Prediction and Expression Analysis of Deleterious Nonsynonymous SNPs of Arabidopsis ACD11 Gene by Combining Computational Algorithms and Molecular Docking Approach

Accelerated cell death 11 (ACD11) is an autoimmune gene that suppresses pathogen infection in plants by preventing plant cells from becoming infected by any pathogen. This gene is widely known for growth inhibition, premature leaf chlorosis, and defense-related programmed cell death (PCD) in seedlings before flowering in Arabidopsis plant. Specific amino acid changes in the ACD11 protein's highly conserved domains are linked to autoimmune symptoms including constitutive defensive responses and necrosis without pathogen awareness. The molecular aspect of the aberrant activity of the ACD11 protein is difficult to ascertain. The purpose of our study was to find the most deleterious mutation position in the ACD11 protein and correlate them with their abnormal expression pattern. Using several computational methods, we discovered PCD vulnerable single nucleotide polymorphisms (SNPs) in ACD11. We analysed the RNA-Seq data, identified the detrimental nonsynonymous SNPs (nsSNP), built genetically mutated protein structures and used molecular docking to assess the impact of mutation. Our results demonstrated that the A15T and A39D variations in the GLTP domain were likely to be extremely detrimental mutations that inhibit the expression of the ACD11 protein domain by destabilizing its composition, as well as disrupt its catalytic effectiveness. When compared to the A15T mutant, the A39D mutant was more likely to destabilize the protein structure. In conclusion, these mutants can aid in the better understanding of the vast pool of PCD susceptibilities connected to ACD11 gene GLTP domain activation.

QTL-seq Analysis of Seed Size Trait in Grape Provides New Molecular Insight on Seedlessness

Background: Seedlessness in grape (Vitis vinifera) is an important commercial trait for both the fresh and drying markets. However, despite numerous studies, the mechanisms and key genes regulating grape seedlessness are mostly unknown.Results: In this study, we sequenced the genomes of the V. vinifera seeded cultivar ‘Red Globe’, the seedless cultivar ‘Centennial’, as well as the derived hybrids. Nonsynonymous SNPs were identified by genome sequencing and analyzed with published transcriptome data. Nonsynonymous SNPs were found in genes which were differential expressed during seeded and seedless grape ovule development, and corresponding Gene Ontology and pathway enrichment were conducted. A potential QTL region associated with seed size was characterized based on SNP-index for both seedless and seeded progeny. Expression analysis of SNP associated candidate genes during ovule development in multiple seeded and seedless grape cultivars were conducted and 3 SNP were further subjected to SNaPshot analysis in 40 progeny for validation.Conclusion: In summary, nonsynonymous SNPs happened in genes related seed development, which identified to be protein kinase, transcription factors, cytochrome P450 and showed differential expression during seeded and seedless grape ovule development. These nonsynonymous SNP associated genes were mainly involved in biological processes like hormone balance, seed coat and endosperm development, reproductive organ development, oxidation and reduction, senescence and cell death. Based on SNP-index and expression pattern analysis, candidate genes in the QTL region were identified and a SNP in G8 showed 67.5% efficiency in the grape progeny validation. Overall, the data cast light on the differences of seed development between seeded and seedless progeny in genomic level, which provides valuable resources for future functional study and grape breeding.

QTL-seq Analysis of Seed Size Trait in Grape Provides New Molecular Insight on Seedlessness

Background Seedlessness in grape ( Vitis vinifera ) is an important commercial trait for both the fresh and drying markets. However, despite numerous studies, the mechanisms and key genes regulating grape seedlessness are mostly unknown. Results In this study, we sequenced the genomes of the V. vinifera seeded cultivar ‘Red Globe’, the seedless cultivar ‘Centennial’, as well as the derived hybrids. Nonsynonymous SNPs were identified and analyzed with respect to published transcriptome data. All the DEGs containing nonsynonymous SNPs were further analyzed in terms of expression patterns, Gene Ontology and pathway enrichment. A potential QTL region associated with seed size was characterized based on SNP indices for both seedless and seeded progeny. Expression analysis of candidate genes during ovule development in multiple seeded and seedless grape cultivars further indicates their potential function in grape seed development. Conclusion In summary, DEGs containing nonsynonymous SNPs were mainly protein kinase, transcription factors, cytochrome P450 and other factors related to seed development, which were mainly involved in biological processes like hormone balance, seed coat and endosperm development, reproductive organ development, oxidation and reduction, senescence and cell death. Based on SNP-index and expression pattern analysis, three genes were further identified as potential seedlessness-related genes. Overall the data cast light on the differences of seed development between seeded and sedless progeny in perspective of both functional variants and expression pattern,which provides valuable candidates for future functional study.

QTL-seq Analysis of Seed Size Trait in Grape Reveal New Insight on The Genetics of Seedlessness

Background Seedlessness in grape ( Vitis vinifera ) is an important commercial trait for both the fresh and drying markets. However, despite numerous studies, the mechanisms and key genes regulating grape seedlessness are mostly unknown. Results In this study, we sequenced the genomes of the V. vinifera seeded cultivar ‘Red Globe’, the seedless cultivar ‘Centennial’, as well as the derived hybrids. Nonsynonymous SNPs were identified and analyzed with respect to published transcriptome data. All the DEGs containing nonsynonymous SNPs were further analyzed in terms of expression patterns, Gene Ontology and pathway enrichment. A potential QTL region associated with seed size was characterized based on SNP indices for both seedless and seeded progeny. Expression analysis of candidate genes during ovule development in multiple seeded and seedless grape cultivars further indicates their potential function in grape seed development. Conclusion In summary, DEGs containing nonsynonymous SNPs were mainly protein kinase, transcription factors, cytochrome P450 and other factors related to seed development, which were mainly involved in biological processes like hormone balance, seed coat and endosperm development, reproductive organ development, oxidation and reduction, senescence and cell death. Based on SNP-index and expression pattern analysis, three genes were further identified as potential seedlessness-related genes. Overall the data cast light on the differences of seed development between seeded and sedless progeny in perspective of both functional variants and expression pattern,which provides valuable candidates for future functional study.

Potential scrapie-associated polymorphisms of the prion protein gene (PRNP) in Korean native black goats

Small ruminants, including sheep and goats are natural hosts of scrapie, and the progression of scrapie pathogenesis is strongly influenced by polymorphisms in the prion protein gene (PRNP). Although Korean native goats have been consumed as meat and health food, the evaluation of the susceptibility to scrapie in these goats has not been performed thus far. Therefore, we investigated the genotype and allele frequencies of PRNP polymorphisms in 211 Korean native goats and compared them with those in scrapie-affected animals from previous studies. We found a total of 12 single nucleotide polymorphisms (SNPs) including 10 nonsynonymous and 2 synonymous SNPs in Korean native goats. Significant differences in allele frequencies of PRNP codons 143 and 146 were found between scrapie-affected goats and Korean native goats (p < 0.01). By contrast, in PRNP codons 168, 211 and 222, there were no significant differences in the genotype and allele frequencies between scrapie-affected animals and Korean native goats. To evaluate structural changes caused by nonsynonymous SNPs, PolyPhen-2, PROVEAN and AMYCO analyses were performed. PolyPhen-2 predicted “possibly damaging” for W102G and R154H, “probably damaging” for G127S. AMYCO predicted relatively low for amyloid propensity of prion protein in Korean native black goats. This is the first study to evaluate the scrapie sensitivity and the first in silico evaluation of nonsynonymous SNPs in Korean native black goats.