Search Results (10)

The Russian Black Pied (RBP) is one of Russia’s most popular dairy cattle breeds. It was developed in the USSR during the 1930s by crossing Russian native cattle with Dutch cattle. Since the mid-1970s, the RBP has been cross-bred with Holstein cattle to enhance milk production. To trace haplotypes and selection signatures in the RBP genomes formed during cross-breeding and selection, we conducted local ancestry inference and scans for selection signatures in 12 resequenced RBP animals. Scans for selection using hapFLK and window-based F_ST identified 65 putatively selected regions across the genome, with 4 identified by both methods. Candidate missense variants were detected within these regions, including KIAA1755, CNBD1, and MPZL3, which may be related to milk traits, pathogen resistance, and climate adaptation. Local ancestry inference and functional annotation analyses suggest that regions with a higher fraction of native haplotypes are enriched for genes associated with keratin filaments, antimicrobial defence, the immune system, protein digestion, and amino acid transporters. The results of our study could be utilised for conservation purposes and the improvement of this and other breeds. Full article

Composite crosses result from the mating of two or more distinct cattle breeds. Breeding performance may improve rapidly using a well-organized composite breeding system and a clear selection index. The KiwiCross^® is a popular composite cross in New Zealand, combining Holstein-Friesian (high milk production) and Jersey (high milk fat). Production efficiency (PR), a key selection index, is calculated by dividing milk solids produced by mature live weight. Over decades of genetic improvement, KiwiCross^® increased milk production significantly. We hypothesized that certain genomic regions from Holstein-Friesian or Jersey breeds were preserved due to artificial selection based on PR. Analysis of genomic regions using XP-EHH, hapFLK, and ROH haplotype statistics revealed selection signatures on BTA 7 and 20 in both high- and low-performance animals, with distinct regions linked to Holstein-Friesian and Jersey ancestry. Our findings suggest that selection acted on different genomic regions across generations and that preserving key ancestry-specific haplotypes is crucial for maintaining performance in composite breeds. Breeders must recognize that selection for specific traits can alter allele frequencies and lead to the loss of beneficial breed-specific haplotypes over time. Full article

Domestication and selection significantly changed phenotypic traits in modern domestic animals. To identify the genomic regions associated with prolificacy in this study, 837 ewes from three Iranian indigenous sheep breeds, consisting of Baluchi, Lori-Bakhtiari, and Zandi uniparous breeds, and one Greek highly prolific dairy sheep, namely Chios, were genotyped using OvineSNP50K arrays. Statistical tests were then performed using different and complementary methods based on either site frequency (F_ST) and haplotype (hapFLK) between populations, followed by a pathway analysis of the genes contained in the selected regions. The results revealed that for the top 0.01 percentile of the obtained F_ST values, 16 genomic regions on chromosomes 2, 3, 4, 7, 8, 9, 13, 14, 16, 18, 19, and 20, and for hapFLK values, 3 regions located on chromosomes 3, 7, and 13, were under selection. A bioinformatic analysis of these genomic regions showed that these loci overlapped with potential candidate genes associated with prolificacy in sheep including GNAQ, COL5A2, COL3A1, HECW1, FBN1, COMMD3, RYR1, CCL28, SERPINA14, and HSPA2. These regions also overlapped with some quantitative trait loci (QTLs) linked to prolificacy traits, milk yield, and body weight. These findings suggest that future research could further link these genomic regions to prolificacy traits in sheep. Full article

Past and ongoing selection shapes the genomes of livestock breeds. Identifying such signatures of selection allows for uncovering the genetic bases of affected phenotypes, including economically important traits and environmental adaptations, for the further improvement of breed genetics to respond to climate and economic challenges. Turano-Mongolian cattle are a group of taurine breeds known for their adaptation to extreme environmental conditions and outstanding production performance. Buryat Turano-Mongolian cattle are among the few breeds adapted to cold climates and poor forage. Wagyu, on the other hand, is famous for high productivity and unique top-quality marbled meat. We used hapFLK, the de-correlated composite of multiple signals (DCMS), PBS, and F_ST methods to search for signatures of selection in their genomes. The scans revealed signals in genes related to cold adaptation (e.g., STAT3, DOCK5, GSTM3, and CXCL8) and food digestibility (SI) in the Buryat breed, and growth and development traits (e.g., RBFOX2 and SHOX2) and marbling (e.g., DGAT1, IQGAP2, RSRC1, and DIP2B) in Wagyu. Several putatively selected genes associated with reproduction, immunity, and resistance to pathogens were found in both breed genomes. The results of our work could be used for creating new productive adapted breeds or improving the extant breeds. Full article

