Field Screen and Genotyping of Phaseolus vulgaris against Two Begomoviruses in Georgia, USA

Abstract

The production and quality of Phaseolusvulgaris (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 spp. 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. We also included two commonly grown Lima bean (Phaseolus lunatus) varieties in our field screening. Twenty Phaseolus spp. genotypes with high to moderate-levels of resistance (disease severity ranging from 5%–50%) to CuLCrV and/or SiGMFV were identified. Twenty-one Phaseolus spp. genotypes were found to be highly susceptible with a disease severity of ≥66%. Furthermore, based on the greenhouse evaluation with two genotypes-each (two susceptible and two resistant; identified in field screen) exposed to viruliferous whiteflies infected with CuLCrV and SiGMFV, we observed that the susceptible genotypes accumulated higher copy numbers of both viruses and displayed severe crumple severity compared to the resistant genotypes, indicating that resistance might potentially be against the virus complex rather than against the whiteflies. Adult whitefly counts differed significantly among Phaseolus genotypes in both years. The whole genome of these Phaseolus spp. [snap bean (n = 82); Lima bean (n = 2)] 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 spp. 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. This phenotypic and genotypic information will be helpful in genome-wide association studies that will aid in identifying the genetic basis of resistance to these begomoviruses in Phaseolus spp.

Differential Transcriptional Responses in Two Old World Bemisia tabaci Cryptic Species Post Acquisition of Old and New World Begomoviruses

“…In the southeastern United States, B. tabaci MEAM1 occurs on field-grown vegetable crops such as tomato, eggplant, snap bean, and cucurbits and on cotton [30,31]. In these cropping systems, B. tabaci MEAM1 is known to transmit tomato yellow leaf curl virus (TYLCV), sida golden mosaic virus (SiGMV), and cucurbit leaf crumple virus (CuLCrV), which cause diseases [32,33]. In laboratory studies, B. tabaci MED tissues accumulated reduced amounts of the two New World begomoviruses compared to B. tabaci MEAM1 and did not transmit SiGMV and CuLCrV, albeit it was an efficient vector of TYLCV [34][35][36].…”

Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

“…As a result, several studies have been conducted to comprehensively explore features specific to each genome. The most widely explored genomic variants used in genome-wide studies are single nucleotide polymorphisms (SNPs) that are utilized in both prokaryotes [ 8 ] and eukaryotes [ 9 , 10 , 11 , 12 , 13 , 14 ]. Another widely used technique to explore variations in prokaryotic genomes is the use of presence and absence variants (PAVs).…”

Improving Whitefly Management

“…Agarwal et al identified several genotypes of snap bean ( Phaseolus vulgaris ) and lima bean ( P . lunatus ) with resistance against two whitefly-transmitted begomoviruses ( Cucurbit leaf crumple virus and Sida golden mosaic Florida virus ) [ 17 ].…”