthologous associated calving interval.
Conclusion: By the way, various genes that were founded within these regions can be considered as candidates under selection based on function. However, will be necessary to carry out more association and functional studies to demonstrate the implication of genes obtained from association analyses. Finally, the results of our research can be used to understand the genetic mechanism controlling litter size trait.
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