Novel putative causal mutations associated with fat traits in Nellore cattle uncovered by eQTLs located in open chromatin regions

Intramuscular fat (IMF) and backfat thickness (BFT) are critical economic traits impacting meat quality. However, the genetic variants controlling these traits need to be better understood. To advance knowledge in this area, we integrated RNA-seq and single nucleotide polymorphisms (SNPs) identified in genomic and transcriptomic data to generate a linkage disequilibrium filtered panel of 553,581 variants. Expression quantitative trait loci (eQTL) analysis revealed 36,916 cis-eQTLs and 14,408 trans-eQTLs. Association analysis resulted in three eQTLs associated with BFT and 24 with IMF. Functional enrichment analysis of genes regulated by these 27 eQTLs revealed noteworthy pathways that can play a fundamental role in lipid metabolism and fat deposition, such as immune response, cytoskeleton remodeling, iron transport, and phospholipid metabolism. We next used ATAC-Seq assay to identify and overlap eQTL and open chromatin regions. Six eQTLs were in regulatory regions, four in predicted insulators and possible CCCTC-binding factor DNA binding sites, one in an active enhancer region, and the last in a low signal region. Our results provided novel insights into the transcriptional regulation of IMF and BFT, unraveling putative regulatory variants.

Integrative Analysis Between Genome-Wide Association Study and Expression Quantitative Trait Loci Reveals Bovine Muscle Gene Expression Regulatory Polymorphisms Associated With Intramuscular Fat and Backfat Thickness

Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle.

Dietary L-arginine supplementation during early gestation of gilts affects conceptuses development

l-arginine supplementation of sows has led to improvement of reproductive performance, but the mechanisms responsible for the positive effects of arginine during gestation on conceptuses survival and development are still poorly understood. Thus, we aimed to evaluate effects of 1.0% l-arginine supplementation (ARG) on phenotypic traits of commercial gilts, embryos and fetuses, concentration of gilts' blood metabolites, expression of developmental and cellular apoptosis genes in conceptuses of 25 and 35 days. At 25 days, IGF1 gene was more expressed in embryos from ARG than in embryos from control gilts (CON) (P = 0.05). At this same gestational age, ARG embryos tended to be heavier compared to CON (P = 0.07) and ARG gilts showed a trend to have a greater arginine concentration in blood plasma (P = 0.06). However, at 35 days of gestation, arginine concentration in blood plasma of ARG gilts tended to be lower compared to CON (P = 0.06) and ARG fetuses showed smaller cephalic-caudal length (P = 0.05). These results indicate that duration of supplementation is determinant for arginine effects, not only on the females performance but also on the conceptuses, since supplementation upregulated IGF1 expression at 25 days, in addition to the reduction of cephalic-caudal length of 35-day fetuses.

Changes in soluble carbohydrates during storage of Caesalpinia echinata LAM. (Brazilwood) seeds, an endangered leguminous tree from the Brazilian Atlantic Forest

Caesalpinia echinata seeds stored in laboratory environmental conditions lose their viability in one month whilst under low temperatures germination is maintained for 18 months of storage. These seeds are tolerant to desiccation, keeping their viability up to 0.08 gH2O.gDW-1. Since soluble carbohydrates are believed to be involved with desiccation tolerance and seed storability, the aim of this work is to analyze the content and composition of soluble carbohydrates in C. echinata seeds during storage in paper bags (PB) and glass flasks (GF) at laboratory room (RT) and cool (CT) temperatures. In freshly harvested seeds, total soluble carbohydrates comprised approximately 10% of the dry weight, decreasing to ca. 8% over 18 months of storage at RT. In seeds stored at CT, sugars varied differently decreasing initially and being restored at the end of the analysis period. The main neutral sugars in seeds from all treatments were sucrose, fructose and glucose. Raffinose and stachyose were present as traces. Free myo-inositol and other cyclitols were also detected. The main tendency observed was the variation in levels of both glucose and fructose in relation to sucrose, the highest levels of monosaccharides which were found in seeds stored at CT. The values of glucose and fructose were practically constant in seeds stored in paper bags for 18 months at CT, decreasing consistently in the other treatments, mainly at RT. Sucrose contents remained relatively stable. Changes in soluble sugars during storage suggest that the loss of germinability of seeds of C. echinata could be associated with low levels of glucose and fructose in relation to sucrose.

A study of chromosome 11p13 translocations involving TCR beta and TCR delta in human T cell leukaemia

A frequent site of translocation damage in human T-ALL has been localized to a specific region of chromosome band 11p13. Five new T-ALL cases are described which break in the major T-ALLbcr region of 11p13, two involving a novel translocation t(7;11)(q35;p13), with breakage at the T cell receptor (TCR) beta gene from 7q35, and three involving TCR delta from 14q11 in the more common t(11;14)(p13;q11). Analysis of the mechanism of one T-ALLbcr/TCR beta translocation and a previously described t(11;14)(p13;q11) was conducted by genomic cloning of translocation breakpoints, using the polymerase chain reaction (PCR). Both seem to have occurred by recombinase error, but only the t(7;11) showed sequence-specific joining. Nonetheless recombinase mediation of the t(11;14) is implied by the presence of N-region addition (a hallmark of recombinase joins) on both derivative chromosomes. These observations reinforce the view that translocations in the T-ALLbcr region of chromosome 11p13 are a major lesion in human T-ALL. In addition, these can occur by mimicry of VDJ joining, but sequence specificity is not obligatory.