Genetic variation at the goat hormone-sensitive lipase ( LIPE ) gene and its association with milk yield and composition

Association analysis for SNPs of LIPE and ITGB4 genes with cashmere production performance, body measurement traits and milk production traits in Liaoning cashmere goats

Liaoning cashmere goat (LCG) is one of the excellent cashmere goat breeds in China. Because of its larger size, better cashmere, and better cashmere production performance, people pay special attention to it. This article mainly studied the relationship between SNP loci of LIPE gene and ITGB4 gene and milk production, cashmere production and body measurement traits of LCGs. We further identified potential SNP loci by PCR-Seq polymorphism detection and gene sequence comparison of LIPE and ITGB4 genes. Further, we use SPSS and SHEsis software to analyze their relationship to production performance. The consequence indicated that CC genotype of LIPE gene T16409C locus was dominant genotype in milk production and cashmere production, while CT genotype of LIPE gene T16409C locus was dominant in body size. The CT genotype of C168T locus of ITGB4 gene is the dominant genotype of body type and cashmere production, while the dominant genotype of milk production is TT genotype. Through joint analysis, in haploid combinations, H1H2:CCCT is the dominant haplotype combination in cashmere fineness. H3H4:TTCT is a dominant haplotype combination of milk production traits and body measurement traits. These dominant genotypes can provide a reliable basis for the study of production performance of LCG.

Detection of two SNPs of the LIPE gene in Holstein-Friesian cows with divergent milk production

The LIPE gene (lipase E, hormone-sensitive type), also known as hormone-sensitive lipase, acts as a primary regulator of lipid metabolism during lactation in cows. We studied a total of two hundred Holstein-Friesian cows and performed sequencing analysis that revealed two synonymous nucleotide changes within the LIPE gene: a transition change, c.276 T > C in exon 2 (g.50631651 T > C; position 351 of GenBank: ON638900) and a transversion change, c.219C > A in exon 6 (g.50635369C > A; position 1070 of GenBank: ON638901). The observed genotypes were TC and CC for the c.276 T > C SNP and CC and CA for the c.219C > A SNP. Notably, the heterozygous TC genotype of the T351C SNP exhibited a significant association with high milk yield. Furthermore, the T351C SNP displayed significant associations with various milk parameters, including temperature, freezing point, density and the percentages of fat, protein, lactose, solids and solids-not-fat, with the homozygous CC genotype showing higher values. The c.219C > A SNP also demonstrated a significant association with milk composition, with heterozygous genotypes (CA) exhibiting higher percentages of fat, protein, and lactose compared to homozygous genotypes (CC). This effect was consistent among both high and low milk producers for fat and lactose percentages, while high milk producers exhibited a higher protein percentage than low milk producers. These findings highlight the importance of considering the detected SNPs in marker-assisted selection and breeding programs for the identification of high milk-producing Holstein-Friesian cows and potentially other breeds. Moreover, this study strongly supports the fundamental role of the LIPE gene in milk production and composition in lactating animals.

Analysis and comparison of lipids in Saanen goat milk from different geographic regions in China based on UHPLC-QTOF-MS lipidomics

The lipids in goat milk from Guangdong Province (GGM), Shaanxi Province (SGM), and Inner Mongolia Province (NGM) were analyzed and compared using untargeted lipidomics. A total of 16 lipid sub-classes and 638 lipid molecules were identified in the three groups. The main lipids were diacylglycerol (DG), triacylglycerol (TG), and glycerophosphatidylethanolamine (PE). The contents of glycerophosphatidylcholine (PC), PE, glycerophosphatidylinositol (PI), sphingomyelin (SM), glucosylceramide (GlcCer), lactosylceramide (LacCer), DG, and TG were significantly different (P < 0.05) in three groups. Moreover, 173 significantly different lipids were screened out, and 13 lipid molecules could be applied as potential lipid markers for identifying the geographic region of goat milk. In addition, the related metabolic pathways were also analyzed. A hypothetical scheme was drawn by linking the most relevant metabolic pathways. This work will provide basics for the establishment of the Saanen goat milk traceability system and provide comprehensive lipid information for the goat milk of different regions.

