Quantitative Trait Loci Mapping for Bacterial Wilt Resistance and Plant Height in Tomatoes.

Bacterial wilt (BW) of tomatoes, caused by , is a devastating disease that results in large annual yield losses worldwide. Management of BW of tomatoes is difficult due to the soil-borne nature of the pathogen. One of the best ways to mitigate the losses is through breeding for disease resistance.

Identification of quantitative trait loci associated with bacterial spot race T4 resistance in intra-specific populations of tomato (Solanum lycopersicum L.).

Bacterial spot of tomato is a serious disease caused by at least four species and four races of Xanthomonas- X. euvesicatoria (race T1), X. vesicatoria (race T2), X.

Molecular mapping of quantitative trait loci for resistance to early blight in tomatoes.

Early blight (EB), caused by (Neerg.) (syn. ) Simmons, is a disease that affects tomatoes ( L.

Coordinated transcriptional regulation of the carotenoid biosynthesis contributes to fruit lycopene content in high-lycopene tomato genotypes.

Lycopene content in tomato fruit is largely under genetic control and varies greatly among genotypes. Continued improvement of lycopene content in elite varieties with conventional breeding has become challenging, in part because little is known about the underlying molecular mechanisms in high-lycopene tomatoes (HLYs). We collected 42 HLYs with different genetic backgrounds worldwide.

Next-generation sequencing-based bulked segregant analysis without sequencing the parental genomes.

Genomic regions that control traits of interest can be rapidly identified using BSA-Seq, a technology in which next-generation sequencing is applied to bulked segregant analysis (BSA). We recently developed the significant structural variant method for BSA-Seq data analysis that exhibits higher detection power than standard BSA-Seq analysis methods. Our original algorithm was developed to analyze BSA-Seq data in which genome sequences of one parent served as the reference sequences in genotype calling and, thus, required the availability of high-quality assembled parental genome sequences.

Detection of Quantitative Trait Loci (QTL) Associated with the Fruit Morphology of Tomato.

Tomato ( L.) is the second most-consumed vegetable in the world. The market value and culinary purpose of tomato are often determined by fruit size and shape, which makes the genetic improvement of these traits a priority for tomato breeders.

Transcriptome-Based Analysis of Tomato Genotypes Resistant to Bacterial Spot ( Race T4.

Bacterial spot (BS) is one of the most devastating foliar bacterial diseases of tomato and is caused by multiple species of . We performed the RNA sequencing (RNA-Seq) analysis of three tomato lines with different levels of resistance to race T4 to study the differentially expressed genes (DEGs) and transcript-based sequence variations. Analysis between inoculated and control samples revealed that resistant genotype accession PI 270443 had more DEGs (834), followed by susceptible genotype tomato ( L) breeding line NC 714 (373), and intermediate genotype tomato breeding line NC 1CELBR (154).

Four bottlenecks restrict colonization and invasion by the pathogen Ralstonia solanacearum in resistant tomato.

Ralstonia solanacearum is a bacterial vascular pathogen causing devastating bacterial wilt. In the field, resistance against this pathogen is quantitative and is available for breeders only in tomato and eggplant. To understand the basis of resistance to R.

PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data.

Background: Bulked segregant analysis (BSA), coupled with next-generation sequencing, allows the rapid identification of both qualitative and quantitative trait loci (QTL), and this technique is referred to as BSA-Seq here. The current SNP index method and G-statistic method for BSA-Seq data analysis require relatively high sequencing coverage to detect significant single nucleotide polymorphism (SNP)-trait associations, which leads to high sequencing cost.

Results: We developed a simple and effective algorithm for BSA-Seq data analysis and implemented it in Python; the program was named PyBSASeq.

Advances and Challenges in Bacterial Spot Resistance Breeding in Tomato ( L.).

