A high-throughput SNP discovery strategy for RNA-seq data

Expression quantitative trait loci associated with performance traits, blood biochemical parameters, and cytokine profile in pigs

Identifying expression Quantitative Trait Loci (eQTL) and functional candidate variants associated with blood biochemical parameters can contribute to the understanding of genetic mechanisms underlying phenotypic variation in complex traits in pigs. We identified eQTLs through gene expression levels in muscle and liver tissues of Large White pigs. The identified eQTL were then tested for association with biochemical parameters, cytokine profiles, and performance traits of pigs. A total of 41,759 SNPs and 15,093 and 15,516 expression gene levels from muscle and liver tissues, respectively, enabled the identification of 1,199 eQTL. The eQTL identified related the SNP rs345667860 as significantly associated with interleukin-6 and interleukin-18 in liver tissue, while the rs695637860 SNP was associated with aspartate aminotransferase and interleukin-6, and rs337362164 was associated with high-density lipoprotein of the blood serum. In conclusion, the identification of three eQTL significantly associated with aspartate aminotransferase and cytokine levels in both serum and liver tissues suggests a potential role for these variants in modulating immune function and overall health in production pigs. Further research is needed to validate these findings and explore their potential for improving pig health and productivity.

Identification of Genetic Relationships and Group Structure Analysis of Yanqi Horses

Background/Objectives: The Yanqi horse is a distinguished local breed in China, known for its robust physique and strong adaptability. However, due to insufficient breeding populations and a loosely structured breeding system, the number of Yanqi horses has been declining annually. To protect its genetic resources and develop scientific breeding strategies, this study aimed to analyze the genetic diversity, parentage relationships, and genetic structure of the Yanqi horse conservation population using microsatellite markers. Materials and Methods: A total of 117 Yanqi horses were selected for genotyping analysis using 16 microsatellite markers. Genetic diversity parameters (e.g., allele number, heterozygosity, F-statistics) were calculated using GeneAIEX (v.6.503) and Fstat software (v.2.9.4). Parentage analysis was conducted using Cervus software. Bayesian clustering analysis was performed using STRUCTURE software (v.2.3.4), and a phylogenetic tree was constructed based on Nei's genetic distance to reveal the population genetic structure. Results: A total of 191 alleles were detected, with an average allele number of 11.969, observed heterozygosity of 0.481, and expected heterozygosity of 0.787. Parentage testing showed a cumulative exclusion probability (CEP) of 0.9652999 when one parent's genotype was known and 0.9996999 when both parents' genotypes were known, achieving an accuracy of 99%. Genetic differentiation analysis revealed moderate genetic divergence among populations (FST = 0.128) and moderate inbreeding levels (FIS = 0.396). Bayesian clustering analysis (K = 4) indicated that the Yanqi horse population could be divided into four genetic clusters, reflecting the impact of geographical isolation on genetic structure. Conclusions: The Yanqi horse conservation population exhibits moderate genetic diversity, high accuracy in parentage identification, and moderate genetic differentiation and inbreeding. The findings provide a scientific basis for the conservation and sustainable utilization of Yanqi horse genetic resources. Future efforts should focus on strengthening conservation measures, optimizing breeding strategies, and further investigating the genetic background using genomic technologies to ensure the sustainable development of the Yanqi horse population.

Investigating the functional and structural effect of non-synonymous single nucleotide polymorphisms in the cytotoxic T-lymphocyte antigen-4 gene: An in-silico study

The cytotoxic T-lymphocyte antigen-4 (CTLA4) is essential in controlling T cell activity within the immune system. Thus, uncovering the molecular dynamics of single nucleotide polymorphisms (SNPs) within the CTLA4 gene is critical. We identified the non-synonymous SNPs (nsSNPs), examined their impact on protein stability, and identified the protein sequences associated with them in the human CTLA4 gene. There were 3134 SNPs (rsIDs) in our study. Out of these, 186 missense variants (5.93%), 1491 intron variants (47.57%), and 91 synonymous variants (2.90%), while the remaining SNPs were unspecified. We utilized SIFT, PolyPhen-2, PROVEAN, and SNAP for identifying deleterious nsSNPs, and SNPs&GO, PhD SNP, and PANTHER for verifying risk nsSNPs in the CTLA4 gene. Following SIFT analysis, six nsSNPs were identified as deleterious and reporting second and third nsSNPs as probably damaging and one as benign, respectively. From upstream analysis, rs138279736, rs201778935, rs369567630, and rs376038796 were found to be deleterious, probably damaging, and disease associated. ConSurf predicted conservation scores for four nsSNPs, and Project Hope suggested that all mutations could disrupt protein interactions. Furthermore, mCSM and DynaMut2 analyses indicated a decrease in ΔΔG stability for the mutants. GeneMANIA and STRING networks highlighted correlations with CD86 and CD80 genes. Finally, MD simulation revealed consistent fluctuation in RMSD and RMSF, consequently Rg, hydrogen bonds, and PCA in the mutant proteins compared with wild-type, which might alter the functional and structural stability of CTLA4 protein. The current comprehensive study shows how various nsSNPs in the CTLA4 gene can modify the structural and functional characteristics of the protein, potentially influencing the pathogenesis of diseases in humans. Further, experimental studies are needed to analyze the effect of these nsSNPs on the susceptibility of pathological phenotype populations.

Integrating dynamic high-throughput phenotyping and genetic analysis to monitor growth variation in foxtail millet

BACKGROUND

Foxtail millet [Setaria italica (L.) Beauv] is a C4 graminoid crop cultivated mainly in the arid and semiarid regions of China for more than 7000 years. Its grain highly nutritious and is rich in starch, protein, essential vitamins such as carotenoids, folate, and minerals. To expand the utilisation of foxtail millet, efficient and precise methods for dynamic phenotyping of its growth stages are needed. Traditional foxtail millet monitoring methods have high labour costs and are inefficient and inaccurate, impeding the precise evaluation of foxtail millet genotypic variation.

RESULTS

This study introduces a high-throughput imaging system (HIS) with advanced image processing techniques to enhance monitoring efficiency and data quality. The HIS can accurately extract a range of key growth feature parameters, such as plant height (PH), convex hull area (CHA), side projected area (SPA) and colour distribution, from foxtail millet images. Compared with traditional manual measurements, this HIS improved data quality and phenotyping of the key foxtail millet growth traits. High-throughput phenotyping combined with a genome-wide association study (GWAS) revealed genetic loci associated with dynamic growth traits, particularly plant height (PH), in foxtail millet. The loci were linked to genes involved in the gibberellic acid (GA) synthesis pathway related to PH.

CONCLUSION

The HIS developed in this study enables the efficient and dynamic monitoring of foxtail millet phenotypic traits. It significantly improves the quality of data obtained for phenotyping key growth traits. The integration of high-throughput phenotyping with GWAS provides new insights into the genetic underpinnings of dynamic growth traits, particularly plant height, by identifying associated genetic loci in the GA synthesis pathway. This methodological advancement opens new avenues for the precise phenotyping and exploration of genetic resources in foxtail millet, potentially enhancing its utilisation.

