Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic regions under selective pressures in sport horse breeds. The major goal of this study was to shed light on genomic regions and biological pathways under selective pressures in sport horses. In this study, whole-genome sequences of 16 modern sport and 35 non-sport horses were used to investigate the genomic selective signals of sport performance, by employing fixation index, nucleotide diversity, and Tajima’s D approaches. A total number of 49 shared genes were identified using these approaches. The functional enrichment analysis for candidate genes revealed novel significant biological processes related to musculoskeletal system development, such as limb development and morphogenesis, having been targeted by selection in sport breeds.

Natural selection and domestication have shaped modern horse populations, resulting in a vast range of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally based on their body type. Understanding the genetic basis of horse type variation and selective pressures related to the evolutionary trend can be particularly important for current selection strategies. Whole-genome sequences were generated for 14 pony and 32 light horses to investigate the genetic signatures of selection of the horse type in pony and light horses. In the overlapping extremes of the fixation index and nucleotide diversity results, we found novel genomic signatures of selective sweeps near key genes previously implicated in body measurements including C4ORF33, CRB1, CPN1, FAM13A, and FGF12 that may influence variation in pony and light horse types. This study contributes to a better understanding of the genetic background of differences between pony and light horse types.

Reducing nitrogen excretion in dairy cattle is crucial for improving the environmental sustainability of livestock production. Milk urea nitrogen (MUN), an established biomarker of nitrogen use efficiency, offers a practical basis for genetic selection. To our knowledge, this is the first study in Iranian Holstein cattle that applies a single-step genome-wide association study (ssGWAS) combined with random regression models to identify genomic regions and candidate genes associated with MUN levels across lactation. The dataset included 347,639 test-day records from 52,219 first-parity cows. After quality control, 41,102 SNPs from 2,187 genotyped bulls were retained for the ssGWAS. Random regression models were used to estimate daily SNP effects, and the top 50 SNPs were categorized into early, mid, and late lactation stages. Functional annotation identified seventeen significant candidate genes, such as PGLYRP3, S100A9, ABCB11, and CYP1A1, which may be involved in nitrogen metabolism, immune regulation, and transmembrane nutrient transport. These findings elucidate the molecular mechanisms underlying MUN variation and highlight candidate genes for genomic selection to improve nitrogen use efficiency in dairy cattle, potentially reducing environmental nitrogen emissions in commercial herds.

Dareshouri, Arabian, and Akhal-Teke are three Middle Eastern horse breeds that have been selected for endurance and adaptation to harsh climates. Deciphering the genetic characteristics of these horses by tracing selection footprints and copy number of variations will be helpful in improving our understanding of equine breeds' development and adaptation. For this purpose, we sequenced the whole-genome of four Dareshouri horses using Illumina Hiseq panels and compared them with publicly available whole-genome sequences of Arabian (n=3) and Akhal-Teke (n=3) horses . Three tests of FLK, hapFLK, and pooled heterozygosity were applied using a sliding window (window size=100kb, step size=50kb) approach to detect putative selection signals. Copy number variation analysis was applied to investigate copy number of variants (CNVs), and the results were used to suggest selection signatures involving CNVs. Whole-genome sequencing demonstrated 8,837,950 single nucleotide polymorphisms (SNPs) in autosomal chromosomes. We suggested 58 genes and three quantitative trait loci (QTLs), including some related to horse gait, insect bite hypersensitivity, and withers height, based on selective signals detected by adjusted p-value of Mahalanobis distance based on the rank-based P-values (Md-rank-P) method. We proposed 12 genomic regions under selection pressure involving CNVs which were previously reported to be associated with metabolism energy (SLC5A8), champagne dilution in horses (SLC36A1), and synthesis of polyunsaturated fatty acids (FAT2). Only 10 Middle Eastern horses were tested in this study; therefore, the conclusions are speculative. Our findings are useful to better understanding the evolution and adaptation of Middle Eastern horse breeds.