Bovine GDF10 gene polymorphism analysis and its association with body measurement traits in Chinese indigenous cattle

Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss)

Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.

Genome-Wide Analysis for Early Growth-Related Traits of the Locally Adapted Egyptian Barki Sheep

Sheep play a critical role in the agricultural and livestock sector in Egypt. For sheep meat production, growth traits such as birth and weaning weights are very important and determine the supply and income of local farmers. The Barki sheep originates from the northeastern coastal zone of Africa, and due to its good adaptation to the harsh environmental conditions, it contributes significantly to the meat production in these semi-arid regions. This study aimed to use a genome-wide SNP panel to identify genomic regions that are diversified between groups of individuals of Egyptian Barki sheep with high and low growth performance traits. In this context, from a phenotyped population of 140 lambs of Barki sheep, 69 lambs were considered for a genome-wide scan with the Illumina OvineSNP50 V2 BeadChip. The selected lambs were grouped into divergent subsets with significantly different performance for birth weight and weaning weight. After quality control, 63 animals and 40,383 SNPs were used for analysis. The fixation index (FST) for each SNP was calculated between the groups. The results verified genomic regions harboring some previously proposed candidate genes for traits related to body growth, i.e., EYA2, GDF2, GDF10, MEF2B, SLC16A7, TBX15, TFAP2B, and TNNC2. Moreover, novel candidate genes were proposed with known functional implications on growth processes such as CPXM2 and LRIG3. Subsequent association analysis showed significant effects of the considered SNPs on birth and weaning weights. Results highlight the genetic diversity associated with performance traits and thus the potential to improve growth traits in the Barki sheep breed.

Yak FOXO1 and FOXO3 SNPs and association with production traits, and their promotes cells apoptosis via RNAi

FOXOs transcription factors not only play key roles in glucose metabolism, muscle atrophy and energy homeostasis but also play crucial transcriptional regulatory roles in the cell's metabolism, orchestrating programs of gene expression that regulate cell apoptosis, cell-cycle progression and oxidative stress resistance. However, the specific function of FOXOs promoting fibroblasts proliferation and apoptosis are still unknown. Thus, we used the High-Resolution Melting (HRM) and RNA interference methods to detect SNPs and function. We found one SNP in the exon of FOXO1, three SNPs were identified in the exon of FOXO3, and three SNPs and production traits were significantly different. The siRNA sequence of yak FOXO1 and FOXO3 were transfected into the yak fibroblasts, and effects were detected by a series of assays to reveal the function in yak fibroblasts. The results demonstrated that down-regulated expression of FOXO1 and FOXO3 resulted in up-regulated the expression of BAX, Caspase9 and Caspase3, and down-regulated the expression level of anti-apoptotic gene of BCL2. The apoptotic situation was consistent with results of the flow cytometry and Tunel test cell cycle and cell vitality results revealed that knockdown FOXO1 and FOXO3 resulted in increased P27 expression level and decreased CyclinD1. Meanwhile, cell vitality was also decreased. These results demonstrated that FOXO1 and FOXO3 are two novel regulatory factors to suppress cells proliferation and promote cells apoptosis. Furthermore, these results provide evidence that FOXO1 and FOXO3 play a functional role in cell apoptosis.

Pleiotropic Genes Affecting Carcass Traits in Bos indicus (Nellore) Cattle Are Modulators of Growth

Two complementary methods, namely Multi-Trait Meta-Analysis and Versatile Gene-Based Test for Genome-wide Association Studies (VEGAS), were used to identify putative pleiotropic genes affecting carcass traits in Bos indicus (Nellore) cattle. The genotypic data comprised over 777,000 single-nucleotide polymorphism markers scored in 995 bulls, and the phenotypic data included deregressed breeding values (dEBV) for weight measurements at birth, weaning and yearling, as well visual scores taken at weaning and yearling for carcass finishing precocity, conformation and muscling. Both analyses pointed to the pleomorphic adenoma gene 1 (PLAG1) as a major pleiotropic gene. VEGAS analysis revealed 224 additional candidates. From these, 57 participated, together with PLAG1, in a network involved in the modulation of the function and expression of IGF1 (insulin like growth factor 1), IGF2 (insulin like growth factor 2), GH1 (growth hormone 1), IGF1R (insulin like growth factor 1 receptor) and GHR (growth hormone receptor), suggesting that those pleiotropic genes operate as satellite regulators of the growth pathway.

