Genomic regions associated with chocolate spot (Botrytis fabae Sard.) resistance in faba bean (Vicia faba L.)

Chocolate spot (CS), caused by Botrytis fabae Sard., is an important threat to global faba bean production. Growing resistant faba bean cultivars is, therefore, paramount to preventing yield loss. To date, there have been no reported quantitative trait loci (QTLs) associated with CS resistance in faba bean. The objective of this study was to identify genomic regions associated with CS resistance using a recombinant inbred line (RIL) population derived from resistant accession ILB 938. A total of 165 RILs from the cross between Melodie/2 and ILB 938/2 were genotyped and evaluated for CS reactions under replicated, controlled climate conditions. QTL analysis identified five loci contributing to CS resistance on faba bean chromosomes 1 and 6, accounting for 5.0-23.4% of the total phenotypic variance. The sequences of SNP markers linked to resistance QTLs on chromosome 1 that have the largest effects encode multiple classes of putative disease and/or defense-related genes. The results of this study not only provide insight into disease-resistance QTLs, but can also be used as potential targets for marker-assisted breeding in faba bean genetic improvement for CS resistance. Keywords: Botrytis fabae; chocolate spot; faba bean; disease resistance; QTL mapping; candidate gene

In silico Structural and Functional Annotation of Tomato Chocolate spot Virus

Aims: The study aims to predict in-silico the structural and functional annotation of Tomato Chocolate Spot Virus (TCSV) retrieved from Uniprotkb with the accession number C7EXM3. Study design: To use the In-silico approach for the structural and functional annotation of the Tomato Chocolate Spot Virus. Place and Duration of Study: The research was conducted at the Bioinformatics Unit, Chevron Biotechnology Centre, Modibbo Adama University Yola, Nigeria. Between August 2021 to September 2021. Methodology: The sequence of the Tomato Chocolate Spot Virus was retrieved from Uniprotkb with accession number C7EXM3, Physicochemical characteristics were computed using the ProtParam tool. The sever SOPMA was used for secondary structure analysis (Helix, Sheets and Coils). The tool CELLO v2.5 was used to predict the subcellular localization of the protein. Four different Homology Modelling tools (trRosetta, Lomet, RaptorX and IntFOLD5) were used to predict the 3D structure of the protein, the quality of the predicted proteins was assessed used PROCHECK. Three tools (InterProScan, NCBI conserved domains and Phobius) were used to get the possible function(s) of the protein. Results: ProtParam tool computed various Physical and Chemical properties such as Molecular weight (MW) 20396.96 Daltons, isoelectric point (pI) of 6.92. Instability Index 41.94, and Grand Average Hydropathy (GRAVY) -0.503. SOPMA was used for calculating the secondary structure parameters of the protein as Helices (Hh) 43.48%, Extended strands (Ee) 18.48%, Random coils (Cc) 38.04%. CELLO v2.5 was used for subcellular localization of the protein, it predicted that the protein can be both Nuclear and Cytoplasmic with the reliability of 1.653 and 1.504 respectively. Different Homology modelling tools were used to obtain the best 3D structure of the protein. Furthermore, PROCHECK was used to assess the quality of the models obtained. Model from trRosetta was found to be the best because of the quality of the Ramachandran Plot obtained from PROCHECK which has more than 90% of amino acid in the most favourable regions. NCBI-CDD and interproScan predicted that protein is a DNA double-strand break repair Rad50 ATPase, which is involved in the early steps of DNA double-strand break (DSB) repair. Furthermore, the Phobius server predicted the protein to be non-cytoplasmic in its domain, which means they help target proteins to their final destinations. Conclusion: The study has helped in obtaining the 3D structure of the protein Tomato Chocolate Spot Virus from different Modelling tools, as well as the possible function of the protein.

Performance and reaction of faba bean genotypes to chocolate spot disease

Background This study aimed to development new faba bean hybrids resistant to chocolate spot disease and using them in breeding programs. Six faba bean genotypes were crossed in a diallel system excluding reciprocals during three growing seasons of 2017/18, 2018/19 and 2019/20 growing seasons. Results Results scored high variability among genotypes (parents and their crosses) in most studied characters. All characters were affected by inbreeding and most crosses recorded high significant in all characters especially the positive significance of resistance to chocolate spot disease (gain) was 5 for all studied resistance characters. Conclusions All studied plant growth and yield characters were affected negatively by chocolate spot disease. Moreover, it can be concluded that the commercial cost of producing hybrid seed can be reduced by growing F1 or directly.

Alternaria yali-inficiens (chocolate spot of Ya Li pear).

A. yali-inficiens is an asexually reproducing, filamentous fungus known only since its isolation in 2001 from infections on fruit of Ya Li pears (Pyrus bretschneideri), exported from a certain region of China. Although most species of Alternaria are air-disseminated, its ability to spread and establish in other temperate fruit-growing regions is not known. This fungus may pose a threat to native or agricultural plants if introduced. Some countries importing pear fruit from China have established regulatory precautions against it.