Characterization of Galacturonic Acid Catabolic Genes in Sclerotinia sclerotiorum

Primary author: Nickisha Pierre-Pierre
Co-author(s): Wei Wei
Faculty sponsor: Weidong Chen

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman

Abstract:

Sclerotinia sclerotiorum is a necrotrophic fungal pathogen causing white mold disease on more than 600 plant species, including many economically important crops. The most prominent symptom of white mold is maceration of host tissue, suggesting the efficiency of pathogen in degrading plant cell wall. Galacturonic acid is the major building block of pectin which is a main component of plant cell wall. Thus, the resulting galacturonic acid after tissue maceration is likely the nutrient source for S. sclerotiorum. The genome of S. sclerotiorum encodes the genes responsible for galacturonic acid catabolism. However, the roles of these galacturonic acid catabolic genes in the biology and virulence of S. sclerotiorum are unknown.
The D-galacturonic acid catabolic pathway in S. sclerotiorum consists of three catalytic steps converting D-galacturonic acid to pyruvate and L-glyceraldehyde. In an effort to characterize the functions of the galacturonic acid catabolic pathway genes, gene deletion mutants of these genes in S. sclerotiorum were generated using targeted mutagenesis.
The wildtype and gene-deletion mutant strains of S. sclerotiorum were tested on media with different carbon sources. For radial growth assays, mycelium of strains were inoculated on Murashige and Skoog media supplemented with Ammonium dihydrogen phosphate and as a carbon source either glucose, D-galacturonic acid, citrus fruit pectin, apple pectin or sodium pectate. The significance of the effects of Sclerotinia sclerotiorum and the characterization of its virulence in host plants will be discussed in efforts to understand the epidemiology of the disease.

Studies on fruit and hard cider chemistry from Eastern WA grown English fruit

Primary author: D. Scott Mattinson

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman

Abstract:

Studies are underway at WSU-Pullman in the postharvest laboratory aimed at unveiling a first analysis of Eastern Washington cider apple fruit chemistry as a means for hard cider makers. The hard cider industry in the USA and WA state steadily increases, as much as 40% since 2008 (Galinato et al., 2016). Apples under study include a desert variety known for its tartness, ‘Improved Red McIntosh’, and 3 English varieties, ‘Dabinette’, ‘Golden Russet’, and ‘Major’. Each of the English varieties are known as high tannin containing fruit. The study revealed that ‘IRM’ had high %TA at 0.62 with low brix, whereas the English apples were 0.248:14.5 for ‘Dabinette’, 0.521:15.0 for ‘Major’, and 0.97:17.9 for ‘Golden Russet’. Blends of ‘NRM’ to English juice, each at 1:1 reveled that the hard ciders blended with more ‘sharp’ chemistry, the highest %TA was ‘IRM’:’Golden Russet’ at 0.89% TA. This cider also had the higher brix at 7.6.
Tannin levels for each juice and each blended cider were analyzed by the Porter assay (Porter et al., 1986). Tannin data revealed that English cider apples grown in Eastern WA due in fact have higher tannin levels than desert varieties, up to 0.139% in ‘Major’, 0.059% in ‘Golden Russet’, and 0.039% in ‘Dabinette’; ‘NRM’ at 0.016%. Tannin carried into the fermented cider, as ‘NRM’ blended with ‘Dabinette’ was highest at 0.045%.

A Rapid and Highly Sensitive Assay for the detection of Dahlia mosaic caulimovirus in Dahlia (Dahlia variabilis)

Primary author: Romana Iftikhar
Authors: Romana Iftikhar, Lindani Moyo, Hanu Pappu

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman

Abstract:

Dahlia (Dahlia variabilis) is a highly valued ornamental plant widely grown in the U.S. and several other countries for its flowers, and the Pacific Northwest boasts more than a dozen dahlia societies. Dahlia mosaic virus (DMV), an aphid-transmitted caulimovirus in the family Caulimoviridae, is an important pathogen of dahlia (Dahlia variabilis). DMV genome consists of a circular, double-stranded DNA, approximately 8kb in size, and the DNA is packaged in spherical virus particles. Development of rapid, and sensitive diagnostic tools is essential in surveillance and management of DMV.

A loop-mediated isothermal amplification (LAMP) assay was developed for DMV detection. The LAMP assay targets the reverse transcriptase region of the DMV genome and is optimal at a temperature of 60°C and run time of 60 min, and amplification was detected through fluorescence detection and by agarose gel electrophoresis. The assay detected DMV in DNA concentration as low as 10 ? 3 ng. The LAMP assay was found to be more sensitive than polymerase chain reaction test. To the best of our knowledge, this is the first report of a LAMP assay for the detection of DMV, a plant DNA virus. This assay will be useful in rapid and sensitive detection of DMV and in reducing the virus incidence through production of virus-free planting material.

