Whole genome scan of selection markers in Holstein, Najdi and Holstein-Najdi hybrids

Introduction: In order to protect native breeds in order to maintain genetic diversity, it is necessary to keep the animal in its place of residence because the cost of protecting genetic resources is high and it is not possible to maintain all genetic resources in laboratories and research institutions. The aim of this research was to identify selection traits in Holstein, Najdi and their hybrids in the herds of Khuzestan province.
Material and Methods: For this purpose, the genomic information of 209 cattle samples including 21, 128 and 60 samples from Holstein, Najdi breeds and their Holstein-Najdi hybrids were used, which were genotyped using Genotyping Array 30K arrays. First, animals with more than 5% missing genotype were excluded from the next steps, and monomorphic genotypes and genotypes with a minimum allelic frequency of less than 5%, as well as loci with more than 5% missing genotype, were excluded. Hardy-Weinberg equilibrium was checked in all loci and loci with P-value less than 6-10 were excluded from the data set. In this study, the signs of selection were investigated using two series of methods, two of which are multi-population (FST, hapFLK ) and the other one is single-population (iHS, nSL). To determine the signs of selection in the studied cattle breeds, FST values for each SNP marker were calculated using the unbiased theta estimator method by Plink and R software. Also, in order to identify the signs of selection in the studied breeds, the FLK Single Marker haplotype expansion method called the hapFLK test was also used. iHS and nSL statistics have been used as intra-population statistics in order to investigate the areas carrying selection signs. To calculate these statistics for each SNP, VCFtools and Selscan version 2.0 were used, respectively.
Results and Discussion: After data editing and imputation of 662,428 SNPs from 329 Najdi, Holstein and their hybrids, and after removing 3,129 SNPs with Hardy-Weinberg 6-10 test and 68,116 SNPs with MAF 0.05, 591,181 SNPs remained for further analysis. In order to identify selection signals at the genome level, the numerical value of fixation index (FST) was used. Only 0.1% of the regions of the genome where all markers had high values. Finally, three regions on the genome were selected for further analysis that passed the threshold. Three regions were located on autosomal chromosomes. These three regions, where the stabilization index had a higher numerical value of 0.38, were located on chromosomes 16, 21, and 8, respectively. A threshold of 0.1% of the high hapFLK value of the population was used to identify the regions under selection by the hapFLK method. Finally, the region of 22774764 to 23377643 base pairs of chromosome 14 and the region of 33981177 to 34039961 base pairs of chromosome 26 had a selection mark at the specified threshold, which was used to identify genes in the next step. The iHS statistic was used to identify signs of selection for alleles that are polymorphic in the population, but have not yet reached the fixation stage. iHS less than zero indicates that the respective haplotype carries the derived allele, and iHS greater than zero indicates that the haplotype in question carries the ancestral gene. In this research, the markers with the highest amount of iHS on chromosomes 3, 7 and 10 were identified as selection markers. By using the nSL statistic which was calculated by Selscan software in the Linux environment and drawing the Manhattan plot diagram of this statistic by R software, it was determined that in the Holstein and Holstein*Najdi hybrids population on chromosome 3 and in the Najdi population 4 and 15 regions have been selected. Some of the areas identified with these statistics are directly and indirectly related to growth traits, reproduction, immune system and other traits related to them.
Conclusion: In this research, four statistics, FST, hapFLK, iHS and nSL, were used to identify the signs of selection in Holstein, Najdi cattle populations and their hybrids. The results of FST and hapFLK statistics, which examine the populations in a multi-population way, showed that the signs of selection detected by these two statistics were on chromosomes 8, 14, 16, 21 and 26, and chromosome 16 was common in each of the two strains. Among the areas identified with these statistics, they are directly or indirectly related to the characteristics of milk production and reproduction in cows. The results of the iHS and nSL statistics, which examine the populations as a single population, showed that the signs of selection detected by these two statistics were on chromosomes 3, 4, 7, 10 and 15, which is the chromosome No. 3 was common in every two races. Some of the areas identified with these statistics are directly and indirectly related to growth traits, reproduction, immune system and other traits related to them. Considering that the statistics used are different in terms of the implementation method and the parameters used (the first two are multi-population based on allele frequency and the second two are single-population based on linkage disequilibrium), consequently their results did not match. But from the total of 59 genes identified by the four methods used, two genes, IQCA1, ACKR3, were jointly identified by iHS and nSL statistics. In addition, it can be concluded that the selection during the past years has been generally focused on traits that have been effective in increasing the production efficiency in addition to increasing the resistance of livestock to the environmental conditions of the place of residence.