Variance of allele balance calculated from low coverage sequencing data infers departure from a diploid state.

Polyploidy and heterokaryosis are common and consequential genetic phenomena that increase the number of haplotypes in an organism and complicate whole-genome sequence analysis. Allele balance has been used to infer polyploidy and heterokaryosis in diverse organisms using read sets sequenced to greater than 50x whole-genome coverage. However, Sequencing to adequate depth is costly if applied to multiple individuals or large genomes. We developed VCFvariance.pl to utilize the variance of allele balance to infer polyploidy and/or heterokaryosis at low sequence coverage. This analysis requires as little as 10x whole-genome coverage and reduces the allele balance profile down to a single value, which can be used to determine if an individual has two or more haplotypes. This approach was validated on simulated, synthetic, and authentic read sets from an oomycete, fungus, and plant. The approach was deployed to ascertain the genome status of multiple isolates of Bremia lactucae and Phytophthora infestans. VCFvariance.pl is a Perl script available at https://github.com/kfletcher88/VCFvariance.

Downy Mildew of Lettuce in Florida

Lettuce Downy Mildew (LDM), caused by the oomycete <i>Bremia lactucae</i>, is the most important disease of lettuce worldwide. LDM has a direct effect on both yield quantity and quality because it may infect lettuce at any growth stage, affecting the marketable portion of the crop. This new 6-page publication of the UF/IFAS Horticultural Sciences Department introduces the LDM disease in Florida lettuce and available control methods and strategies. This publication also introduces the work on LDM in the UF/IFAS Lettuce Breeding Program, which was created to release cultivars adapted to Florida conditions. Written by Lis Rodrigues-Porto, Richard N. Raid, and Germán V. Sandoya.https://edis.ifas.ufl.edu/hs1403

Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif

Pathogens that infect plants and animals use a diverse arsenal of effector proteins to suppress the host immune system and promote infection. Identification of effectors in pathogen genomes is foundational to understanding mechanisms of pathogenesis, for monitoring field pathogen populations, and for breeding disease resistance. We identified candidate effectors from the lettuce downy mildew pathogen Bremia lactucae by searching the predicted proteome for the WY domain, a structural fold found in effectors that has been implicated in immune suppression as well as effector recognition by host resistance proteins. We predicted 55 WY domain containing proteins in the genome of B. lactucae and found substantial variation in both sequence and domain architecture. These candidate effectors exhibit several characteristics of pathogen effectors, including an N-terminal signal peptide, lineage specificity, and expression during infection. Unexpectedly, only a minority of B. lactucae WY effectors contain the canonical N-terminal RXLR motif, which is a conserved feature in the majority of cytoplasmic effectors reported in Phytophthora spp. Functional analysis of 21 effectors containing WY domains revealed 11 that elicited cell death on wild accessions and domesticated lettuce lines containing resistance genes, indicative of recognition of these effectors by the host immune system. Only two of the 11 recognized effectors contained the canonical RXLR motif, suggesting that there has been an evolutionary divergence in sequence motifs between genera; this has major consequences for robust effector prediction in oomycete pathogens.

Comparison of methods to evaluate resistance of lettuce genotypes against Bremia lactucae

For the lettuce crop, there is no specific or standard methodology to evaluate genotype resistance of lettuce against downy mildew. Therefore, the aim of this work was to compare three methodologies for the identification of resistance to downy mildew. The experiment was carried out at Universidade Federal de Uberlândia, Monte Carmelo Campus between 2017 and 2018. The statistical method used was a completely randomized design with 12 treatments (cultivar Solaris, used as a control; and 11 genotypes of lettuce F5: 6: UFU-Crespa 75 # 2, UFU-Crespa 189 # 2, UFU-Crespa 206 # 1, UFU-Lisa 66 # 3, UFU-Lisa 66 # 7, UFU-Lisa 215 # 3, UFU-Lisa 215 # 6, UFU-Lisa 215 # 10, UFU-Lisa 215 # 12, UFU-Lisa 215 # 13, UFU-Lisa 215 # 14) and four replications. The seeding of genotypes was carried out in transparent boxes and after 15 days the inoculation was performed using a spore suspension (1x104 sporangia/ml) and sterile deionized water for the controls. The disease progression was assessed by three methods: Mesquita, Dickinson & Crute and Horsfall & Barrat. The data were standardized and submitted to the univariate analysis of variance by the F test and multivariate analyzes. The univariate clustering results allowed the separation of the genotypes into two distinct resistance groups for the Dickinson & Crute and Mesquita methods. In the multivariate analysis, more formation of groups among genotypes with different levels of resistance to downy mildew in the Mesquita method was observed. The methodology proposed by Mesquita was more efficient in discriminating genotypes with different levels of resistance to downy mildew, separating them in a larger number of groups.

Essential Tea Tree Oil Activity against Bremia lactucae in Lettuce

Downy mildew caused by the oomycete Bremia lactucae Regel is a serious disease of lettuce in field and greenhouse production. Here we report on the antifungal activity of essential Australian tea tree oil (TTO) derived from Melaleuca alternifolia against downy mildew in lettuce. Preventive treatments with Timorex Gold (STK Ltd., Petach Tikva, Israel), fungicide containing TTO, suppressed the development of B. lactucae on cotyledons and young lettuce plants. Epifluorescence microscopy showed that TTO had a moderate inhibitory effect on spore germination of the pathogen but a strong inhibitory effect on sporophore emergence and hence on sporulation. Timorex Gold (22.3 EC W/V) was as effective as copper hydroxide in controlling the disease in organic field plots. It was as effective as the fungicides Bellis (Boscalid + Pyraclostrobin; BASF, Germany) and Commet (pyraclostrobin; BASF, Germany) in conventional production. The results demonstrate that Timorex Gold effectively suppresses the development of downy mildew in lettuce in growth chambers as well as in the field, and thus suitable biopesticide for its control.