A novel polymorphism of the myogenin gene is associated with body measurement traits in native Chinese breeds

Genome-wide insights into selection signatures for transcription factor binding sites in cattle ROH regions

Runs of Homozygosity (ROH) regions are characterized by homozygous genotypes inherited from a common ancestor, often arising from positive selection for adaptive traits. These homozygous regions may arise due to inbreeding, selective breeding, or demographic events like population bottlenecks. Transcription factor binding sites (TFBS) are short, specific DNA sequences where transcription factors bind to regulate the expression of nearby genes. These sites are essential for controlling biological processes such as development, metabolism, and immune response. TFBS act as key regulatory elements, and their variations can influence gene activity, contributing to phenotypic differences and adaptation. ROH often encompass regulatory elements, including TFBS, suggesting a functional connection between these genomic features. This study investigates TFBS within ROH regions in 297 animals of six cattle breeds: Gir (48), Tharparkar (72), Vrindavani (72), Frieswal (14), Holstein Friesian (63), and Jersey (28). Utilizing genotyped data of these animals, we identified genomic regions enriched with ROH. We focused on the central 10 kb regions of 50 ROH regions common across all breeds. Within these regions, 450 motifs were examined, identifying 168 transcription factors potentially binding to these regions. The results emphasize the role of TFBS in gene regulation and adaptive processes. By linking ROH patterns to regulatory elements, this study enhances our understanding of the genetic architecture underlying phenotypic traits and their adaptation to environmental pressures. These findings provide insights into the molecular mechanisms influencing genetic variation in cattle populations.

Genomic patterns of selection in morphometric traits across diverse Indian cattle breeds

This study seeks a comprehensive exploration of genome-wide selective processes impacting morphometric traits across diverse cattle breeds, utilizing an array of statistical methods. Morphometric traits, encompassing both qualitative and quantitative variables, play a pivotal role in characterizing and selecting livestock breeds based on their external appearance, size, and physical attributes. While qualitative traits, such as color, horn structure, and coat type, contribute to adaptive features and breed identification, quantitative traits like body weight and conformation measurements bear a closer correlation with production characteristics. This study employs advanced genotyping technologies, including the Illumina BovineSNP50 Bead Chip and next-generation sequencing methods like Reduced Representation sequencing, to identify genomic signatures associated with these traits. We applied four intra-population methods to find evidence of selection, such as Tajima's D, CLR, iHS, and ROH. We found a total of 40 genes under the selection signature, that were associated with morphometric traits in five cattle breeds (Kankrej, Tharparkar, Nelore, Sahiwal, and Gir). Crucial genes such as ADIPDQ, DPP6, INSIG1, SLC35D2 in Kankrej, LPL, ATP6V1B2, CDC14B in Tharparkar, HPSE2, PLAG1 in Nelore, PCSK1, PRKD1 in Sahiwal, and GNAQ, HPCAL1 in Gir were identified in our study. This approach provides valuable insights into the genetic basis of variations in body weight and conformation traits, facilitating informed selection processes and offering a deeper understanding of the evolutionary and domestication processes in diverse cattle breeds.

Polymorphisms in coding and non-coding regions of rabbit (Oryctolagus cuniculus) myogenin (MyoG) gene

In animal breeding, selection based on growth is very often used, as this trait affects the profitability of animal production. Identification of  polymorphisms within the genes affecting the growth process seems to be very important. Therefore, we decided to analyse rabbit myogenin (<em>MyoG</em> gene) for potential polymorphic sites and their association with growth and carcass traits in Termond White (TER), Belgian Giant Grey (BGG) and crossbred New Zealand White×Belgian Giant Grey (NZW×BGG) rabbits. We found three single nucleotide polymorphisms (SNPs) – in 5’ upstream sequence g.68679476 C&gt;T, in exon 1 – silent mutation g.68680096 T&gt;C and g.68680097 G&gt;A resulting in change of GTG triplet (valine) into ATG triplet (methionine). Association analysis showed that GG genotype weaning weight was statistically higher compared to GA in TER population (<em>P</em>=0.005), and that the hind parts for GG genotypes were heavier compared to those of GA (<em>P</em>=0.024), but association analysis of dissectible parts showed this was caused by higher bone weight (<em>P</em>=0.015). For g.68679476 C&gt;T in NZW×BGG population, the CC genotypes for fore (678±35) and hind part (615±29) weights were heavier compared to CT (588±16 and 549±13, respectively); moreover, association analysis of dissectible parts showed that weight of dissectible meat in hind part. Unfortunately, we did not find similar associations for other analysed breeds. For g.68679476 C&gt;T in NZWxBGG musculus longissimus lumborum pH leg after 24 h chilling (pH24L) were statistically lower for CC genotypes compared to CT (<em>P</em>=0.027). For g.68680097 G&gt;A in Termond White population L* value on the hind leg after 24 h chilling (L*24H) was higher for GA genotypes compared to GG (<em>P</em>=0.03), while for g.68679476 C&gt;T for musculus longissimus lumborum L* value after 24 h (L*24L) CC genotypes had higher value compared to CT (<em>P</em>=0.016) in BGG population. Moreover, in BGG population CT genotypes had higher weaning weight compared to CC (<em>P</em>=0.018). Our results show that SNPs within the <em>MyoG </em>gene may influence growth traits in some rabbit breeds, but the evolutionary conserved sequence may not be favourable for changes within coding sequences. For a better understanding thereof, additional analysis is required.