Molecular targets and strategies in the development of nucleic acid cancer vaccines: from shared to personalized antigens

Recent breakthroughs in cancer immunotherapies have emphasized the importance of harnessing the immune system for treating cancer. Vaccines, which have traditionally been used to promote protective immunity against pathogens, are now being explored as a method to target cancer neoantigens. Over the past few years, extensive preclinical research and more than a hundred clinical trials have been dedicated to investigating various approaches to neoantigen discovery and vaccine formulations, encouraging development of personalized medicine. Nucleic acids (DNA and mRNA) have become particularly promising platform for the development of these cancer immunotherapies. This shift towards nucleic acid-based personalized vaccines has been facilitated by advancements in molecular techniques for identifying neoantigens, antigen prediction methodologies, and the development of new vaccine platforms. Generating these personalized vaccines involves a comprehensive pipeline that includes sequencing of patient tumor samples, data analysis for antigen prediction, and tailored vaccine manufacturing. In this review, we will discuss the various shared and personalized antigens used for cancer vaccine development and introduce strategies for identifying neoantigens through the characterization of gene mutation, transcription, translation and post translational modifications associated with oncogenesis. In addition, we will focus on the most up-to-date nucleic acid vaccine platforms, discuss the limitations of cancer vaccines as well as provide potential solutions, and raise key clinical and technical considerations in vaccine development.

Identification of Single-Nucleotide Polymorphisms in Differentially Expressed Genes Favoring Soybean Meal Tolerance in Higher-Growth Zebrafish (Danio rerio)

Genetic variability within the same fish species could confer soybean meal (SBM) tolerance in some individuals, thus favoring growth. This study investigates the single-nucleotide polymorphisms (SNPs) in differentially expressed genes (DEGs) favoring SBM tolerance in higher-growth zebrafish (Danio rerio). In a previous work, nineteen families of zebrafish were fed a fish meal diet (100FM control diet) or SBM-based diets supplemented with saponin (50SBM + 2SPN-experimental diet), from juvenile to adult stages. Individuals were selected from families with a genotype-by-environment interaction higher (170 ± 18 mg) or lower (76 ± 10 mg) weight gain on 50SBM + 2SPN in relation to 100FM. Intestinal transcriptomic analysis using RNA-seq revealed six hundred and sixty-five differentially expressed genes in higher-growth fish fed 50SBM + 2SPN diet. In this work, using these results, 47 SNPs in DEGs were selected. These SNPs were genotyped by Sequenom in 340 zebrafish that were fed with a 50SBM + 2SPN diet or with 100FM diet. Marker-trait analysis revealed 4 SNPs associated with growth in 3 immunity-related genes (aif1l, arid3c, and cst14b.2) in response to the 50SBM + 2SPN diet (p-value < 0.05). Two SNPs belonging to aif1l y arid3c produce a positive (+19 mg) and negative (-26 mg) effect on fish growth, respectively. These SNPs can be used as markers to improve the early selection of tolerant fish to SBM diet or other plant-based diets. These genes can be used as biomarkers to identify SNPs in commercial fish, thus contributing to the aquaculture sustainability.

Random mutations induced by a sub-sterilizing dose of gamma ray on Aedes albopictus male pupae and transmission to progeny

The application of the Sterile Insect Technique (SIT) to mosquito control is based on the systematic release of large numbers of adult males that have been previously sterilized by irradiation. Ionizing radiation doses inducing full sterility also cause somatic damages that reduce the capacity of the treated males to compete with wild males. The optimal dose inducing high levels of male sterility and minimal impact on competitiveness can be assessed by establishing a dose-response curve. Sub-sterile males are, to a variable degree, still fertile and might be able to transmit to the progeny and following generation(s) sub-lethal random mutations resulting from irradiation. To investigate this, we treated Ae. albopictus male pupae with a sub-sterilizing (2-4 % of egg hatching) dose of gamma rays and explored expressed mutated genes in treated males and their progeny using RNA-seq. Single nucleotide polymorphisms (SNPs) were called using two independent pipelines. Only SNPs common to both pipelines (less than 5 % of the total SNPs predicted) were considered reliable and were annotated to genes. Over 600 genes with mutations likely induced by irradiation were found in the treated Ae. albopictus males. A part of the genes found mutated in irradiated males were also found in (and therefore probably passed on to) males of the F1 and F2 progeny, indicating that genetic variations induced by irradiation may be transmitted along generations. The mutated genes in irradiated males did not seem to significantly affect biological processes, except in one case (i.e., oxidative phosphorylation). Only in four cases (i.e., oxidative phosphorylation, UDP-glucose metabolic process, proton transmembrane transport and riboflavin metabolism) we found biological processes to be significantly affected by mutated genes that were likely transmitted to the male progeny. Our results suggest that random mutations induced by a sub-sterilizing dose of gamma ray in Ae. albopictus male pupae and transmitted to the male progeny of the irradiated mosquitoes do not affect biological processes potentially harmful, from a public-health point of view.

In Silico Functional and Structural Analysis of Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in Human Paired Box 4 Gene

In human genome, members of Paired box (PAX) transcription factor family are highly sequence-specific DNA-binding proteins. Among PAX gene family members, PAX4 gene has significant role in growth, proliferation, differentiation, and insulin secretion of pancreatic β-cells. Single nucleotide polymorphisms (SNPs) in PAX4 gene progress in the pathogenesis of various human diseases. Hence, the molecular mechanism of how these SNPs in PAX4 gene significantly progress diseases pathogenesis needs to be elucidated. For the reason, a series of bioinformatic analyzes were done to identify the SNPs of PAX4 gene that contribute in diseases pathogenesis. From the analyzes, 4145 SNPs (rsIDs) in PAX4 gene were obtained, where, 362 missense (8.73%), 169 synonymous (4.08%), and 2323 intron variants (56.04%). The rest SNPs were unspecified. Among the 362 missense variants, 118 nsSNPs were found as deleterious in SIFT analysis. Among those, 25 nsSNPs were most probably damaging and 23 were deleterious as observed in PolyPhen-2 and PROVEAN analyzes, respectively. Following all analyzes, 14 nsSNPs (rs149708455, rs115887120, rs147279315, rs35155575, rs370095957, rs373939873, rs145468905, rs121917718, rs2233580, rs3824004, rs372751660, rs369459316, rs375472849, rs372497946) were common and observed as deleterious, probably damaging, affective and diseases associated. Following structural analyzes, 11 nsSNPs guided proteins were found as most unstable and highly conserved. Among these, R20W, R39Q, R45Q, R60H, G65D, and A223D mutated proteins were highly harmful. Hence, the results from above-mentioned integrated comprehensive bioinformatic analyzes guide how different nsSNPs in PAX4 gene alter structural and functional characteristics of the protein that might progress diseases pathogenesis in human including type 2 diabetes.

Transcriptome variations in hybrids of wild emmer wheat (Triticum turgidum ssp. dicoccoides)

BACKGROUND

Wild emmer wheat is a great candidate to revitalize domesticated wheat genetic diversity. Recent years have seen intensive investigation into the evolution and domestication of wild emmer wheat, including whole-genome DNA and transcriptome sequencing. However, the impact of intraspecific hybridization on the transcriptome of wild emmer wheat has been poorly studied. In this study, we assessed changes in methylation patterns and transcriptomic variations in two accessions of wild emmer wheat collected from two marginal populations, Mt. Hermon and Mt. Amasa, and in their stable F4 hybrid.

