Whole-genome sequencing and phenotyping revealed structural variants and varied level of resistance against leaf crumple disease in diverse lines of snap bean (Phaseolus vulgaris)

Authors: AGARWAL, GAURAV - University Of Georgia; KAVALAPPARA, SARITHA - University Of Georgia; GAUTAM, SAURABH - University Of Georgia; DA SILVA, ANDRE - University Of Georgia; Simmons, Alvin; SRINIVASAN, RAJAGOPALBABU - University Of Georgia; DUTTA, BHABESH - University Of Georgia

Submitted to: Insects
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/4/2021
Publication Date: 1/10/2021
Citation: Agarwal, G., Kavalappara, S.R., Gautam, S., da Silva, A., Simmons, A., Srinivasan, R., Dutta, B. 2021. Field screen and genotyping of Phaseolus vulgaris against two begomoviruses in Georgia, USA. Insects. 12:49
DOI: https://doi.org/10.3390/insects12010049

Interpretive Summary: Snap bean plants are damaged by whiteflies and whitefly-transmitted diseases including the cucurbit leaf crumple virus (CuLCrV) and sida golden mosaic Florida virus (SiGMFV). These diseases often appear together in fields in Georgia. Using cultivars that are resistance is the most economical management strategy against whitefly-transmitted viruses, but information is lacking about plant resistance for these two viruses in commercial cultivars. Across two field seasons, screening was done on CuLCrV and SiGMFV for snap bean genotypes (84 in 2018 and 80 in 2019). Twenty genotypes were identified with high- to moderate-levels of resistance (disease severity ranging from 5-50%) to CuLCrV and/or SiGMF; conversely, 21 genotypes were highly susceptible with a disease severity of =66%. Adult whitefly counts differed significantly among snap bean genotypes for both years. The whole genome of these snap bean genotypes (n=82) was sequenced and genetic variability among them was identified. This plant and genetic information will be helpful to scientists in developing snap beans that have resistance to whitefly-transmitted viruses.

Technical Abstract: The production and quality of Phaseolus vulgaris (snap bean) have been negatively impacted by leaf crumple disease caused by two whitefly-transmitted begomoviruses; cucurbit leaf crumple virus (CuLCrV) and sida golden mosaic Florida virus (SiGMFV), which often appear as a mixed infection in Georgia. Host resistance is the most economical management strategy against whitefly-transmitted viruses. Currently, information is not available with respect to resistance to these two viruses in commercial cultivars. In two field seasons (2018 and 2019), we screened Phaseolus sp. genotypes (n = 84 in 2018; n = 80 in 2019; most of the genotypes were common in both years with a few exceptions) for resistance against CuLCrV and/or SiGMFV. Twenty genotypes with high- to moderate-levels of resistance (disease severity ranging from 5-50%) to CuLCrV and/or SiGMFV were identified. Twenty-one genotypes were found to be highly susceptible with a disease severity of =66%. Adult whitefly counts differed significantly among snap bean genotypes for both years. The whole genome of these Phaseolus sp. (n=82) genotypes was sequenced and genetic variability among them was identified. Over 900 giga-base (Gb) of filtered data were generated and >88% of the resulting data were mapped to the reference genome, and SNP and Indel variants in Phaseolus genotypes were obtained. A total of 645,729 SNPs and 68,713 Indels including 30,169 insertions and 38,543 deletions were identified, which were distributed in 11 chromosomes with chromosome 02 harboring the maximum number of variants. These phenotypic and genotypic information will be helpful in genome-wide association studies that will aid in identifying genetic basis of resistance to these begomoviruses in Phaseolus sp.