Combined effects of three novel SNPs within goat LHX3 gene on milk performance

The landscape of long noncoding RNA expression in the goat brain

The brain regulates multiple metabolic processes, such as food intake, energy expenditure, insulin secretion, hepatic glucose production, and glucose and fatty acid metabolism in adipose tissue, which are fundamental for the maintenance of energy and glucose homeostasis during lactation and pregnancy. In addition, brain expression has a fundamental impact on the development of maternal behavior. Although brain functions are partly regulated by long noncoding RNAs (lncRNAs), their expression profiles have not been characterized in depth in any ruminant species. We have sequenced the transcriptome of 12 brain tissues from 3 goats that were 1 mo pregnant and 4 nonpregnant goats to investigate their lncRNA expression patterns. Between 4,363 (adenohypophysis) and 4,604 (olfactory bulb) lncRNAs were expressed in brain tissues, leading us to establish a set of 794 already annotated lncRNAs and 5,098 novel lncRNA candidates. The detected lncRNAs shared features with those of other mammals, and tissue-specific lncRNAs were enriched in brain development-related terms. Differential expression analyses between goats that were 1 mo pregnant and nonpregnant goats showed that the lncRNA expression profiles of certain brain regions experience substantial changes associated with early pregnancy (238 lncRNAs are differentially expressed in the olfactory bulb), but others do not. Enrichment analysis showed that differentially expressed lncRNAs from the olfactory bulb are co-expressed with genes previously linked to behavioral changes related to pregnancy. These findings provide a first characterization of the landscape of lncRNA expression in the goat brain and provides valuable clues to understand the molecular events triggered by early pregnancy in the central nervous system.

Distribution of DGAT1 copy number variation in Chinese goats and its associations with milk production traits

Goat is an important sector for meat and dairy products. Diacylglycerol O-acyltransferase 1 (DGAT1), which is a key gene in milk production, has been recently detected to overlap with a novel copy number variation (CNV) in goats. CNVs could be genetic markers providing new insights into the genetic basis of phenotypic variation. Up to now, there are no reports on the DGAT1-related CNV (DGAT1 CNV) in Chinese goats. This study first detected the distribution of the DGAT1 CNV in Chinese seven goat breeds, finding substantial differences among dairy, meat, and fiber goats (P < 0.01). The association analysis between the DGAT1 CNV and milk production traits revealed significant associations: Xinong Sannen (XS) dairy goat with copy number loss type had higher freezing point depression (FPD) (P < 0.01) and milk solids-not-fat (SNF) content (P < 0.05). Overall, our study unraveled the distribution of DGAT1 CNV in Chinese goats for the first time and found the potential role of this CNV in the marker-assisted selection of dairy goat breeding.

Transcriptome Analysis Reveals the Potential Role of Long Non-coding RNAs in Mammary Gland of Yak During Lactation and Dry Period

The mammary gland is a remarkably dynamic organ of milk synthesis and secretion, and it experiences drastic structural and metabolic changes during the transition from dry periods to lactation, which involves the expression and regulation of numerous genes and regulatory factors. Long non-coding RNA (lncRNA) has considered as a novel type of regulatory factors involved in a variety of biological processes. However, their role in the lactation cycle of yak is still poorly understood. To reveal the involved mechanism, Ribo-zero RNA sequencing was employed to profile the lncRNA transcriptome in mammary tissue samples from yak at two physiological stages, namely lactation (LP) and dry period (DP). Notably, 1,599 lncRNA transcripts were identified through four rigorous steps and filtered through protein-coding ability. A total of 59 lncRNAs showed significantly different expression between two stages. Accordingly, the results of qRT-PCR were consistent with that of the transcriptome data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that target genes of differentially expressed lncRNAs (DELs) were involved in pathways related to lactation, such as ECM-receptor interaction, PI3K-Akt signaling pathway, biosynthesis of amino acids and focal adhesion etc. Finally, we constructed a lncRNA-gene regulatory network containing some well known candidate genes for milk yield and quality traits. This is the first study to demonstrate a global profile of lncRNA expression in the mammary gland of yak. These results contribute to a valuable resource for future genetic and molecular studies on improving milk yield and quality, and help us to gain a better understanding of the molecular mechanisms underlying lactogenesis and mammary gland development of yak.

Differential Expression of ACTL8 Gene and Association Study of Its Variations with Growth Traits in Chinese Cattle

Simple Summary

Marker-assisted selection has a great influence on livestock molecular breeding development. The discovery of key molecular markers that are significantly associated with body size data will accelerate molecular breeding in livestock. In this study, the cattle ACTL8 gene is a critical candidate gene. It was found that there are multiple mutations in the ACTL8 gene that may be used as molecular markers. Our results have shown that the mutations of the ACTL8 gene could have important reference value in molecular breeding for beef cattle.