RESULTS

Methylation-Sensitive Amplified Polymorphism (MSAP) detected significant cytosine demethylation in F4 hybrids vs. parental lines, suggesting potential transcriptome variation. After a detailed analysis, we examined nine RNA-Seq samples, which included three biological replicates from the F4 hybrid and its parental lines. RNA-Seq databases contained approximately 200 million reads, with each library consisting of 15 to 25 million reads. There are a total of 62,490 well-annotated genes in these databases, with 6,602 genes showing differential expression between F4 hybrid and parental lines Mt. Hermon and Mt. Amasa. The differentially expressed genes were classified into four main categories based on their expression patterns. Gene ontology (GO) analysis revealed that differentially expressed genes are associated with DNA/RNA metabolism, photosynthesis, stress response, phosphorylation and developmental processes.

CONCLUSION

This study highlights the significant transcriptomic changes resulting from intraspecific hybridization within natural plant populations, which might aid the nascent hybrid in adapting to various environmental conditions.

Assessing Privacy Vulnerabilities in Genetic Data Sets: Scoping Review

BACKGROUND

Genetic data are widely considered inherently identifiable. However, genetic data sets come in many shapes and sizes, and the feasibility of privacy attacks depends on their specific content. Assessing the reidentification risk of genetic data is complex, yet there is a lack of guidelines or recommendations that support data processors in performing such an evaluation.

OBJECTIVE

This study aims to gain a comprehensive understanding of the privacy vulnerabilities of genetic data and create a summary that can guide data processors in assessing the privacy risk of genetic data sets.

METHODS

We conducted a 2-step search, in which we first identified 21 reviews published between 2017 and 2023 on the topic of genomic privacy and then analyzed all references cited in the reviews (n=1645) to identify 42 unique original research studies that demonstrate a privacy attack on genetic data. We then evaluated the type and components of genetic data exploited for these attacks as well as the effort and resources needed for their implementation and their probability of success.

RESULTS

From our literature review, we derived 9 nonmutually exclusive features of genetic data that are both inherent to any genetic data set and informative about privacy risk: biological modality, experimental assay, data format or level of processing, germline versus somatic variation content, content of single nucleotide polymorphisms, short tandem repeats, aggregated sample measures, structural variants, and rare single nucleotide variants.

CONCLUSIONS

On the basis of our literature review, the evaluation of these 9 features covers the great majority of privacy-critical aspects of genetic data and thus provides a foundation and guidance for assessing genetic data risk.

In silico functional, structural and pathogenicity analysis of missense single nucleotide polymorphisms in human MCM6 gene

Single nucleotide polymorphisms (SNPs) are one of the most common determinants and potential biomarkers of human disease pathogenesis. SNPs could alter amino acid residues, leading to the loss of structural and functional integrity of the encoded protein. In humans, members of the minichromosome maintenance (MCM) family play a vital role in cell proliferation and have a significant impact on tumorigenesis. Among the MCM members, the molecular mechanism of how missense SNPs of minichromosome maintenance complex component 6 (MCM6) contribute to DNA replication and tumor pathogenesis is underexplored and needs to be elucidated. Hence, a series of sequence and structure-based computational tools were utilized to determine how mutations affect the corresponding MCM6 protein. From the dbSNP database, among 15,009 SNPs in the MCM6 gene, 642 missense SNPs (4.28%), 291 synonymous SNPs (1.94%), and 12,500 intron SNPs (83.28%) were observed. Out of the 642 missense SNPs, 33 were found to be deleterious during the SIFT analysis. Among these, 11 missense SNPs (I123S, R207C, R222C, L449F, V456M, D463G, H556Y, R602H, R633W, R658C, and P815T) were found as deleterious, probably damaging, affective and disease-associated. Then, I123S, R207C, R222C, V456M, D463G, R602H, R633W, and R658C missense SNPs were found to be highly harmful. Six missense SNPs (I123S, R207C, V456M, D463G, R602H, and R633W) had the potential to destabilize the corresponding protein as predicted by DynaMut2. Interestingly, five high-risk mutations (I123S, V456M, D463G, R602H, and R633W) were distributed in two domains (PF00493 and PF14551). During molecular dynamics simulations analysis, consistent fluctuation in RMSD and RMSF values, high Rg and hydrogen bonds in mutant proteins compared to wild-type revealed that these mutations might alter the protein structure and stability of the corresponding protein. Hence, the results from the analyses guide the exploration of the mechanism by which these missense SNPs of the MCM6 gene alter the structural integrity and functional properties of the protein, which could guide the identification of ways to minimize the harmful effects of these mutations in humans.

Verification of Key Target Molecules for Intramuscular Fat Deposition and Screening of SNP Sites in Sheep from Small-Tail Han Sheep Breed and Its Cross with Suffolk

Intramuscular fat (IMF) is vital for meat tenderness and juiciness. This study aims to explore the IMF deposition mechanism and the related molecular markers in sheep. Two populations, Small-tail Han Sheep (STH) and STH × Suffolk (SFK) F1 (SFK × STH), were used as the research object. Histological staining techniques compared the differences in the longissimus dorsi muscle among populations. A combination of transcriptome sequencing and biological information analysis screened and identified IMF-related target genes. Further, sequencing technology was employed to detect SNP loci of target genes to evaluate their potential as genetic markers. Histological staining revealed that the muscle fiber gap in the SFK × STH F1 was larger and the IMF content was higher. Transcriptome analysis revealed that PIK3R1 and PPARA were candidate genes. Histological experiments revealed that the expressions of PIK3R1 mRNA and PPARA mRNA were lower in SFK × STH F1 compared with the STH. Meanwhile, PIK3R1 and PPARA proteins were located in intramuscular adipocytes and co-located with the lipid metabolism marker molecule (FASN). SNP locus analysis revealed a mutation site in exon 7 of the PIK3R1 gene, which served as a potential genetic marker for IMF deposition. This study's findings will provide a new direction for meat quality breeding in sheep.

Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs

BACKGROUND

Mapping expression quantitative trait loci (eQTLs) in skeletal muscle tissue in pigs is crucial for understanding the relationship between genetic variation and phenotypic expression of carcass traits in meat animals. Therefore, the primary objective of this study was to evaluate the impact of different sets of single nucleotide polymorphisms (SNP), including scenarios removing SNPs pruned for linkage disequilibrium (LD) and SNPs derived from SNP chip arrays and RNA-seq data from liver, brain, and skeletal muscle tissues, on the identification of eQTLs in the Longissimus lumborum tissue, associated with carcass and body composition traits in Large White pigs. The SNPs identified from muscle mRNA were combined with SNPs identified in the brain and liver tissue transcriptomes, as well as SNPs from the GGP Porcine 50 K SNP chip array. Cis- and trans-eQTLs were identified based on the skeletal muscle gene expression level, followed by functional genomic analyses and statistical associations with carcass and body composition traits in Large White pigs.

RESULTS

The number of cis- and trans-eQTLs identified across different sets of SNPs (scenarios) ranged from 261 to 2,539 and from 29 to 13,721, respectively. Furthermore, 6,180 genes were modulated by eQTLs in at least one of the scenarios evaluated. The eQTLs identified were not significantly associated with carcass and body composition traits but were significantly enriched for many traits in the "Meat and Carcass" type QTL. The scenarios with the highest number of cis- (n = 304) and trans- (n = 5,993) modulated genes were the unpruned and LD-pruned SNP set scenarios identified from the muscle transcriptome. These genes include 84 transcription factor coding genes.