Polymorphisms in hormone-sensitive lipase and leptin receptor genes and their association with growth traits in Barki lambs

Background and Aim

Marker-assisted selection has many advantages over conventional selection in animal breeding. The candidate gene approach has been applied to identify genetic markers associated with economically important traits in livestock. This study was established to investigate variation in the hormone-sensitive lipase (HSL) and leptin receptor (LEPR) genes, and their association with growth traits in Barki lambs.

Materials and Methods

Records for birth weight (BW), pre-weaning average daily gain (ADG1), weaning weight (WW), post-weaning average daily gain (ADG2), and marketing weight (MW) were obtained from 247 Barki lambs. Polymerase chain reaction-single-stranded conformational polymorphism analyses were used to detect variation in exon 9 of HSL and exon 19 of LEPR. General linear models were used to test for associations between the variation in ovine HSL and LEPR, and growth traits.

Results

The SSCP banding patterns for HSL showed three variants (H1, H2, and H3), which contained two nucleotide-sequence differences (c.1865C>T and c.2038T>C). Two SSCP banding patterns (L1 and L2) were observed for LEPR and these contained two nucleotide-sequence differences (c.2800G>A and c.2978C>G). The HSL genotype showed no effect on the studied traits. The LEPR genotype was proven to have significant effects (p<0.05) on ADG2 and MW. The presence of the L1 variant was associated (p<0.01) with decreased ADG2 and MW.

Conclusion

The finding of an association between LEPR gene variation and growth rate after weaning in Barki lambs warrants efforts to improve this trait.

Co-inherited novel SNPs of the LIPE gene associated with increased carcass dressing and decreased fat-tail weight in Awassi breed

The lipase E hormone-sensitive (LIPE) enzyme is one of the lipolytic enzymes, and it plays a key role in the regulation of adipose tissue deposition. This study was conducted to investigate the possible association between the LIPE gene variations and the main body weight measurements in Awassi sheep. A total of 160 of sexually mature Awassi rams (Ovis aries) that aged between 2 and 3 years were included in the present study. Genomic DNA was extracted and two specific PCR amplicons were designed to amplify two coding regions within the LIPE gene. Genotyping experiments were performed using polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP). Two different SSCP banding patterns were identified, CC and CD in exon 2, and AA and AT in exon 9. Five novel single-nucleotide polymorphisms (SNPs) were detected by sequencing, namely g.151C > A and g.198C > T in exon 2, and g.213G > C, g.226G > T, and g.232A > C in exon 9. Haplotype block analysis showed strong linkage disequilibrium values between the two SNPs in exon 2 and the three SNPs in exon 9. Association analysis of haplotypes with carcass traits demonstrated a significantly higher dressing percentage (P < 0.05) and lower fat tail weight (FTW) in CACT and GCGTAC haplotypes made these haplotypes more favorable for human consumption. The current research is the first one to report a tight association between the LIPE genetic polymorphism and the dressing percentage and FTW traits, suggesting a pivotal role played by these co-inherited SNPs in the metabolism of carcass traits in sheep.

Comprehensive profiling of transcriptional networks specific for lactogenic differentiation of HC11 mammary epithelial stem-like cells

The development of mammary gland as a lactogenic tissue is a highly coordinated multistep process. The epithelial cells of lactiferous tubules undergo profound changes during the developmental window of puberty, pregnancy, and lactation. Several hormones including estrogen, progesterone, glucocorticoids and prolactin act in concert, and orchestrate the development of mammary gland. Understanding the gene regulatory networks that coordinate proliferation and differentiation of HC11 Mammary Epithelial stem-like Cells (MEC) under the influence of lactogenic hormones is critical for elucidating the mechanism of lactogenesis in detail. In this study, we analyzed transcriptome profiles of undifferentiated MEC (normal) and compared them with Murine Embryonic Stem Cells (ESC) using next-generation mRNA sequencing. Further, we analyzed the transcriptome output during lactogenic differentiation of MEC following treatment with glucocorticoids (primed state) and both glucocorticoids and prolactin together (prolactin state). We established stage-specific gene regulatory networks in ESC and MEC (normal, priming and prolactin states). We validated the top up-and downregulated genes in each stage of differentiation of MEC by RT-PCR and found that they are comparable with that of RNA-seq data. HC11 MEC display decreased expression of Pou5f1 and Sox2, which is crucial for the differentiation of MEC, which otherwise ensure pluripotency to ESC. Cited4 is induced during priming and is involved in milk secretion. MEC upon exposure to both glucocorticoids and prolactin undergo terminal differentiation, which is associated with the expression of several genes, including Xbp1 and Cbp that are required for cell growth and differentiation. Our study also identified differential expression of transcription factors and epigenetic regulators in each stage of lactogenic differentiation. We also analyzed the transcriptome data for the pathways that are selectively activated during lactogenic differentiation. Further, we found that selective expression of chromatin modulators (Dnmt3l, Chd9) in response to glucocorticoids suggests a highly coordinated stage-specific lactogenic differentiation of MEC.