Abstract

Mutations are heritable changes at the base level of genomic DNA. Furthermore, mutations lead to genetic polymorphisms and may alter animal growth phenotypes. Our previous study found that mutations in the bovine Actin-like protein 8 (ACTL8) gene may be involved in muscle growth and development. This study explored several mutations of the ACTL8 gene and their influence on body size in Chinese beef cattle, as well as tested the tissue expression profile of the ACTL8 gene in Qinchuan cattle at different ages. Five single nucleotide polymorphisms (SNPs) (including one synonymous mutation (c.2135552895G > A)) and two insertion/deletion polymorphisms (indels) were identified in the ACTL8 gene from 1138 cattle by DNA-seq, RFLP and other methods. Then, the expression profile of the ACTL8 gene in Qinchuan cattle showed that it was expressed in heart, spleen, lung, liver, muscle, and fat tissues. Moreover, the expression level of ACTL8 was increased with cattle growth (p < 0.01). The ACTL8 mRNA expression level in kidney and muscle tissues was the highest in the calves, while lowest in the fetal stage. Overall, we showed that the mutations could act as markers in beef molecular breeding and selection of the growth traits of cattle.

Two New Insertion/Deletion Variants of the PITX2 Gene and their Effects on Growth Traits in Sheep

In China, Tong sheep (TS) and Lanzhou fat-tailed sheep (LFTS) are two closely relative endanger breeds for low meat production and low fecundity, finding some marker-assisted selected (MAS) is our first priority for improving their growth traits. For this purpose, Hu sheep (HS) and small-tailed Han sheep (STHS) were compared with two endangered breeds (TS and LFTS). Paired-liked homeodomain transcription factor 2 (PITX2) gene was the important member of PITX family, which could adjust animal growth through hypothalamic-pituitary-adrenal axis. During the past years, insertion/deletion (indel) has become increasingly popular in application as MAS. In this study, two novel indel loci were identified, and five significant differences, including chest width, hip width, chest depth, chest circumference, and body height, were found between different breeds. Interestingly, there was no DD genotype and smaller number of ID genotye. All the ID genotypes were significantly greater than II genotype, which was to say the allele of "D" was dominant variation and its frequency was lower, which demonstrated that it has huge space for selection. Briefly, the two indel were potential and useful DNA markers for selecting excellent individuals in relation to growth traits in sheep.

A novel 29 bp insertion/deletion (indel) variant of the <i>LHX3</i> gene and its influence on growth traits in four sheep breeds of various fecundity

Abstract. Belonging to the same LIM homeobox (LHX) family, LHX3 and LHX4 are key transcription factors in animal growth and reproduction. Insertion/deletion (indel) is a relatively simple and effective DNA marker. Therefore, four sheep breeds of various fecundity were used to explore the novel indel variants within the sheep LHX3 and LHX4 gene, as well as to evaluate their effects on growth traits. Herein, only one novel 29 bp indel (NC_019460.2:g.3107494-3107522delGGCCTGGACTGTGATGGGCACCCTCCGGG) within the sheep LHX3 gene was found, and three genotypes were detected. Interestingly, the increasing trends of II (insertion/insertion) genotype frequency and I allelic frequency were the same as the growth of the fertility character. Genotypic frequency and allelic frequency distributions were significantly different between the high-fecundity breeds (HS, STHS and LFTS) and low-fecundity breed (TS) based on a χ2 test (P < 0.05). Association analyses showed that body length was significantly different in female TS and STHS and that chest width was significantly different for the female TS and male STHS (P < 0.05). These findings suggested that the 29 bp indel could extend the spectrum of genetic variations of the LHX3 gene in sheep and provide a valuable theoretical basis for the marker-assisted selection (MAS) in sheep breeding and genetics.

A novel 28-bp insertion–deletion polymorphism within goat PRNP gene and its association with production traits in Chinese native breeds

In this study, a novel 28-bp insertion–deletion (indel) polymorphism (AJ298878:g.47836–47853insCCTCAGACACTGAGTCTCCCCAACAGCA) was found in goat prion protein (PRNP) gene in 2373 goats from 13 Chinese native breeds. The frequencies of allele “ins” varied from 0.500 to 1.000 in different breeds. The establishment of association of the 28-bp indel polymorphism with production traits was performed in Inner Mongolia white cashmere (IMWC) and Xinong Sannen dairy (XNSN) breeds. Two significant associations between this polymorphism and 1-year-old body mass (P = 0.011) and average body mass (P = 0.024) were observed in IMWC breed, as well as wool thickness of 3-year-olds (P < 0.001). Furthermore, the novel 28-bp indel polymorphism was significantly associated with total solids in the evening (%) (P = 0.009) and milk yield (P = 0.016) in XNSN breed. These findings suggested that the 28-bp indel polymorphism was a potential DNA marker for eliminating or selecting preferred individuals in relation to production traits in goat marker-assisted selection breeding while carrying out preventing scrapie project.