CONCLUSIONS

After LD pruning, the set of SNPs identified based on the transcriptome of the skeletal muscle tissue of pigs resulted in the highest number of genes modulated by eQTLs. Most eQTLs are of the trans type and are associated with genes influencing complex traits in pigs, such as transcription factors and enhancers. Furthermore, the incorporation of SNPs from other genomic regions to the set of SNPs identified in the porcine skeletal muscle transcriptome contributed to the identification of eQTLs that had not been identified based on the porcine skeletal muscle transcriptome alone.

A reference transcriptome for walnut anthracnose pathogen, Ophiognomonia leptostyla, guides the discovery of candidate virulence genes

Despite the economic losses due to the walnut anthracnose, Ophiognomonia leptostyla is an orphan fungus with respect to genomic resources. In the present study, the transcriptome of O. leptostyla was assembled for the first time. RNA sequencing was conducted for the fungal mycelia grown in a liquid media, and the inoculated leaf samples of walnut with the fungal conidia sampled at 48, 96 and 144 h post inoculation (hpi). The completeness, correctness, and contiguity of the de novo transcriptome assemblies generated with Trinity, Oases, SOAPdenovo-Trans and Bridger were compared to identify a single superior reference assembly. In most of the assessment criteria including N50, Transrate score, number of ORFs with known description in gene bank, the percentage of reads mapped back to the transcript (RMBT), BUSCO score, Swiss-Prot coverage bin and RESM-EVAL score, the Bridger assembly was the superior and thus used as a reference for profiling the O. leptostyla transcriptome in liquid media vs. during walnut infection. The k-means clustering of transcripts resulted in four distinct transcription patterns across the three sampling time points. Most of the detected CAZy transcripts had elevated transcription at 96 hpi that is hypothetically concurrent with the start of intracellular growth. The in-silico analysis revealed 103 candidate effectors of which six were members of Necrosis and Ethylene Inducing Like Protein (NLP) gene family belonging to three distinct k-means clusters. This study provided a complex and temporal pattern of the CAZys and candidate effectors transcription during six days post O. leptostyla inoculation on walnut leaves, introducing a list of candidate virulence genes for validation in future studies.

Transcriptome analysis of flower colour reveals the correlation between SNP and differential expression genes in Phalaenopsis

BACKGROUND

Phalaenopsis is an important ornamental plant that has great economic value in the world flower market as one of the most popular flower resources.

OBJECTIVE

To investigate the flower colour formation of Phalaenopsis at the transcription level, the genes involved in flower color formation were identified from RNA-seq in this study.

METHODS

In this study, white and purple petals of Phalaenopsis were collected and analyzed to obtained (1) differential expression genes (DEGs) between white and purple flower color and (2) the association between single nucleotide polymorphisms (SNP) mutations and DEGs at the transcriptome level.

RESULTS

The results indicated that a total of 1,175 DEGs were identified, and 718 and 457 of them were up- and down-regulated genes, respectively. Gene Ontology and pathway enrichment showed that the biosynthesis of the secondary metabolites pathway was key to color formation, and the expression of 12 crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase, and E1.11.17) that are involved in the regulation of flower color in Phalaenopsis.

CONCLUSION

This study reported the association between the SNP mutations and DEGs for color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.

Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion Zone

BACKGROUND

Individual functional modifications shape the ability of wildlife populations to cope with anthropogenic environmental changes. But instead of adaptive response, human-altered environments can generate a succession of deleterious functional changes leading to the extinction of the population. To study how persistent anthropogenic changes impacted local species' population status, we characterised population structure, genetic diversity and individual response of gene expression in the tree frog Hyla orientalis along a gradient of radioactive contamination around the Chernobyl nuclear power plant.

RESULTS

We detected lower effective population size in populations most exposed to ionizing radiation in the Chernobyl Exclusion Zone that is not compensated by migrations from surrounding areas. We also highlighted a decreased body condition of frogs living in the most contaminated area, a distinctive transcriptomics signature and stop-gained mutations in genes involved in energy metabolism. While the association with dose will remain correlational until further experiments, a body of evidence suggests the direct or indirect involvement of radiation exposure in these changes.

CONCLUSIONS

Despite ongoing migration and lower total dose rates absorbed than at the time of the accident, our results demonstrate that Hyla orientalis specimens living in the Chernobyl Exclusion Zone are still undergoing deleterious changes, emphasizing the long-term impacts of the nuclear disaster.

Whole-genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen-free ducks

Specific pathogen-free ducks are important high-grade laboratory animals, with a key role in research related to poultry biosecurity, production, and breeding. However, the genetic characteristics of experimental duck varieties remain poorly explored. Herein we performed whole-genome resequencing to construct a single nucleotide polymorphism genetic map of the genomes of 3 experimental duck varieties [Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)] to determine their genetic characteristics and identify selection signatures. Subsequent analyses of population structure and genetic diversity revealed that each duck variety formed a monophyletic group, with SM showing richer genetic diversity than JD and SX. Further, on exploring shared selection signatures, we found 2 overlapping genomic regions on chromosome Z of all experimental ducks, which comprised immune response-related genes (IL7R and IL6ST). Moreover, growth and skeletal development (IGF1R and GDF5), meat quality (FoxO1), and stress resistance (HSP90B1 and Gpx8-b) candidate gene loci were identified in strongly selected signatures specific to JD, SM, and SX, respectively. Our results identified the population genetic basis of experimental ducks at the whole-genome level, providing a framework for future molecular investigations of genetic variations and phenotypic changes. We believe that such studies will eventually contribute to the management of experimental animal resources.

Assessment of single-nucleotide variant discovery protocols in RNA-seq data from human cells exposed to mycotoxins

Food and feed contamination by nonlegislated mycotoxins beauvericin (BEA) and enniatin B (ENB) is a worldwide health concern in the present. The principal objective of this work is to assess some of the existing protocols to discover the single nucleotide variants (SNVs) in transcriptomic data obtained by RNA-seq from Jurkat cells in vitro samples individually exposed to BEA and ENB at three concentration levels (1.5, 3 and 5 µM). Moreover, previous transcriptomic results will be compared with new findings obtained using a different protocol. SNVs rs201003509 in BEA exposed cells and the rs36045790 in ENB were found in the differentially expressed genes in all doses compared to controls by means of the Genome Analysis Toolkit (GATK) Best Practices workflow. SNV-RNA-seq complementary pipeline did not show any SNV. Concerning gene expression, discrepant results were found for 1.5 µM BEA exposed cells compared with previous findings. However, 354 overlapped differentially expressed genes (DEGs) were identified in the three ENB concentrations used, with 147 matches with respect to the 245 DEGs found in the previous results. In conclusion, the two discovery SNVs protocols based on variant calling from RNA-seq used in this work displayed very different results and there were SNVs found manually not identified by any pipeline. Additionally, the new gene expression analysis reported comparable but non identical DEGs to the previous transcriptomic results obtained from these RNA-seq data.

