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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)
Agarwal, G.; Kavalappara, S.R.; Gautam, S.; Silva, A.; Simmons, A.; Srinivasan, R.; Dutta, B. Field Screen and Genotyping of Phaseolus vulgaris against Two Begomoviruses in Georgia, USA. Insects2021, 12, 49.
Agarwal, G.; Kavalappara, S.R.; Gautam, S.; Silva, A.; Simmons, A.; Srinivasan, R.; Dutta, B. Field Screen and Genotyping of Phaseolus vulgaris against Two Begomoviruses in Georgia, USA. Insects 2021, 12, 49.
Agarwal, G.; Kavalappara, S.R.; Gautam, S.; Silva, A.; Simmons, A.; Srinivasan, R.; Dutta, B. Field Screen and Genotyping of Phaseolus vulgaris against Two Begomoviruses in Georgia, USA. Insects2021, 12, 49.
Agarwal, G.; Kavalappara, S.R.; Gautam, S.; Silva, A.; Simmons, A.; Srinivasan, R.; Dutta, B. Field Screen and Genotyping of Phaseolus vulgaris against Two Begomoviruses in Georgia, USA. Insects 2021, 12, 49.
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.
Keywords
Cucurbit leaf crumple virus, Sida golden mosaic Florida virus, Whitefly, Snap beans, Lima beans
Subject
Biology and Life Sciences, Agricultural Science and Agronomy
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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