Bacterial spot is a serious disease of tomato caused by at least four species of . These include (race T1), (race T2), (races T3 and T4), and with the distinct geographical distribution of each group. Currently, and are two major bacterial pathogens of tomato in North America, with (race T4) dominating in east-coast while dominating in the Midwest.

Phenotypic and Genetic Diversity of Populations from Tomato in North Carolina.

Bacterial spot caused by spp. is one of the most devastating diseases of tomato in North Carolina (NC). In total, 290 strains of spp.

Filter paper-based spin column method for cost-efficient DNA or RNA purification.

We describe herein a method of recharging used commercial spin columns or assembling homemade spin columns using filter paper as binding material for cost-effective, low throughput nucleic acid purification. The efficiency of filter paper-based spin columns was evaluated for purification of nucleic acids from various sources. Following protocols of commercial kits, we found filter paper to be a useful binding material for purification of nucleic acids, including plant genomic DNA, plant total RNA, PCR products, and DNA from agarose gels.

Current Status of Early Blight Resistance in Tomato: An Update.

Early blight (EB) is one of the dreadful diseases of tomato caused by several species of including (which includes and ), as well as In some instances, annual economic yield losses due to EB have been estimated at 79%. are known only to reproduce asexually, but a highly-virulent isolate has the potential to overcome existing resistance genes. Currently, cultural practices and fungicide applications are employed for the management of EB due to the lack of strong resistant cultivars.

Mapping Quantitative Trait Loci (QTL) for Resistance to Late Blight in Tomato.

Late blight caused by (Montagne, Bary) is a devastating disease of tomato worldwide. There are three known major genes, , , and , conferring resistance to late blight. In addition to these three genes, it is also believed that there are additional factors or quantitative trait loci (QTL) conferring resistance to late blight.

A novel plant DNA extraction method using filter paper-based 96-well spin plate.

A simple, low cost and safe method using homemade filter paper-based 96-well spin plates and homemade solutions was developed for high throughput plant DNA extraction to use in molecular marker analysis. A low cost and safe method was developed for high throughput extraction of plant DNA for molecular marker analysis. In this method, we describe a simple way to prepare 96-well spin plate using filter paper, a plant material product for DNA binding.

Differential response of tomato genotypes to Xanthomonas-specific pathogen-associated molecular patterns and correlation with bacterial spot (Xanthomonas perforans) resistance.

Plants depend on innate immune responses to retard the initial spread of pathogens entering through stomata, hydathodes or injuries. These responses are triggered by conserved patterns in pathogen-encoded molecules known as pathogen-associated molecular patterns (PAMPs). Production of reactive oxygen species (ROS) is one of the first responses, and the resulting 'oxidative burst' is considered to be a first line of defense.

Natural variation for responsiveness to flg22, flgII-28, and csp22 and Pseudomonas syringae pv. tomato in heirloom tomatoes.

Tomato (Solanum lycopersicum L.) is susceptible to many diseases including bacterial speck caused by Pseudomonas syringae pv. tomato.

High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.

The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA) and pairwise estimates of F(st) supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S.

Genomics of fungal disease resistance in tomato.

Tomato (Solanum lycopersicum) is an important vegetable crop worldwide. Often times, its production is hindered by fungal diseases. Important fungal diseases limiting tomato production are late blight, caused by Phytophthora infestans, early blight, caused by Alternaria solanii, and septoria leaf spot, caused by Septoria lycopersici, fusarium wilt caused by Fusarium oxysporium fsp.

Differential expression of genes in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow) is soybean growth stage-specific.

Understanding plant host response to a pathogen such as Phakopsora pachyrhizi, the causal agent of Asian soybean rust (ASR), under different environmental conditions and growth stages is crucial for developing a resistant plant variety. The main objective of this study was to perform global transcriptome profiling of P. pachyrhizi-exposed soybean (Glycine max) with susceptible reaction to the pathogen from two distinct developmental growth stages using whole genome Affymetrix microarrays of soybean followed by confirmation using a resistant genotype.