Intra- and Interspecies RNA-Seq Based Variants in the Lactation Process of Ruminants

The RNA-Seq data provides new opportunities for the detection of transcriptome variants' single nucleotide polymorphisms (SNPs) in various species and tissues. Herein, milk samples from two sheep breeds and two cow breeds were utilized to characterize the genetic variation in the coding regions in three stages (before-peak (BP), peak (P), and after-peak (AP)) of the lactation process. In sheep breeds Assaf and Churra, 100,462 and 97,768, 65,996 and 62,161, and 78,656 and 39,245 variants were observed for BP, P, and AP lactation stages, respectively. The number of specific variants was 59,798 and 76,419, 11,483 and 49,210, and 104,033 and 320,817 in cow breeds Jersy and Kashmiri, respectively, for BP, P, and AP stages. Via the transcriptome analysis of variation in regions containing QTL for fat, protein percentages, and milk yield, we detected a number of pathways and genes harboring mutations that could influence milk production attributes. Many SNPs detected here can be regarded as appropriate markers for custom SNP arrays or genotyping platforms to conduct association analyses among commercial populations. The results of this study offer new insights into milk production genetic mechanisms in cow and sheep breeds, which can contribute to designing suitable breeding systems for optimal milk production.

Time Course RNA-seq Reveals Soybean Responses against Root-Lesion Nematode and Resistance Players

Pratylenchus brachyurus causes serious damage to soybean production and other crops worldwide. Plant molecular responses to RLN infection remain largely unknown and no resistance genes have been identified in soybean. In this study, we analyzed molecular responses to RLN infection in moderately resistant BRSGO (Chapadões-BRS) and susceptible TMG115 RR (TMG) Glycine max genotypes. Differential expression analysis revealed two stages of response to RLN infection and a set of differentially expressed genes (DEGs) in the first stage suggested a pattern-triggered immunity (PTI) in both genotypes. The divergent time-point of DEGs between genotypes was observed four days post-infection, which included the activation of mitogen-activated protein kinase (MAPK) and plant-pathogen interaction genes in the BRS, suggesting the occurrence of an effector-triggered immunity response (ETI) in BRS. The co-expression analyses combined with single nucleotide polymorphism (SNP) uncovered a key element, a transcription factor phytochrome-interacting factor (PIF7) that is a potential regulator of moderate resistance to RLN infection. Two genes for resistance-related leucine-rich repeat (LRR) proteins were found as BRS-specific expressed genes. In addition, alternative splicing analysis revealed an intron retention in a myo-inositol oxygenase (MIOX) transcript, a gene related to susceptibility, may cause a loss of function in BRS.

Whole Transcriptome Sequencing Unveils the Genomic Determinants of Putative Somaclonal Variation in Mint (Mentha L.)

Mint (Mentha L., Lamiaceae) is a strongly scented herb of the family Lamiaceae that is grown mostly by clonal propagation, making it a valuable species for the study of somaclonal variation and its phenotypic consequences. The recent introduction of a few species of mint in South America, followed by a presumably rampant propagation, make this region particularly ideal for studying the extent of somaclonal genetic diversity. Hence, the objective of this work was to offer a preliminary characterization of somaclonal genetically coding diversity of the mint in the northern Andes in order to address the question of whether somaclonal variants may have emerged despite relatively recent introductions in a region where mint is not native. A total of 29 clonally propagated specimens, collected in mint export farms in the province of Antioquia, a major region for mint production in the northwest Andes of Colombia, were genotyped using RNA sequencing (RNA-Seq). SNP calling was carried out from the leaves’ transcriptome profiles of each plant by combining the GATK4 and TRINITY protocols, obtaining a total of 2033 loci across 912 transcripts with a minimum read depth of 20X and 4% of missing data. Unsupervised machine learning algorithms considered the K-means, AGNES and UPGMA approaches, all of which suggested three genetic clusters for M. spicata and a unique cluster for M. × piperita. The results indicate that at least two different origins of M. spicata reached the eastern region of the Antioquia province, clonally propagated in the locality ever since for local consumption and export. One of these ancestries had more population structure, possibly due to environmental or anthropological pressures that intervened in the fragmentation of this genetic group or to a higher somaclonal mutation rate. This work offers a first step into the study of the accumulation and transmission of presumably quasi-neutral somatic mutations at coding regions in an herbaceous clonally propagated scented species such as mint, likely favored by an expected population expansion after its Andean introduction. These ad hoc hypotheses warrant further study as part of future research.

Functional genomics data: privacy risk assessment and technological mitigation

The generation of functional genomics data by next-generation sequencing has increased greatly in the past decade. Broad sharing of these data is essential for research advancement but poses notable privacy challenges, some of which are analogous to those that occur when sharing genetic variant data. However, there are also unique privacy challenges that arise from cryptic information leakage during the processing and summarization of functional genomics data from raw reads to derived quantities, such as gene expression values. Here, we review these challenges and present potential solutions for mitigating privacy risks while allowing broad data dissemination and analysis.

Differential gene expression reveals host factors for viral shedding variation in mallards (Anas platyrhynchos) infected with low-pathogenic avian influenza virus

Intraspecific variation in pathogen shedding impacts disease transmission dynamics; therefore, understanding the host factors associated with individual variation in pathogen shedding is key to controlling and preventing outbreaks. In this study, ileum and bursa of Fabricius tissues of wild-bred mallards (Anas platyrhynchos) infected with low-pathogenic avian influenza (LPAIV) were evaluated at various post-infection time points to determine genetic host factors associated with intraspecific variation in viral shedding. By analysing transcriptome sequencing data (RNA-seq), we found that LPAIV-infected wild-bred mallards do not exhibit differential gene expression compared to uninfected birds, but that gene expression was associated with cloacal viral shedding quantity early in the infection. In both tissues, immune gene expression was higher in high/moderate shedding birds compared to low shedding birds, and significant positive relationships with viral shedding were observed. In the ileum, expression for host genes involved in viral cell entry was lower in low shedders compared to moderate shedders at 1 day post-infection (DPI), and expression for host genes promoting viral replication was higher in high shedders compared to low shedders at 2 DPI. Our findings indicate that viral shedding is a key factor for gene expression differences in LPAIV-infected wild-bred mallards, and the genes identified in this study could be important for understanding the molecular mechanisms driving intraspecific variation in pathogen shedding.

