Genetic diversity and signatures of selection in four indigenous horse breeds of Iran.

Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish breeds, respectively. By analysis of the population genetic structure, we classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using the de-correlated composite of multiple selection signal statistics based on pairwise comparisons, we detected a different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05). The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation, and fitness traits. Our results showed HMGA2 and LLPH as strong candidate genes for height variation between Caspian horses with a small size and the other studied breeds with a medium size. Using the results of studies on human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results provide a genomewide map of selection signatures in the studied breeds, which represent valuable information for formulating genetic conservation and improved breeding strategies for the breeds.

Changes in the gene expression profile of the mammary gland lipogenic enzymes in Saanen goats in response to dietary fats.

BACKGROUND: The second half of the first pregnancy is a critical period in the growth and development of the mammary gland. The use of functional compounds during this period may positively impact livestock performance. OBJECTIVES: In this study, changes in lipogenic enzyme gene expression in the mammary gland of Saanen goats in response to different dietary fat sources were analysed. METHODS: Goats from four groups (10 each) received these diets from the last two months of pregnancy through four months of lactation: C-, no added fat (negative control group), C+, with saturated palm oil (positive control group), SB, with roasted soybeans (omega-6 group) and FS, with extruded flaxseed (omega-3 group). The fat content was about 4% of dry matter. Milk yield, milk fatty acid profile, milk health index (HI) and gene expression of four lipogenic enzymes in mammary tissue were measured. RESULTS: The FS group had significantly higher milk production with lower omega-6 to omega-3, monounsaturated to polyunsaturated, and total saturated fatty acids compared to other groups. The shorter and longer than16-carbon chain of total milk fatty acid indicates significantly higher values for the C- and C+ groups, respectively. The milk HI for the SB group was significantly higher. The gene expression profile for acetyl-coenzyme A carboxylase was higher in the C- group than other experimental groups. CONCLUSIONS: The results show that manipulation of the diet with unsaturated fat supplements improved milk production, synthesis of milk fat and molecular expression of lipogenic enzymes in mammary tissue in primiparous Saanen goats.

A Genome-Wide Scan for Signatures of Selection in Kurdish Horse Breed.

The genetic diversity and genomic regions being under putative natural selection in Kurdish horse population were studied. The samples from 72 horses were genotyped by using GGP Equine 70K SNP arrays. The Ne Slope (NeS) analyses revealed that a sharp decline in Ne has probably occurred around four generations ago, and high frequency of ROH with 2-4 Mbp in length suggested that the inbreeding has probably occurred around 20 generations ago. The effective population size (Ne) was 104 horses up to three generations ago and the average inbreeding (FROH) was 0.047(± 0.045). Using de-correlated composite of multiple selection signals (DCMS) and runs of homozygosity (ROH) analyses the genomic regions being under putative selection were detected. By using DCMS, a total of 148 significant SNP (FDR < 0.05) were identified, 40% of which were located on ECA9, where the greatest peak was observed. This genomic region harbors several known QTL which are associated with withers height (body size). Also, significant genomic regions (FDR < 0.05), harboring QTL associated with insect bite hypersensitivity (IBH), hair density and coat texture, alternate gaits, guttural pouch tympany and temperament were identified. By using outputs of ROH analyses, two hotspot regions (i.e., 30% of individuals was considered as threshold), were identified on ECA7 (50.11-54.36 Mbp) and ECA11 (26.10-29.07 Mbp) harboring QTL associated with withers height, alternate gait and IBH. In summary, the genomic regions being under putative natural selection which harbors known QTL associated with body size and IBH, among others, were introduced. Nevertheless, additional functional and comparative studies are necessary to corroborate their effect on the observed genetic and phenotypic diversity of the Kurdish horses.

Bottleneck study and genetic structure of Iranian Caspian horse population using microsatellites.

Genetic diversity within the Iranian Caspian horse was evaluated using 8 different microsatellite pairs on 45 Caspian horse blood samples. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks, if any, in this breed. The number of alleles per locus varied from 3 to 5 with mean value of 4.125. All markers have relatively high PIC value (> 0.6), observed heterozygosity; 0.9433, expected Levene's heterozygosity 0.6856 and expected Nei's heterozygosity equal to 0.6762. This study indicated the existence of substantial genetic diversity in the Caspian horse. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A mode-shifted distribution, significant heterozygote excess on the basis of different mutation models, as revealed from Sign, Standardized differences and Wilcoxon rank tests suggested that there was recent bottleneck in the existing Caspian horse. Urgent conservational strategies on this population, is recommended.

Genetic relationships among six Iranian goat populations based on random amplified polymorphic DNA markers.

The objectives of this study were to assess the genetic variability among six Iranian goat breeds including: Markhoz (MR), Korki of South Khorasan (KK), Black Lori (BL), Najdi (NJ), Korki of Raeini (KR), Tali (TL) and to evaluate the genetic relationships between populations using RAPD markers. The genetic characterization of these genetic resources is essential to conservation and breeding programs. Blood sample (50 individuals per breeds) were collected from spreading location of these breeds. DNA extraction was carried out by Salting-Out method. Initially, a total of 16 ten and eleven-nucleotide arbitrary primers were used but 10 of 16 primers revealed a pattern with scorable amplified bands. From a total number of 115 scored bands 62 (53.9%) and 53 (46.1%) were described as polymorphic and monomorphic, respectively. The average number of bands per primer 11/5 and with sizes varying from 220 to 2310 bp in length. Nei's genetic distances varied between 0.081 and 0.227 in the populations. The phylogenetic tree was reconstructed on Neighbor-Joining method and showed two main separated groups. One includes KK, TL, KR in a branch and then NJ. Another consists BL and MR. This research was showed that RAPD technique is an useful tool for evaluation of genetic variation among of domesticated animals.