The application of gene marker-assisted selection and proteomics for the best meat quality criteria and body measurements in Qinchuan cattle breed

In the past few decades, enhancement of animal productivity has been gaining increasing attention among decisions-makers, politicians, mangers, and breeders, because of the increasing of world population and shortage of natural resources. The selection of high productivity animals is the main goal, through the application of genetic improvement programs. The use of molecular genetics has conferred significant breeding advantages over conventional breeding techniques. In this regard, many economic characteristics are controlled by a small number of multiple gene loci, each of which is responsible for trait diversity and hence they are referred to as quantitative trait loci (QTL). Single-nucleotide polymorphisms (SNPs), which have recently been discovered through DNA sequencing, are considered one of the most useful types of genetic marker. SNPs are found where different nucleotides occur at the same position in the DNA sequence. They are found in both coding and noncoding regions of the genome and are present at one SNP in every 1000 b. Strategies for the identification and application of markers are based on reference to examples of loci that can control various traits. Furthermore, markers for growth, body measurements, and meat quality traits are preferred, because they can be used to predict the performance of animals, via blood samples, in the first few days of animal life. Marker-assisted selection using SNPs, such asSIRT1, SIRT2, LPL, CRTC2, SIX4, UCPs, and ZBTB38as selection criteria of body measurements and meat traits in beef cattle, will be beneficial in selection and breeding programs. The proteomic is a novel marker and a new approache of biotechnology which increases the understanding of the biological processes, besides being a remarkable biomarker that interrelated to growth and meat quality traits. Proteomics is a vigorous tool as usage for deduces molecular processes between quality traits and muscle proteins, which are helpful in analyzing the mechanisms of biochemistry that influence quality. So they could be potential biomarker for some meat quality traits. Among them, Actin, Myosin, Heat shock proteins are used a novel approaches in the field of biotechnology to understand the proteomics changes. This review article highlights the novel findings on the potential use of MAS and proteomics as biomarker for the selection for meat quality and carcass traits in Qinchuan cattle breed.

Exploring polymorphisms and potential application roles of the bovine Nfix gene in breeding

The aim of this study was to detect mutations of the nuclear factor I/X (Nfix) gene and examine the association of its polymorphisms with growth traits in cattle. Six sequence variants (SVs) including five single-nucleotide mutations and an indel with multiple alleles were detected, among which four polymorphisms within the Nfix gene were identified in 1159 individuals of five cattle breeds by sequencing and forced PCR–RFLP methods. The results of haplotype analysis showed 14 haplotypes within the breeds. Three haplotypes were shared by the five cattle breeds. Hap1 (ACAI) was extremely predominant in all test populations, which suggested that individuals with Hap1 (ACAI) were more adapted to the steppe environment. Association analysis in Nanyang cattle showed that two SVs of the Nfix gene were significantly associated with growth traits at different ages. In addition, the locations of the SVs showed that the 3′ terminal of the bovine Nfix gene was unstable. Combining this instability with its characteristic of multiple alternative splicing, we conjectured that some SVs might have a relationship with the formation of the splices through which growth traits are modulated. This study will provide useful information for the selection and detection of multiple forms of alternative splicing of the bovine Nfix gene.

Genetic polymorphisms of lipoprotein lipase gene and their associations with growth traits in Xiangxi cattle

Lipoprotein lipase (LPL), involved in the metabolism and transport of lipids, regulate energy balance, fat deposition and growth traits. The objective of this study was to investigate the single nucleotide polymorphisms (SNPs) of LPL gene and to determine their associations between these polymorphisms and growth traits in Xiangxi cattle breed. In this study, six novel SNPs (C355157T, T355169C, T355186G, A355210G, T355348A and T355420C) and one reported SNP (A355427T, has been recorded in dbSNP, ID rs110590698) were detected using polymerase chain reaction and DNA sequencing method. Genotyping and genetic diversity analysis were performed in 240 Xiangxi cattle on the basis of sequence alignment, which indicated that five SNPs (C355157T, 355186G, T355348A, T355420C, A355427T) were in abundant genetic diversity, and the other two SNPs (T355169C and TA355210G) were in low genetic diversity. Linkage disequilibrium analysis showed that 18 different haplotypes were identified in these animals. Moreover, the results of the association between LPL gene polymorphisms and growth traits indicated that the individuals with H1H1 haplotype combination had higher BW and HG than those with other haplotype combinations (P < 0.05). The animals with CC genotype maintain higher mean values for BW than those with the CT and TT genotypes (P < 0.05) at T355420C locus. The animals with the AA genotype have lower mean values for WH, BL, HG and BW than those with the AT and TT genotypes at A355427T locus (P < 0.05). The results suggested that the SNPs of the LPL gene might be useful genetic markers for growth traits in the bovine reproduction and breeding.