scholarly journals Potential Application of Genomic Technologies in Breeding for Fungal and Oomycete Disease Resistance in Pea

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1260
Author(s):  
Ambuj B. Jha ◽  
Krishna K. Gali ◽  
Zobayer Alam ◽  
V. B. Reddy Lachagari ◽  
Thomas D. Warkentin
Keyword(s):  
Disease Resistance ◽  
Genome Sequence ◽  
Potential Application ◽  
Ascochyta Blight ◽  
Gene Families ◽  
Snp Markers ◽  
Growth And Yield ◽  
Current Status ◽  
Genomic Technologies ◽  
Sequencing Platforms

Growth and yield of pea crops are severely affected by various fungal diseases, including root rot, Ascochyta blight, powdery mildew, and rust, in different parts of the world. Conventional breeding methods have led to enhancement of host plant resistance against these diseases in adapted cultivars, which is the primary option to minimize the yield losses. To support the breeding programs for marker-assisted selection, several successful attempts have been made to detect the genetic loci associated with disease resistance, based on SSR and SNP markers. In recent years, advances in next-generation sequencing platforms, and resulting improvements in high-throughput and economical genotyping methods, have been used to make rapid progress in identification of these loci. The first reference genome sequence of pea was published in 2019 and provides insights on the distribution and architecture of gene families associated with disease resistance. Furthermore, the genome sequence is a resource for anchoring genetic linkage maps, markers identified in multiple studies, identification of candidate genes, and functional genomics studies. The available pea genomic resources and the potential application of genomic technologies for development of disease-resistant cultivars with improved agronomic profile will be discussed, along with the current status of the arising improved pea germplasm.

scholarly journals Paper-containing 1-methylcyclopropene treatment suppresses fruit decay of fresh Anxi persimmons by enhancing disease resistance

2021 ◽  
Vol 5 ◽  
Author(s):  
Lingzhen Zeng ◽  
Lili Shi ◽  
Hetong Lin ◽  
Yuzhao Lin ◽  
Yixiong Lin ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Decay Rate ◽  
Potential Application ◽  
Total Phenolics ◽  
Lignin Content ◽  
Related Substances ◽  
Postharvest Treatment ◽  
Cent Relative Humidity ◽  
Fruit Decay ◽  
Fruit Disease

Abstract Objectives The purpose of this work was to evaluate the potential application of papers containing 1-methylcyclopropene (1-MCP) postharvest treatment for suppressing fruit decay of fresh Anxi persimmons and its possible mechanism. Materials and methods Anxi persimmon fruit were treated with papers containing 1-MCP at the dosage of 1.35 μL/L and stored at 25 ± 1 °C and 85 per cent relative humidity for 35 days. During storage, the fruit decay rate and lignin content were evaluated, and the content of total phenolics, the activities of phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO), peroxidase (POD), chitinase (CHI), and β-1,3-glucanase (GLU) were determined by spectrophotometry. Results The 1-MCP–treated persimmons displayed a lower fruit decay rate, but higher contents of lignin and total phenolics, higher activities of PAL, PPO, POD, CHI, and GLU. Conclusions The treatment with 1-MCP could inhibit the fruit decay of postharvest Anxi persimmons, which might be because 1-MCP enhanced fruit disease resistance by increasing the activities of disease resistance-associated enzymes and retaining higher contents of disease resistance-related substances in postharvest fresh Anxi persimmons. These findings indicate that papers containing 1-MCP at the dosage of 1.35 μL/L have potential application in suppressing fruit decay and extending storage life of postharvest fresh Anxi persimmons.

scholarly journals Chromosome-scale genome assembly of Cucumis hystrix—a wild species interspecifically cross-compatible with cultivated cucumber

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Xiaodong Qin ◽  
Zhonghua Zhang ◽  
Qunfeng Lou ◽  
Lei Xia ◽  
Ji Li ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Wild Species ◽  
Genomic Analysis ◽  
Gene Families ◽  
Comparative Genomic ◽  
Disease Resistance Gene ◽  
Introgression Breeding ◽  
Interspecific Introgression ◽  
Cucumber Genome ◽  
Cucumis Hystrix

