Molecular characterization of the Rocky Mountain elk (Cervus elaphus nelsoni) PRNP putative promoter

Transcriptome analysis of green and purple fruited pepper provides insight into novel regulatory genes in anthocyanin biosynthesis

Background

Pepper (Capsicum annuum L.) is a valuable horticultural crop with economic significance, and its purple fruit color is attributed to anthocyanin, a phytonutrient known for its health-promoting benefits. However, the mechanisms regulating anthocyanin biosynthesis in pepper have yet to be fully elucidated.

Methods

RNA sequencing (RNA-seq) was utilized to analyze the transcriptome of fruits from three purple-fruited varieties (HN191, HN192, and HN005) and one green-fruited variety (EJT) at various developmental stages. To determine the relationships between samples, Pearson correlation coefficients (PCC) and principal component analysis (PCA) were calculated. Differential expression analysis was performed using the DESeq2 package to identify genes that were expressed differently between two samples. Transcription factors (TF) were predicted using the iTAK program. Heatmaps of selected genes were generated using Tbtools software.

Results

The unripe fruits of HN191, HN192, and HN005, at the stages of 10, 20, and 30 days after anthesis (DAA), display a purple color, whereas the unripe fruits of variety EJT remain green. To understand the molecular basis of this color difference, five transcriptome comparisons between green and purple fruits were conducted: HN191-10 vs EJT-10, HN191-20 vs EJT-20, HN191-30 vs EJT-30, HN192-30 vs EJT-30, and HN005-30 vs EJT-30. Through this analysis, 503 common differentially expressed genes (DEGs) were identified. Among these DEGs, eight structural genes related to the anthocyanin biosynthesis pathway and 24 transcription factors (TFs) were detected. Notably, one structural gene (MSTRG.12525) and three TFs (T459_25295, T459_06113, T459_26036) exhibited expression patterns that suggest they may be novel candidate genes involved in anthocyanin biosynthesis. These results provide new insights into the regulation of anthocyanin biosynthesis in purple pepper fruit and suggest potential candidate genes for future genetic improvement of pepper germplasm with enhanced anthocyanin accumulation.

Geographic variation in the PRNP gene and its promoter, and their relationship to chronic wasting disease in North American deer

PRNP genotypes, number of octarepeats (PHGGGWGQ) and indels in the PRNP promoter can influence the progression of prion disease in mammals. We found no relationship between presence of promoter indels in white-tailed deer and mule deer from Nebraska and CWD presence. White-tailed deer with the 95 H allele and G20D mule deer were more likely to be CWD-free, but unlike other studies white-tailed deer with the 96S allele(s) were equally likely to be CWD-free. We provide the first information on PRNP genotypes and indels in the promoter for Key deer (all homozygous 96SS) and Coues deer (lacked 95 H and 96S alleles, but possessed a uniquely high frequency of 103 T). All deer surveyed were homozygous for three tandem octarepeats.

Accurate Genomic Predictions for Chronic Wasting Disease in U.S. White-Tailed Deer

The geographic expansion of chronic wasting disease (CWD) in U.S. white-tailed deer (Odocoileus virginianus) has been largely unabated by best management practices, diagnostic surveillance, and depopulation of positive herds. Using a custom Affymetrix Axiom single nucleotide polymorphism (SNP) array, we demonstrate that both differential susceptibility to CWD, and natural variation in disease progression, are moderately to highly heritable (h2=0.337±0.079─0.637±0.070) among farmed U.S. white-tailed deer, and that loci other than PRNP are involved. Genome-wide association analyses using 123,987 quality filtered SNPs for a geographically diverse cohort of 807 farmed U.S. white-tailed deer (n = 284 CWD positive; n = 523 CWD non-detect) confirmed the prion gene (PRNP; G96S) as a large-effect risk locus (P-value < 6.3E-11), as evidenced by the estimated proportion of phenotypic variance explained (PVE ≥ 0.05), but also demonstrated that more phenotypic variance was collectively explained by loci other than PRNP. Genomic best linear unbiased prediction (GBLUP; n = 123,987 SNPs) with k-fold cross validation (k = 3; k = 5) and random sampling (n = 50 iterations) for the same cohort of 807 farmed U.S. white-tailed deer produced mean genomic prediction accuracies ≥ 0.81; thereby providing the necessary foundation for exploring a genomically-estimated CWD eradication program.

Association analysis of PRNP gene region with chronic wasting disease in Rocky Mountain elk

Background

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy (TSE) of cervids including white-tailed (Odocoileus virginianus) and mule deer (Odocoileus hemionus), Rocky Mountain elk (Cervus elaphus nelsoni), and moose (Alces alces). A leucine variant at position 132 (132L) in prion protein of Rocky Mountain elk confers a long incubation time with CWD, but not complete resistance. However, variants in regulatory regions outside the open reading frame of PRNP have been associated with varying degrees of susceptibility to prion disease in other species, and some variants have been observed in similar regions of Rocky Mountain elk PRNP. Thus, additional genetic variants might provide increased protection, either alone or in combination with 132L.

Findings

This study provided genomic sequence of all exons for PRNP of Rocky Mountain elk. Many functional sites in and around the PRNP gene region were sequenced, and this report approximately doubled (to 75) the number of known variants in this region. A haplotype-tagging approach was used to reduce the number of genetic variants required to survey this variation in the PRNP gene region of 559 Rocky Mountain elk. Eight haplotypes were observed with frequencies over 1.0%, and one haplotype was present at 71.2% frequency, reflecting limited genetic diversity in the PRNP gene region.

Conclusions

The presence of 132L cut odds of CWD by more than half (Odds Ratio = 0.43; P = 0.0031), which was similar to a previous report. However after accounting for 132L, no association with CWD was found for any additional variants in the PRNP region (P > 0.05).