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZF_ST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits. Full article

South Africa boasts a diverse range of pig populations, encompassing intensively raised commercial breeds, as well as indigenous and village pigs reared under low-input production systems. The aim of this study was to investigate how natural and artificial selection have shaped the genomic landscape of South African pig populations sampled from different genetic backgrounds and production systems. For this purpose, the integrated haplotype score (iHS), as well as cross population extended haplotype homozygosity (XP-EHH) and Lewontin and Krakauer’s extension of the Fst statistic based on haplotype information (HapFLK) were utilised. Our results revealed several population-specific signatures of selection associated with the different production systems. The importance of natural selection in village populations was highlighted, as the majority of genomic regions under selection were identified in these populations. Regions under natural and artificial selection causing the distinct genetic footprints of these populations also allow for the identification of genes and pathways that may influence production and adaptation. In the context of intensively raised commercial pig breeds (Large White, Kolbroek, and Windsnyer), the identified regions included quantitative loci (QTLs) associated with economically important traits. For example, meat and carcass QTLs were prevalent in all the populations, showing the potential of village and indigenous populations’ ability to be managed and improved for such traits. Results of this study therefore increase our understanding of the intricate interplay between selection pressures, genomic adaptations, and desirable traits within South African pig populations. Full article

The Luxi gamecock developed very unique morphological and behavioral features under the special artificial selection of the most famous Chinese gamecocks. There are very few research studies on the genetics and selection of the Luxi gamecock. We used six methods (Fst, Tajima’s D, hapFLK, iHS, XP-EHH, and Runs of homozygosity) to detect selective sweeps in whole-genome resequencing data of 19 Luxi gamecocks compared to other Chinese indigenous chickens. Eleven genes that were highly related to nervous system development (CDH18, SLITRK1, SLITRK6, NDST3, ATP23, LRIG3, IL1RAPL1, GADL1, C5orf22, UGT8, WISP1, and WNT9A) appeared in at least four methods and were regarded as the most significant genes under selection. Differentially expressed gene (DEG) analysis based on the RNA sequencing data of the cerebral cortex and middle brain between six Luxi gamecocks, Tibetan chickens, and white leghorns found that most differentially expressed genes were enriched in pathways with nervous system functions. Genes associated with aggressiveness-related neurotransmitters (SLC4A2, DRD1, DRD2, ADRA2A, and ADRA2B) showed differential expression rates in Luxi gamecocks as well. Combined results showed that most genes in selective sweep regions were also differentially expressed in Luxi gamecocks including the most significant genes (SLITRK6, IL1RAPL1, GADL1, WISP1, and LRIG3). This study provides more insight into molecular mechanisms of the aggressiveness of gamecocks and aims to promote further studies on animal and human aggression. Full article

Cold stress is an important factor affecting cattle health, production performance, and reproductive efficiency. Understanding of the potential mechanism underlying genetic adaptation to local environments, particularly extreme cold environment, is limited. Here, by using FLK and hapFLK methods, we found that the Zinc finger CCCH-type containing 10 (ZC3H10) gene underwent positive selection in the Menggu, Fuzhou, Anxi, and Shigatse humped cattle breeds that are distributed in the cold areas of China. Furthermore, ZC3H10 expression significantly increased in bovine fetal fibroblast (BFF) cells at 28 °C for 4 h. ZC3H10 knockout BFFs were generated using CRISPR/Cas9. Wild and ZC3H10-deleted BFFs were treated at two temperatures and were divided into four groups (WT, wild and cultured at 38 °C; KO, ZC3H10^−/− and 38 °C; WT_LT, wild, and 28 °C for 4 h; and KO_LT, ZC3H10^−/− and 28 °C for 4 h. A total of 466, 598, 519, and 650 differently expressed genes (two-fold or more than two-fold changes) were identified by determining transcriptomic difference (KO_LT vs. KO, WT_LT vs. WT, KO vs. WT, and KO_LT vs. WT_LT, respectively). Loss of ZC3H10 dysregulated pathways involved in thermogenesis and immunity, and ZC3H10 participated in immunity-related pathways induced by cold stress and regulated genes involved in glucose and lipid metabolism and lipid transport (PLTP and APOA1), thereby facilitating adaptability to cold stress. Our findings provide a foundation for further studies on the function of ZC3H10 in cold stress and development of bovine breeding strategies for combatting the influences of cold climate. Full article

Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by F_ST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding. Full article

It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep. Full article