AbstractCucumis hystrix Chakr. (2n = 2x = 24) is a wild species that can hybridize with cultivated cucumber (C. sativus L., 2n = 2x = 14), a globally important vegetable crop. However, cucumber breeding is hindered by its narrow genetic base. Therefore, introgression from C. hystrix has been anticipated to bring a breakthrough in cucumber improvement. Here, we report the chromosome-scale assembly of C. hystrix genome (289 Mb). Scaffold N50 reached 14.1 Mb. Over 90% of the sequences were anchored onto 12 chromosomes. A total of 23,864 genes were annotated using a hybrid method. Further, we conducted a comprehensive comparative genomic analysis of cucumber, C. hystrix, and melon (C. melo L., 2n = 2x = 24). Whole-genome comparisons revealed that C. hystrix is phylogenetically closer to cucumber than to melon, providing a molecular basis for the success of its hybridization with cucumber. Moreover, expanded gene families of C. hystrix were significantly enriched in “defense response,” and C. hystrix harbored 104 nucleotide-binding site–encoding disease resistance gene analogs. Furthermore, 121 genes were positively selected, and 12 (9.9%) of these were involved in responses to biotic stimuli, which might explain the high disease resistance of C. hystrix. The alignment of whole C. hystrix genome with cucumber genome and self-alignment revealed 45,417 chromosome-specific sequences evenly distributed on C. hystrix chromosomes. Finally, we developed four cucumber–C. hystrix alien addition lines and identified the exact introgressed chromosome using molecular and cytological methods. The assembled C. hystrix genome can serve as a valuable resource for studies on Cucumis evolution and interspecific introgression breeding of cucumber.

scholarly journals Draft Genome Sequence of Xylella fastidiosa subsp. fastidiosa Strain Stag’s Leap

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
J. Chen ◽  
F. Wu ◽  
Z. Zheng ◽  
X. Deng ◽  
L. P. Burbank ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Genome Sequence ◽  
Gene Function ◽  
Xylella Fastidiosa ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Pierce's Disease ◽  
Pierce’S Disease ◽  
Knockout Mutants ◽  
Fastidiosa Strain

Xylella fastidiosa subsp. fastidiosa causes Pierce’s disease of grapevine. Presented here is the draft genome sequence of the Stag’s Leap strain, previously used in pathogenicity/virulence assays to evaluate grapevine germplasm bearing Pierce’s disease resistance and a phenotypic assessment of knockout mutants to determine gene function.

scholarly journals Experience of using modern genomic technologies to study microorganisms and their communities

2021 ◽  
pp. 159-167
Author(s):  
E. V. Voropaev ◽  
I. O. Stoma ◽  
D. V. Tapalski
Keyword(s):  
Risk Groups ◽  
Metagenomic Analysis ◽  
Minimal Amount ◽  
Genomic Technologies ◽  
Bacterial Microbiome ◽  
Genomic Studies ◽  
H Pylori ◽  
Sequencing Platforms ◽  
Modern Genomic ◽  
Medical University

Objective. The aim of this work was to review the main results of genomic studies of microorganisms and their communities performed on the base of the Research Laboratory of Gomel State Medical University.Materials and methods. Genomic, transcriptomic and metagenomic analysis of the microorganisms of the stomach and respiratory tract.Results. The capabilities of modern next-generation sequencing platforms have been analyzed, and the authors` own results of the use of genomic, transcriptomic and metagenomic analysis of the microbiota in patients with various gastric and respiratory pathologies have been described.Conclusion. The analysis of the obtained data has revealed peculiarities of the structure of the microbial communities of the stomach of the patients infected with H. pylori with different gastric pathology: the proportion participation of H. pylori in the metagenome of the samples with different forms of gastric cancer did not exceed 25 %, of gastritis — 6 %, of peptic ulcer — 1 %. At the same time, the minimal amount of H. pylori in all the cases could reach 0.1 %. A signifcant degree of CagA and CagY loci variability of H. pylori was detected. Streptoccocus genus bacteria dominated (36 %) in the bacterial microbiome of a patient diagnosed with the coronavirus disease, and in the viral microbiome, SARS-CoV-2 constituted 59 % of the total number of viruses in the material. The analysis of 13 strains of Klebsiella pneumoniae with multiple and extreme resistance to antibiotics has found that the studied strains belong to fve MLST-types, three of which are classifed as high epidemic risk groups.

scholarly journals Full-Length Transcriptome Sequences by A Combination of Sequencing Platforms Applied to Isoflavonoid and Triterpenoid Saponin Biosynthesis of Astragalus Mongholicus Bunge

2020 ◽  
Author(s):  
Minzhen Yin ◽  
Shanshan Chu ◽  
Tingyu Shan ◽  
Liangping Zha ◽  
Huasheng Peng
Keyword(s):  
Single Molecule ◽  
Molecular Genetic ◽  
Gene Families ◽  
Triterpenoid Saponin ◽  
Smrt Sequencing ◽  
Triterpenoid Saponins ◽  
Saponin Biosynthesis ◽  
Medicinal Value ◽  
Long Time ◽  
Sequencing Platforms

