Genome-wide identification and expression profiling analysis of Wnt family genes affecting adipocyte differentiation in cattle

Transcriptomic Analysis of Newborn Hanwoo Calves: Effects of Maternal Overnutrition during Mid- to Late Pregnancy on Subcutaneous Adipose Tissue and Liver

This study investigated the transcriptomic responses of subcutaneous adipose tissue (SAT) and liver in newborn Hanwoo calves subjected to maternal overnutrition during mid- to late gestation. Eight Hanwoo cows were randomly assigned to control and treatment groups. The treatment group received a diet of 4.5 kg of concentrate and 6.5 kg of rice straw daily, resulting in intake levels of 8.42 kg DMI, 5.69 kg TDN, and 0.93 kg CP-higher than the control group (6.07 kg DMI, 4.07 kg TDN, and 0.65 kg CP), with respective NEm values of 9.56 Mcal and 6.68 Mcal. Following birth, newly born calves were euthanized humanely as per ethical guidelines, and SAT and liver samples from newborn calves were collected for RNA extraction and analysis. RNA sequencing identified 192 genes that were differentially expressed in the SAT (17 downregulated and 175 upregulated); notably, HSPA6 emerged as the most significantly upregulated gene in the SAT and as the singular upregulated gene in the liver (adj-p value < 0.05). Additionally, differential gene expression analysis highlighted extensive changes across genes associated with adipogenesis, fibrogenesis, and stress response. The functional enrichment pathway and protein-protein interaction (PPI) unraveled the intricate networks and biological processes impacted by overnutrition, including extracellular matrix organization, cell surface receptor signaling, and the PI3K-Akt signaling pathway. These findings underscore maternal overnutrition's substantial influence on developmental pathways, suggesting profound cellular modifications with potential lasting effects on health and productivity. Despite the robust insights that are provided, the study's limitations (sample size) underscore the necessity for further research.

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo cattle

Cattle traits like average daily weight gain (ADG) greatly impact profitability. Selecting based on ADG considering genetic variability can lead to economic and genetic advancements in cattle breeding. This study aimed to unravel genetic influences on ADG variation in Hanwoo cattle at the skeletal muscle transcriptomic level. RNA sequencing was conducted on longissimus dorsi (LD), semimembranosus (SB), and psoas major (PM) muscles of 14 steers assigned to same feed, grouped by low (≤ 0.71 kg) and high (≥ 0.77 kg) ADG. At P ≤ 0.05 and log2fold > 1.5, the distinct pattern of gene expression was identified with 184, 172, and 210 differentially expressed genes in LD, SB, and PM muscles, respectively. Tissue-specific responses to ADG variation were evident, with myogenesis and differentiation associated JAK-STAT signaling pathway and prolactin signaling pathways enriched in LD and SB muscles, while adipogenesis-related PPAR signaling pathways were enriched in PM muscle. Key hub genes (AXIN2, CDKN1A, MYC, PTGS2, FZD5, SPP1) were upregulated and functionally significant in muscle growth and differentiation. Notably, DPP6, CDKN1A, and FZD5 emerged as possible candidate genes linked to ADG variation. These findings enhance our understanding of genetic factors behind ADG variation in Hanwoo cattle, illuminating skeletal muscle mechanisms influencing ADG.

Effects of maternal calcium propionate supplementation on offspring productivity and meat metabolomic profile in sheep

This study determined the effect of dietary calcium propionate (CaPr) as a source of energy supplementation during the First Half of Gestation (FMG), the Second Half of Gestation (SMG), and during All Gestation (AG), on offspring post-weaning growth performance, meat quality, and meat metabolomic profile. Thirty-one pregnant ewes were assigned to one of four treatments: a) supplementation of 30 gd-1 of CaPr during the first half of gestation (day 1 to day 75, n = 8) (FMG); b) supplementation of 30 gd-1 of CaPr during the second half of gestation (day 76 to day 150, n = 8) (SMG); c) supplementation of 30 gd-1 of CaPr during all gestation (AG, n = 8); d) no CaPr supplementation (control; CS, n = 7). The ewes were ad libitum fed a basal diet based on oat hay and corn silage. Ewes were distributed in a completely randomized unbalanced design to four treatments. The FMG group had lower (P ≤ 0.05) birth weight and weaning weight than the CS group. However, the average daily gain was similar across all treatments. Empty body weight and FMG had lower values (P ≤ 0.05) than the other groups. Both FMG and AG had lower hot carcass weight (P ≤ 0.05) compared to CS, while CaPr treatments resulted in reduced hot carcass yield (P ≤ 0.05). Meat color and texture were similar among treatments. A principal component analysis between gestation stages showed a trend for separating CS and FMG from SMG and AG, and that was explained by 93.7% of the data variability (PC1 = 87.9% and PC2 = 5.8%). Regarding meat metabolomic profile, 23 compounds were positively correlated between all treatments. Only 2 were negatively correlated (eicosane and naphthalene 1,2,3); but tetradecanoic acid, hexadecane, undecane 5-methyl, (-)-alpha, hexadecenoic acid, octadecanoic acid, and octadecane had a highly significant correlation (P ≤ 0.05). Overall, dam supplementation with CaPr during different periods of gestation provoked changes in meat metabolites related to the biosynthesis of fatty acids in lambs without negative changes in lamb's growth performance and carcass quality.