Comparison of seven SNP calling pipelines for the next-generation sequencing data of chickens

Single nucleotide polymorphisms (SNPs) are widely used in genome-wide association studies and population genetics analyses. Next-generation sequencing (NGS) has become convenient, and many SNP-calling pipelines have been developed for human NGS data. We took advantage of a gap knowledge in selecting the appropriated SNP calling pipeline to handle with high-throughput NGS data. To fill this gap, we studied and compared seven SNP calling pipelines, which include 16GT, genome analysis toolkit (GATK), Bcftools-single (Bcftools single sample mode), Bcftools-multiple (Bcftools multiple sample mode), VarScan2-single (VarScan2 single sample mode), VarScan2-multiple (VarScan2 multiple sample mode) and Freebayes pipelines, using 96 NGS data with the different depth gradients of approximately 5X, 10X, 20X, 30X, 40X, and 50X coverage from 16 Rhode Island Red chickens. The sixteen chickens were also genotyped with a 50K SNP array, and the sensitivity and specificity of each pipeline were assessed by comparison to the results of SNP arrays. For each pipeline, except Freebayes, the number of detected SNPs increased as the input read depth increased. In comparison with other pipelines, 16GT, followed by Bcftools-multiple, obtained the most SNPs when the input coverage exceeded 10X, and Bcftools-multiple obtained the most when the input was 5X and 10X. The sensitivity and specificity of each pipeline increased with increasing input. Bcftools-multiple had the highest sensitivity numerically when the input ranged from 5X to 30X, and 16GT showed the highest sensitivity when the input was 40X and 50X. Bcftools-multiple also had the highest specificity, followed by GATK, at almost all input levels. For most calling pipelines, there were no obvious changes in SNP numbers, sensitivities or specificities beyond 20X. In conclusion, (1) if only SNPs were detected, the sequencing depth did not need to exceed 20X; (2) the Bcftools-multiple may be the best choice for detecting SNPs from chicken NGS data, but for a single sample or sequencing depth greater than 20X, 16GT was recommended. Our findings provide a reference for researchers to select suitable pipelines to obtain SNPs from the NGS data of chickens or nonhuman animals.

DNA-Based Tools to Certify Authenticity of Rice Varieties—An Overview

Rice (Oryza sativa L.) is one of the most cultivated and consumed crops worldwide. It is mainly produced in Asia but, due to its large genetic pool, it has expanded to several ecosystems, latitudes and climatic conditions. Europe is a rice producing region, especially in the Mediterranean countries, that grow mostly typical japonica varieties. The European consumer interest in rice has increased over the last decades towards more exotic types, often more expensive (e.g., aromatic rice) and Europe is a net importer of this commodity. This has increased food fraud opportunities in the rice supply chain, which may deliver mixtures with lower quality rice, a problem that is now global. The development of tools to clearly identify undesirable mixtures thus became urgent. Among the various tools available, DNA-based markers are considered particularly reliable and stable for discrimination of rice varieties. This review covers aspects ranging from rice diversity and fraud issues to the DNA-based methods used to distinguish varieties and detect unwanted mixtures. Although not exhaustive, the review covers the diversity of strategies and ongoing improvements already tested, highlighting important advantages and disadvantages in terms of costs, reliability, labor-effort and potential scalability for routine fraud detection.

Machine learning applications for therapeutic tasks with genomics data

Thanks to the increasing availability of genomics and other biomedical data, many machine learning algorithms have been proposed for a wide range of therapeutic discovery and development tasks. In this survey, we review the literature on machine learning applications for genomics through the lens of therapeutic development. We investigate the interplay among genomics, compounds, proteins, electronic health records, cellular images, and clinical texts. We identify 22 machine learning in genomics applications that span the whole therapeutics pipeline, from discovering novel targets, personalizing medicine, developing gene-editing tools, all the way to facilitating clinical trials and post-market studies. We also pinpoint seven key challenges in this field with potentials for expansion and impact. This survey examines recent research at the intersection of machine learning, genomics, and therapeutic development.

Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing

KEY MESSAGE

Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies. Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. However, no reference genome is currently available due to its very large genome size (approximately 13 Gb) and limited single nucleotide polymorphism (SNP) markers as well as highly efficient genotyping tools have been reported for faba bean. In this study, 16.7 billion clean reads were obtained from transcriptome libraries of flowers and leaves of 102 global faba bean accessions. A total of 243,120 unigenes were de novo assembled and functionally annotated. Moreover, a total of 1,579,411 SNPs were identified and further filtered according to a selection pipeline to develop a high-throughput, flexible, low-cost Faba_bean_130K targeted next-generation sequencing (TNGS) genotyping platform. A set of 69 Chinese faba bean accessions were genotyped with the TNGS genotyping platform, and the average mapping rate of captured reads to reference transcripts was 93.14%, of which 53.23% were located in the targeted regions. The TNGS genotyping results were validated by Sanger sequencing and the average consistency rate reached 93.6%. Comprehensive population genetic analysis was performed on the 69 Chinese faba bean accessions and identified four genetic subgroups correlated with the geographic distribution. This study provides valuable genomic resources and a reliable genotyping tool that could be implemented in genetic and molecular breeding studies to accelerate new cultivar development and improvement in faba bean.

A forward genetics approach integrating genome-wide association study and expression quantitative trait locus mapping to dissect leaf development in maize (Zea mays)

The characterization of the genetic basis of maize (Zea mays) leaf development may support breeding efforts to obtain plants with higher vigor and productivity. In this study, a mapping panel of 197 biparental and multiparental maize recombinant inbred lines (RILs) was analyzed for multiple leaf traits at the seedling stage. RNA sequencing was used to estimate the transcription levels of 29 573 gene models in RILs and to derive 373 769 single nucleotide polymorphisms (SNPs), and a forward genetics approach combining these data was used to pinpoint candidate genes involved in leaf development. First, leaf traits were correlated with gene expression levels to identify transcript-trait correlations. Then, leaf traits were associated with SNPs in a genome-wide association (GWA) study. An expression quantitative trait locus mapping approach was followed to associate SNPs with gene expression levels, prioritizing candidate genes identified based on transcript-trait correlations and GWAs. Finally, a network analysis was conducted to cluster all transcripts in 38 co-expression modules. By integrating forward genetics approaches, we identified 25 candidate genes highly enriched for specific functional categories, providing evidence supporting the role of vacuolar proton pumps, cell wall effectors, and vesicular traffic controllers in leaf growth. These results tackle the complexity of leaf trait determination and may support precision breeding in maize.

Single-Cell RNA Sequencing Approaches for Tracing T Cell Development

T cell development occurs in the thymus, where uncommitted progenitors are directed into a range of sublineages with distinct functions. The goal is to generate a TCR repertoire diverse enough to recognize potential pathogens while remaining tolerant of self. Decades of intensive research have characterized the transcriptional programs controlling critical differentiation checkpoints at the population level. However, greater precision regarding how and when these programs orchestrate differentiation at the single-cell level is required. Single-cell RNA sequencing approaches are now being brought to bear on this question, to track the identity of cells and analyze their gene expression programs at a resolution not previously possible. In this review, we discuss recent advances in the application of these technologies that have the potential to yield unprecedented insight to T cell development.

Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants

BACKGROUND

An individual's genetics play a role in how RNA transcripts are generated from DNA and consequently in their translation into protein. Transcriptional and translational profiling of patients furnishes the information that a specific marker is present; however, it fails to provide evidence whether the marker correlates with response to a therapeutic agent. A comparative analysis of the frequency of genetic variants, such as single nucleotide polymorphisms (SNPs), in diseased and general populations can identify pathogenic variants in individual patients. This is in part because SNPs have considerable effects on protein function and gene expression when they occur in coding regions and regulatory sequences, respectively. Therefore, a tool that can help users to obtain the allele frequency for a corresponding transcript is the need of the day. Several annotation tools such as SNPnexus and VariED are publicly available; however, none of them can use transcript IDs as input and provide the corresponding genomic positions of variants.