Abstract Background: Astragalus mongholicus Bunge is an important medicinal plant and has been used in traditional Chinese medicine for a long history, which is rich in isoflavonoids and triterpenoid saponins. Although these active constituents in A. mongholicus have been discovered for a long time, the molecular genetic basis of the isoflavonoid and triterpenoid saponin biosynthesis pathways is virtually unknown due to the lack of a reference genome. The combination of next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing to analyze genes involved in the biosynthetic pathways of secondary metabolites in medicinal plants has been widely recognized.Results: In this study, NGS, SMRT sequencing, and targeted compounds were combined to investigate the association between isoflavonoids and triterpenoid saponins and gene expression in roots, stems and leaves of A. mongholicus. A total of four main isoflavonoids and four astragalosides (belong to triterpenoid saponins) were measured, and 44 differentially expressed genes (DEGs) of nine gene families, 44 DEGs of 16 gene families that encode for enzymes involved in isoflavonoid and triterpenoid saponin biosynthesis were identified, separately. Additionally, transcription factors (TFs) associated with isoflavonoid and triterpenoid saponin biosynthesis were analyzed, including 72 MYBs, 53 bHLHs, 64 AP2-EREBPs and 11 bZIPs. The above transcripts exhibit different expression trends in different organs.Conclusions: Our study provides important genetic information for the essential genes of isoflavonoid and triterpenoid saponin biosynthesis in A. mongholicus, and provides a basis for developing its medicinal value.

scholarly journals Effect of Some Agronomic Practices on Ascochyta Blight Severity and Yield of Faba Bean (Vicia faba L.) in Tunisia

2021 ◽  
Author(s):  
A. Ouji ◽  
S. Chekali ◽  
M. Rouaissi
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Ascochyta Blight ◽  
Growth And Yield ◽  
Row Spacing ◽  
Seed Rate ◽  
Agronomic Practices ◽  
Vicia Faba L ◽  
Cropping Seasons ◽  
Effect On Yield

Background: In Tunisia, faba bean (Vicia faba L.) is the first major food legume. The development of faba bean production is facing several biotic constraints. Faba bean Ascochyta blight caused by Ascochyta fabae is one of the most destructive diseases of faba bean and can cause significant yield loss under favorable conditions. As only incomplete resistance ABL varieties are available, some agronomic practices should be applied to control and reduce Ascochyta blight incidence wherever possible. Therefore, this work was undertaken to evaluate the effect of spacing row and seed rate on ABL severity, growth and yield of faba bean. Methods: A split-plot design with three replications was adopted to carry out this study during 2018 and 2019 cropping seasons. ‘Bachaar’ faba bean variety was sown at 40 and 60 cm row spacing and at three seed rates (100, 140 and 200 kg ha-1). ABL severity was assessed visually on a 0-9 scale and agro-morphological traits were measured. Analysis of variance was used to analyze the data. Correlations between agronomic traits, row spacing, seed rate and ABL severity were investigated. Result: Results showed that seed rate has a larger effect on yield than row spacing. In both cropping seasons, the highest grain yield was recorded in 60 cm row spacing and 140 kg ha-1 seed rate treatment. So, this treatment is recommended for obtaining high yield of faba bean. Most of the variation in disease severity was associated with seed rate (r=0.62). The highest ABL score severity was noted at 200 kg ha-1 rate. Over both years, wide row spacing and low seed rate reduced ABL severity. In this study, the small amounts of ABL disease (which reached a score of 5.3 and 4.7 in 2018 and 2019, respectively) had little or no effect on yield.

scholarly journals Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1359
Author(s):  
Esther Camacho ◽  
Sandra González-de la Fuente ◽  
Jose C. Solana ◽  
Alberto Rastrojo ◽  
Fernando Carrasco-Ramiro ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Leishmania Major ◽  
De Novo ◽  
Gene Annotation ◽  
Leishmania Species ◽  
De Novo Genome Assembly ◽  
Sequencing Platforms

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

scholarly journals Precision phenotyping reveals novel loci for quantitative resistance to septoria tritici blotch in European winter wheat

2018 ◽  
Author(s):  
Steven Yates ◽  
Alexey Mikaberidze ◽  
Simon Krattinger ◽  
Michael Abrouk ◽  
Andreas Hund ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Winter Wheat ◽  
High Throughput ◽  
Quantitative Resistance ◽  
Small Chromosome ◽  
Snp Markers ◽  
Automated Image Analysis ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Limiting Factor

Accurate, high-throughput phenotyping for quantitative traits is the limiting factor for progress in plant breeding. We developed automated image analysis to measure quantitative resistance to septoria tritici blotch (STB), a globally important wheat disease, enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance. 335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population. More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform a GWAS. We identified 26 chromosome intervals explaining 1.9-10.6% of the variance associated with four resistance traits. Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes, including many genes associated with disease resistance. Five intervals contained four or fewer genes, providing high priority targets for functional validation. Ten chromosome intervals were not previously associated with STB resistance. Our experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance. The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes.

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