Genetic Diversity of Mop-top Virus: An Emerging Threat to the US Potato Production

Primary author: Ying Zhai

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman

Abstract:

Potato mop-top virus (PMTV; Genus: Pomovirus; Family: Virgaviridae), a soil-borne RNA Virus, is an emerging threat to potato production in the US. PMTV is known to exist as two distinct strains; however, there is limited information on the population structure, strain incidence and distribution in the U.S. The complete genome of six isolates of PMTV collected from three states in the USA were sequenced, analyzed, and compared with a previously characterized isolate from Washington and all known PMTV sequences available in GenBank.

Genome-wide nucleotide sequence identities of the U.S. isolates ranged from 96% to 100%. Based on the coat protein amino acid sequence, all the U.S. isolates clustered with known severe (S) strains. Genetic diversity test showed that the S strain to be more diverse than the mild (M) strain and the PMTV recombinant strain. Population selection analysis revealed that most of the codons were generally negatively selected in the PMTV isolates studied. However, positive selection was detected at codon 689 in the RT domain, which could be an adaptation to facilitate vector transmission and to overcome host plant resistance.

The sequence characteristics and the observed genetic diversity would be useful in developing improved virus diagnostics to detect the virus in aerial plant parts, tubers, soil and the soil-borne vector.

Phenotyping tree architecture using proximal and remote sensing techniques

Primary author: Chongyuan Zhang
Co-author(s): Juan José Quirós Vargas; Sara Serra; Stefano Musacch; Worasit Sangjan; Sindhuja Sankaran
Faculty sponsor: Dr. Sindhuja Sankaran

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman

Abstract:

Tree architecture optimizes the light interception and improves tree growth, fruit quality, and yield with the goal of simplify orchard management and harvest. However, currently tree architectural traits are measured manually by researchers or growers. In this study, both proximal and remote sensing techniques were evaluated to phenotype critical architectural traits with the final goal to assist tree fruit breeders, physiologists and growers in collecting architectural traits easily and efficiently. A red-green-blue (RGB) camera was used to collect proximal side-images of apple tree, while an unmanned aerial system integrated with RGB camera was programmed to image tree canopy at 15 m above ground level. The data were processed to extract architectural features from 2D images (proximal) and 3D digital surface model (remote sensing). The sensing data were compared to ground reference data that have three training systems (Spindle, V-trellis, Bi-axis), two rootstocks (‘WA38’ trees grafted on G41 and M9-Nic29) and two pruning methods (Bending and Click). The results from proximal sensing indicated that there was a significant (P < 0.0001) difference in box-counting fractal dimension (DBs) between Spindle and V-trellis training systems, and correlations between DBs with tree height (r = 0.78) and total yield per unit area in Mton/hectare (r = 0.70) was significant (P < 0.05). Moreover, correlations between average or total tree row volume and ground reference data, such as trunk area, total fruit yield per tree, were significant (P < 0.05). This study demonstrated the potential of sensing or phenotyping techniques in detecting tree architectural traits.

Understanding the Molecular Basis of Fusarium solani Mediated Root Rot in Pisum sativum

Primary author: Bruce Williamson-Benavides
Faculty sponsor: Amit Dhingra

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman

Abstract:

Pisum sativum (pea) yields have declined significantly over the last decades predominantly due to root rot caused by the fungus, Fusarium solani f. sp. pisi (Fsp). Yield losses caused by Fsp range from 15 to 60%. We hypothesize genes exhibiting differential expression and associated polymorphisms in response to Fsp challenge, will confer tolerance or susceptibility of pea to Fsp. To gain a comprehensive insight into the molecular changes that accompany Fsp infection, we performed a comparative time-course gene expression analysis of tolerant and susceptible P. sativum genotypes challenged with the Fsp pathogen. Differential gene expression and molecular pathway analyses revealed that transcription factors, pattern recognition receptors, disease-related genes, as well as genes that participate in the production of hormones and metabolites such as salicylic acid, jasmonate, ethylene, lignin, and flavonoids were differentially expressed between tolerant and susceptible genotypes. 769 differentially expressed genes with single nucleotide polymorphisms (SNPs) were identified and the putative SNPs were evaluated for being polymorphic across four tolerant and four susceptible P. sativum genotypes. The total set of SNPs with validated polymorphisms was used to screen two segregating populations generated from sets of tolerant and susceptible parents and currently a linkage-analysis is being performed. This work is expected to facilitate an understanding of the complex relationship between a host plant and its native pathogen. It is also expected to result in the identification of gene-linked molecular markers that will provide a cost-effective avenue to breed peas for resistance to root rot.