RESULTS

In this study, we developed an R package, called transcript annotation tool (TransAT), that provides (i) SNP ID and genomic position for a user-provided transcript ID from patients, and (ii) allele frequencies for the SNPs from publicly available global populations. All data elements are extracted, collected, and displayed in an easily downloadable format in two simple command lines. TransAT is available on Windows/Linux/MacOS and is operative for R version 4.0.4 or later. It is available at https://github.com/ShihChingYu/TransAT and can be downloaded and installed using devtools::install_github("ShihChingYu/TransAT", force=T) on the R execution page. Thereafter, all functions can be executed by loading the package into R with library(TransAT).

CONCLUSIONS

TransAT is a novel tool that seamlessly provides genetic annotations for queried transcripts. Such easily obtainable information would be greatly advantageous for physicians, assisting them to make individualized decisions about specific drug treatments. Moreover, allele frequencies from user-chosen global ethnic populations will highlight the importance of ethnicity and its effect on patient pathogenicity.

New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies

During the last (15) years, improved omics sequencing technologies have expanded the scale and resolution of various biological applications, generating high-throughput datasets that require carefully chosen software tools to be processed. Therefore, following the sequencing development, bioinformatics researchers have been challenged to implement alignment algorithms for next-generation sequencing reads. However, nowadays selection of aligners based on genome characteristics is poorly studied, so our benchmarking study extended the “state of art” comparing 17 different aligners. The chosen tools were assessed on empirical human DNA- and RNA-Seq data, as well as on simulated datasets in human and mouse, evaluating a set of parameters previously not considered in such kind of benchmarks. As expected, we found that each tool was the best in specific conditions. For Ion Torrent single-end RNA-Seq samples, the most suitable aligners were CLC and BWA-MEM, which reached the best results in terms of efficiency, accuracy, duplication rate, saturation profile and running time. About Illumina paired-end osteomyelitis transcriptomics data, instead, the best performer algorithm, together with the already cited CLC, resulted Novoalign, which excelled in accuracy and saturation analyses. Segemehl and DNASTAR performed the best on both DNA-Seq data, with Segemehl particularly suitable for exome data. In conclusion, our study could guide users in the selection of a suitable aligner based on genome and transcriptome characteristics. However, several other aspects, emerged from our work, should be considered in the evolution of alignment research area, such as the involvement of artificial intelligence to support cloud computing and mapping to multiple genomes.

The caffeoyl-CoA O-methyltransferase gene SNP replacement in Russet Burbank potato variety enhances late blight resistance through cell wall reinforcement

Metabolic pathway gene editing in tetraploid potato enhanced resistance to late blight. Multiallelic mutation correction of a caffeoyl-CoA O-methyltransferase gene increased accumulation of resistance metabolites in Russet Burbank potato. Late blight of potato is a devastating disease worldwide and requires weekly applications of fungicides to manage. Genetic improvement is the best option, but the self-incompatibility and inter-specific incompatibility makes potato breeding very challenging. Immune receptor gene stacking has increased resistance, but its durability is limited. Quantitative resistance is durable, and it mainly involves secondary cell wall thickening due to several metabolites and their conjugates. Deleterious mutations in biosynthetic genes can hinder resistance metabolite biosynthesis. Here a probable resistance role of the StCCoAOMT gene was first confirmed by an in-planta transient overexpression of the functional StCCoAOMT allele in late blight susceptible Russet Burbank (RB) genotype. Following this, a precise single nucleotide polymorphism (SNP) mutation correction of the StCCoAOMT gene in RB potato was carried out using CRISPR-Cas9 mediated homology directed repair (HDR). The StCCoAOMT gene editing increased the transcript abundance of downstream biosynthetic resistance genes. Following pathogen inoculation, several phenylpropanoid pathway genes were highly expressed in the edited RB plants, as compared to the non-edited. The disease severity (fold change = 3.76) and pathogen biomass in inoculated stems of gene-edited RB significantly reduced (FC = 21.14), relative to non-edited control. The metabolic profiling revealed a significant increase in the accumulation of resistance-related metabolites in StCCoAOMT edited RB plants. Most of these metabolites are involved in suberization and lignification. The StCCoAOMT gene, if mutated, can be edited in other potato cultivars to enhance resistance to late blight, provided it is associated with other functional genes in the metabolic pathway network.

Modified "Allele-Specific qPCR" Method for SNP Genotyping Based on FRET

The proposed method is a modified and improved version of the existing "Allele-specific q-PCR" (ASQ) method for genotyping of single nucleotide polymorphism (SNP) based on fluorescence resonance energy transfer (FRET). This method is similar to frequently used techniques like Amplifluor and Kompetitive allele specific PCR (KASP), as well as others employing common universal probes (UPs) for SNP analyses. In the proposed ASQ method, the fluorophores and quencher are located in separate complementary oligonucleotides. The ASQ method is based on the simultaneous presence in PCR of the following two components: an allele-specific mixture (allele-specific and common primers) and a template-independent detector mixture that contains two or more (up to four) universal probes (UP-1 to 4) and a single universal quencher oligonucleotide (Uni-Q). The SNP site is positioned preferably at a penultimate base in each allele-specific primer, which increases the reaction specificity and allele discrimination. The proposed ASQ method is advanced in providing a very clear and effective measurement of the fluorescence emitted, with very low signal background-noise, and simple procedures convenient for customized modifications and adjustments. Importantly, this ASQ method is estimated as two- to ten-fold cheaper than Amplifluor and KASP, and much cheaper than all those methods that rely on dual-labeled probes without universal components, like TaqMan and Molecular Beacons. Results for SNP genotyping in the barley genes HvSAP16 and HvSAP8, in which stress-associated proteins are controlled, are presented as proven and validated examples. This method is suitable for bi-allelic uniplex reactions but it can potentially be used for 3- or 4-allelic variants or different SNPs in a multiplex format in a range of applications including medical, forensic, or others involving SNP genotyping.

Identification and functional characterisation of late blight resistance polymorphic genes in Russet Burbank potato cultivar

In plants, the biosynthesis of the phenylpropanoid, flavonoid and fatty acid pathway monomers, polymers and conjugated metabolites play a vital role in disease resistance. These are generally deposited to reinforce cell walls to contain the pathogen to the site of infection. Identification of sequence variants in genes that biosynthesise these resistance metabolites can explain the mechanisms of disease resistance. The resistant and susceptible genotypes inoculated with Phytophthora infestans were RNA sequenced to identify the single nucleotide polymorphisms (SNPs) and insertion/deletion (InDel) variations. The SNPs/InDels were annotated and classified into different categories based on their effect on gene functions. In the selected 25 biosynthetic genes overlapping 39 transcripts, a total of 52 SNPs/InDels were identified in the protein-coding (CDS) regions. These were categorised as deleterious based on prediction of their effects on protein structure and function. The SNPs/InDels data obtained in this study can be used in genome editing to enhance late blight resistance in Russet Burbank and other potato cultivars.

Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize

Maize is the third most important cereal crop worldwide. However, its production is vulnerable to heat stress, which is expected to become more and more severe in coming years. Germplasm resilient to heat stress has been identified, but its underlying genetic basis remains poorly understood. Genomic mapping technologies can fill the void, provided robust markers are available to tease apart the genotype-phenotype relationship. In the present investigation, we used data from an RNA-seq experiment to identify single nucleotide polymorphisms (SNPs) between two contrasting lines, LM11 and CML25, sensitive and tolerant to heat stress, respectively. The libraries for RNA-seq were made following heat stress treatment from three separate tissues/organs, comprising the top leaf, ovule, and pollen, all of which are highly vulnerable to damage by heat stress. The single nucleotide variants (SNVs) calling used STAR mapper and GATK caller pipelines in a combined approach to identify highly accurate SNPs between the two lines. A total of 554,423, 410,698, and 596,868 SNVs were discovered between LM11 and CML25 after comparing the transcript sequence reads from the leaf, pollen, and ovule libraries, respectively. Hundreds of these SNPs were then selected to develop into genome-wide Kompetitive Allele-Specific PCR (KASP) markers, which were validated to be robust with a successful SNP conversion rate of 71%. Subsequently, these KASP markers were used to effectively genotype an F₂ mapping population derived from a cross of LM11 and CML25. Being highly cost-effective, these KASP markers provide a reliable molecular marker toolkit to not only facilitate the genetic dissection of the trait of heat stress tolerance but also to accelerate the breeding of heat-resilient maize by marker-assisted selection (MAS).

Role of NGS and SNP genotyping methods in sugarcane improvement programs

Sugarcane (Saccharum spp.) is one of the most economically significant crops because of its high sucrose content and it is a promising biomass feedstock for biofuel production. Sugarcane genome sequencing and analysis is a difficult task due to its heterozygosity and polyploidy. Long sequence read technologies, PacBio Single-Molecule Real-Time (SMRT) sequencing, the Illumina TruSeq, and the Oxford Nanopore sequencing could solve the problem of genome assembly. On the applications side, next generation sequencing (NGS) technologies played a major role in the discovery of single nucleotide polymorphism (SNP) and the development of low to high throughput genotyping platforms. The two mainstream high throughput genotyping platforms are the SNP microarray and genotyping by sequencing (GBS). This paper reviews the NGS in sugarcane genomics, genotyping methodologies, and the choice of these methods. Array-based SNP genotyping is robust, provides consistent SNPs, and relatively easier downstream data analysis. The GBS method identifies large scale SNPs across the germplasm. A combination of targeted GBS and array-based genotyping methods should be used to increase the accuracy of genomic selection and marker-assisted breeding.

Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset

BACKGROUND

Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species.

RESULTS

We identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves' transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including "Terpenoid backbone biosynthesis", "Valine, leucine and isoleucine biosynthesis", "Butanoate metabolism", "C5-Branched dibasic acid metabolism" "Pantothenate and CoA biosynthesis". We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species.

CONCLUSION

Some important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.

Transcriptional analyses of differential cultivars during resistant and susceptible interactions with Peronospora effusa, the causal agent of spinach downy mildew

Downy mildew of spinach is caused by the obligate oomycete pathogen, Peronospora effusa. The disease causes significant economic losses, especially in the organic sector of the industry where the use of synthetic fungicides is not permitted for disease control. New pathotypes of this pathogen are increasingly reported which are capable of breaking resistance. In this study, we took advantage of new spinach genome resources to conduct RNA-seq analyses of transcriptomic changes in leaf tissue of resistant and susceptible spinach cultivars Solomon and Viroflay, respectively, at an early stage of pathogen establishment (48 hours post inoculation, hpi) to a late stage of symptom expression and pathogen sporulation (168 hpi). Fold change differences in gene expression were recorded between the two cultivars to identify candidate genes for resistance. In Solomon, the hypersensitive inducible genes such as pathogenesis-related gene PR-1, glutathione-S-transferase, phospholipid hydroperoxide glutathione peroxidase and peroxidase were significantly up-regulated uniquely at 48 hpi and genes involved in zinc finger CCCH protein, glycosyltransferase, 1-aminocyclopropane-1-carboxylate oxidase homologs, receptor-like protein kinases were expressed at 48 hpi through 168 hpi. The types of genes significantly up-regulated in Solomon in response to the pathogen suggests that salicylic acid and ethylene signaling pathways mediate resistance. Furthermore, many genes involved in the flavonoid and phenylpropanoid pathways were highly expressed in Viroflay compared to Solomon at 168 hpi. As anticipated, an abundance of significantly down-regulated genes was apparent at 168 hpi, reflecting symptom development and sporulation in cultivar Viroflay, but not at 48 hpi. In the pathogen, genes encoding RxLR-type effectors were expressed during early colonization of cultivar Viroflay while crinkler-type effector genes were expressed at the late stage of the colonization. Our results provide insights on gene expression in resistant and susceptible spinach-P. effusa interactions, which can guide future studies to assess candidate genes necessary for downy mildew resistance in spinach.

MYCN and PRC1 cooperatively repress docosahexaenoic acid synthesis in neuroblastoma via ELOVL2

Background

The MYCN amplification is a defining hallmark of high-risk neuroblastoma. Due to irregular oncogenes orchestration, tumor cells exhibit distinct fatty acid metabolic features from non-tumor cells. However, the function of MYCN in neuroblastoma fatty acid metabolism reprogramming remains unknown.

Methods

Gas Chromatography-Mass Spectrometer (GC-MS) was used to find the potential target fatty acid metabolites of MYCN. Real-time PCR (RT-PCR) and clinical bioinformatics analysis was used to find the related target genes. The function of the identified target gene ELOVL2 on cell growth was detected through CCK-8 assay, Soft agar colony formation assay, flow Cytometry assay and mouse xenograft. Chromatin immunoprecipitation (ChIP) and Immunoprecipitation-Mass Spectrometer (IP-MS) further identified the target gene and the co-repressor of MYCN.

Results

The fatty acid profile of MYCN-depleted neuroblastoma cells identified docosahexaenoic acid (DHA), an omega-3 polyunsaturated fatty acid with anti-tumor activity, significantly increased after MYCN depletion. Compared with MYCN single-copy neuroblastoma cells, DHA level was significantly lower in MYCN-amplified neuroblastoma cells. RT-PCR and clinical bioinformatics analysis discovered that MYCN interfered DHA accumulation via ELOVL fatty acid elongase 2 (ELOVL2) which is a rate-limiting enzyme of cellular DHA synthesis. Enforced ELOVL2 expression in MYCN-amplified neuroblastoma cells led to decreased cell growth and counteracted the growth-promoting effect of MYCN overexpression both in vitro and vivo. ELOVL2 Knockdown showed the opposite effect in MYCN single-copy neuroblastoma cells. In primary neuroblastoma, high ELOVL2 transcription correlated with favorable clinical tumor biology and patient survival. The mechanism of MYCN-mediated ELOVL2 inhibition contributed to epigenetic regulation. MYCN recruited PRC1 (Polycomb repressive complex 1), catalysed H2AK119ub (histone 2A lysine 119 monoubiquitination) and inhibited subsequent ELOVL2 transcription.

Conclusions

The tumor suppressive properties of DHA and ELOVL2 are repressed by the MYCN and PRC1 jointly, which suggests a new epigenetic mechanism of MYCN-mediated fatty acid regulation and indicates PRC1 inhibition as a potential novel strategy to activate ELOVL2 suppressive functions.

Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

Background

Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant.

Results

In this study, we investigated the genome-wide genetic variations between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on 46 tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes.

Conclusion

The identified genome-wide genetic variations and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.