The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

Goat genomics has evolved at a low pace because of a lack of molecular tools and sufficient investment. Whilst thousands and hundreds of quantitative trait loci (QTL) have been identified in cattle and sheep, respectively, about nine genome scans have been performed in goats dealing with traits as conformation, growth, fiber quality, resistance to nematodes, and milk yield and composition. In contrast, a great effort has been devoted to the characterization of candidate genes and their association with milk, meat, and reproduction phenotypes. In this regard, causal mutations have been identified in the αS1-casein gene that has a strong effect on milk composition and the PIS locus that is linked to intersexuality and polledness. In recent times, the development of massive parallel sequencing technologies has allowed to build a reference genome for goats as well as to monitor the expression of mRNAs and microRNAs in a broad array of tissues and experimental conditions. Besides, the recent design of a 52K SNP chip is expected to have a broad impact in the analysis of the genetic architecture of traits of economic interest as well as in the study of the population structure of goats at a worldwide scale.

Cholesterol transport and regulation in the mammary gland

The milk-producing alveolar epithelial cells secrete milk that remains after birth the principal source of nutrients for neonates. Milk secretion and composition are highly regulated processes via integrated actions of hormones and local factors which involve specific receptors and downstream signal transduction pathways. Overall milk composition is similar among mammalian species, although the content of individual constituents such as lipids may significantly differ from one species to another. The milk lipid fraction is essentially composed of triglycerides, which represent more than 95 % of the total lipids in human and commercialized bovine milk. Though sterols, including cholesterol, which is the major milk sterol, represent less than 0.5 % of the total milk lipid fraction, they are of key importance for several biological processes. Cholesterol is required for the formation of biological membranes especially in rapidly growing organisms, and for the synthesis of sterol-based compounds. Cholesterol found in milk originates predominantly from blood uptake and, to a certain extent, from local synthesis in the mammary tissue. The present review summarizes current knowledge on cellular mechanisms and regulatory processes determining intra- and transcellular cholesterol transport in the mammary gland. Cholesterol exchanges between the blood, the mammary alveolar cells and the milk, and the likely role of active cholesterol transporters in these processes are discussed. In this context, the hormonal regulation and signal transduction pathways promoting active cholesterol transport as well as potential regulatory crosstalks are highlighted.

Genome-wide detection of signatures of selection in Korean Hanwoo cattle

The Korean Hanwoo cattle have been intensively selected for production traits, especially high intramuscular fat content. It is believed that ancient crossings between different breeds contributed to forming the Hanwoo, but little is known about the genomic differences and similarities between other cattle breeds and the Hanwoo. In this work, cattle breeds were grouped by origin into four types and used for comparisons: the Europeans (represented by six breeds), zebu (Nelore), African taurine (N'Dama) and Hanwoo. All animals had genotypes for around 680 000 SNPs after quality control of genotypes. Average heterozygosity was lower in Nelore and N'Dama (0.22 and 0.21 respectively) than in Europeans (0.26-0.31, with Shorthorn as outlier at 0.24) and Hanwoo (0.29). Pairwise FST analyses demonstrated that Hanwoo are more related to European cattle than to Nelore, with N'Dama in an intermediate position. This finding was corroborated by principal components and unsupervised hierarchical clustering. Using genome-wide smoothed FST , 55 genomic regions potentially under positive selection in Hanwoo were identified. Among these, 29 were regions also detected in previous studies. Twenty-four regions were exclusive to Hanwoo, and a number of other regions were shared with one or two of the other groups. These regions overlap a number of genes that are related to immune, reproduction and fatty acid metabolism pathways. Further analyses are needed to better characterize the ancestry of the Hanwoo cattle and to define the genes responsible to the identified selection peaks.