Genome-wide scan for runs of homozygosity in South American Camelids

BACKGROUND

Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection.

RESULTS

A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively.

CONCLUSIONS

The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.

Uncovering the candidate genes related to sheep body weight using multi-trait genome-wide association analysis

In sheep, body weight is an economically important trait. This study sought to map genetic loci related to weaning weight and yearling weight. To this end, a single-trait and multi-trait genome-wide association study (GWAS) was performed using a high-density 600 K single nucleotide polymorphism (SNP) chip. The results showed that 43 and 56 SNPs were significantly associated with weaning weight and yearling weight, respectively. A region associated with both weaning and yearling traits (OARX: 6.74-7.04 Mb) was identified, suggesting that the same genes could play a role in regulating both these traits. This region was found to contain three genes (TBL1X, SHROOM2 and GPR143). The most significant SNP was Affx-281066395, located at 6.94 Mb (p = 1.70 × 10-17), corresponding to the SHROOM2 gene. We also identified 93 novel SNPs elated to sheep weight using multi-trait GWAS analysis. A new genomic region (OAR10: 76.04-77.23 Mb) with 22 significant SNPs were discovered. Combining transcriptomic data from multiple tissues and genomic data in sheep, we found the HINT1, ASB11 and GPR143 genes may involve in sheep body weight. So, multi-omic anlaysis is a valuable strategy identifying candidate genes related to body weight.

Presence of KREMEN receptors for DKK1 in the preimplantation bovine embryo

The WNT inhibitory protein DKK1 has been shown to regulate development of the preimplantation embryo to the blastocyst stage. In cattle, DKK1 increases the number of trophectoderm cells that are the precursor of the placenta. DKK1 can affect cells by blocking WNT signaling through its receptors KREMEN1 and KREMEN2. Here it was shown that the mRNA for KREMEN1 and KREMEN2 decline as the embryo advances in development. Nonetheless, immunoreactive KREMEN1 was identified in blastocysts using Western blotting. DKK1 also decreased amount of immunoreactive CTNNB1 in blastocysts, as would be expected if DKK1 was signaling through a KREMEN-mediated pathway. Thus, it is likely that KREMEN1 functions as a receptor for DKK1 in the preimplantation bovine embryo.

Identification of HQT gene family and their potential function in CGA synthesis and abiotic stresses tolerance in vegetable sweet potato

Hydroxycinnamate-CoA quinate hydroxycinnamoyl transferase (HQT) enzyme affect plant secondary metabolism and are crucial for growth and development. To date, limited research on the genome-wide analysis of HQT family genes and their regulatory roles in chlorogenic acid (CGA) accumulation in leafy vegetable sweet potato is available. Here, a total of 58 HQT family genes in the sweet potato genome (named IbHQT) were identified and analyzed. We studied the chromosomal distribution, phylogenetic relationship, motifs distribution, collinearity, and cis-acting element analysis of HQT family genes. This study used two sweet potato varieties, high CGA content Fushu 7-6-14-7 (HC), and low CGA content Fushu 7-6 (LC). Based on the phylogenetic analysis, clade A was unique among the identified four clades as it contained HQT genes from various species. The chromosomal location and collinearity analysis revealed that tandem gene duplication may promote the IbHQT gene expansion and expression. The expression patterns and profile analysis showed changes in gene expression levels at different developmental stages and under cold, drought, and salt stress conditions. The expression analysis verified by qRT-PCR revealed that IbHQT genes were highly expressed in the HC variety leaves than in the LC variety. Furthermore, cloning and gene function analysis unveiled that IbHQT family genes are involved in the biosynthesis and accumulation of CGA in sweet-potato. This study expands our understanding of the regulatory role of HQT genes in sweet-potato and lays a foundation for further functional characterization and genetic breeding by engineering targeted HQT candidate genes in various sweet-potato varieties and other species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01299-4.

Identification of potential miRNA-mRNA regulatory network and the key miRNAs in intramuscular and subcutaneous adipose

Intramuscular fat (IMF) is an important indicator for evaluating meat quality. Breeds with high IMF content are often accompanied by high subcutaneous fat (SCF), severely affecting the meat rate of pigs. Studying the mechanisms of miRNAs related to lipogenesis and lipid metabolism has important implications for pig breeding. We constructed two small RNA libraries from intramuscular and subcutaneous fat to evaluate the patterns of lipogenesis in Laiwu pig, a Chinese breed. A total of 286 differentially expressed miRNAs (DEmiRNAs), including 193 known miRNA and 93 novel miRNAs, were identified from two types of adipose. GO and KEGG enrichment analysis for DEmiRNAs showed that their target genes involved in many adipogenesis and lipid metabolism biological processes and signaling pathways, such as Wnt signaling pathway,MAPK signaling pathway, Hippo signaling pathway, PI3K-Akt signaling pathway, Melanogenesis, Signaling pathways regulating pluripotency of stem cells and so on. Then, we constructed a miRNA-mRNA interaction network to find out which miRNAs were the key miRNAs of regulation in Wnt signaling pathway. In this pathway, miR-331-3p, miR-339-5p, miR-874 and novel346_mature target PPARD, WNT10B, RSPO3, WNT2B. This study provides a theoretical basis for further understanding the post-transcriptional regulation mechanism of meat quality formation and predicting and treating diseases caused by ectopic fat.