Molecular Characterization of Bovine SMO Gene and Effects of Its Genetic Variations on Body Size Traits in Qinchuan Cattle (Bos taurus)

Smoothened (Smo)-mediated Hedgehog (Hh) signaling pathway governs the patterning, morphogenesis and growth of many different regions within animal body plans. This study evaluated the effects of genetic variations of the bovine SMO gene on economically important body size traits in Chinese Qinchuan cattle. Altogether, eight single nucleotide polymorphisms (SNPs: 1-8) were identified and genotyped via direct sequencing covering most of the coding region and 3'UTR of the bovine SMO gene. Both the p.698Ser.>Ser. synonymous mutation resulted from SNP1 and the p.700Ser.>Pro. non-synonymous mutation caused by SNP2 mapped to the intracellular C-terminal tail of bovine Smo protein; the other six SNPs were non-coding variants located in the 3'UTR. The linkage disequilibrium was analyzed, and five haplotypes were discovered in 520 Qinchuan cattle. Association analyses showed that SNP2, SNP3/5, SNP4 and SNP6/7 were significantly associated with some body size traits (p < 0.05) except SNP1/8 (p > 0.05). Meanwhile, cattle with wild-type combined haplotype Hap1/Hap1 had significantly (p < 0.05) greater body length than those with Hap2/Hap2. Our results indicate that variations in the SMO gene could affect body size traits of Qinchuan cattle, and the wild-type haplotype Hap1 together with the wild-type alleles of these detected SNPs in the SMO gene could be used to breed cattle with superior body size traits. Therefore, our results could be helpful for marker-assisted selection in beef cattle breeding programs.

Expression of the SIRT2 gene and its relationship with body size traits in Qinchuan cattle (Bos taurus)

Silent information regulator 2 (SIRT2) is a member of the sirtuin family of class III NAD (nicotinamide adenine dinucleotide)-dependent protein deacetylases and may regulate senescence, metabolism and apoptosis. The aims of this study were to investigate whether the SIRT2 gene could be used as a candidate gene in the breeding of Qinchuan cattle. Real-time polymerase chain reaction (RT-PCR) results showed that among all types of tissue that were analyzed, the highest mRNA expression levels of the gene were found in subcutaneous fat. DNA sequencing of 468 individual Qinchuan cattle identified two novel, single nucleotide polymorphisms (g.19501 C > T and g.19518 C > T) in the 3' untranslated region (3'UTR) of the SIRT2 gene. The frequencies of SNP g.19501 C > T and g.19518 C > T were in Hardy-Weinberg disequilibrium in all the samples (chi-square test, χ² < χ_0.05²). An association analysis showed that the two loci were significantly correlated with some body size traits and the H₂H₂ (-CT-CT-) diplotypes performed better than other combinations. These results indicated that the variations in the SIRT2 gene and their corresponding genotypes may be considered as molecular markers for economic traits in cattle breeding.

The polymorphisms of LYRM1 gene and their association with body measurement and ultrasound traits of Qinchuan cattle

Body measurement and meat quality traits which play important roles in the assessment of productivity and economy in cattle were influenced by genes and environmental factors. Latest studies showed that LYR motif containing 1 (LYRM1) may be involved in influencing fatness deposition in animals. The objective of this study was to detect bovine LYRM1 gene polymorphism and analyze its association with body measurement and meat quality traits of cattle. Blood samples were taken from a total of 404 Qinchuan cattle aged from 18-24 months. Created restriction site-polymerase chain reaction-restriction fragment length polymorphism (CRS-PCR-RFLP) and DNA sequencing were used to find out LYRM1 single polymorphism nucleotide (SNPs). Sequence analysis of LYRM1 gene revealed two SNPs (g.165 C > A, g.193 A > G) in 3' untranslated region (3'UTR) of exon 3. And g.165 C > A showed two genotypes namely AC and CC while g.193 A > G showed three genotypes: AA, AG and GG. Analysis results showed that there were significant associations between polymorphism of these two and body measurement and meat quality traits in Qinchuan cattle population. Based on the results obtained from this study, it is inferred that LYRM1 gene may have potential effects on body measurement and meat quality traits in Qinchuan cattle population and could be used for marker-assisted selection.

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.