Loading...
Please wait, while we are loading the content...
Similar Documents
MULTI-LOCUS SIMPLE SEQUENCE REPEATS AND SINGLE NUCLEOTIDE POLYMORPHISM MARKERS FOR GENOTYPING AND ASSESSING GENETIC DIVERSITY OF XYLELLA FASTIDIOSA IN CALIFORNIA Project Leader:
| Content Provider | Semantic Scholar |
|---|---|
| Author | Doddapaneni, Harshavardhan Walker, Andrew T. |
| Copyright Year | 2007 |
| Abstract | In California, information regarding the population structure and genetic diversity as well as the genetic evolutionary and epidemiological relationships among Xylella fastidiosa (Xf) strains in agricultural populations is not clear. To develop effective management strategies, we need to understand pathogen population structure and genetic diversity in the agricultural ecosystem. Here we report development and utilization of two multilocous marker systems, Simple Sequence Repeats (SSR) and single nucleotide polymorphism (SNP) for genotyping and assessing genetic diversity of Xf in California. Strain diversity studies using SSRs on samples from different geographic populations and/or from different hosts demonstrated that host selection plays an important role in Xf genetic differentiation among agricultural populations in California. Whole-genome comparison of four sequenced strains identified 12,754 potential SNPs in coding sequences and 20,779 SNPs in non-coding regions across four Xf strains. Small scale validation (16 loci) tests showed that SNP genotype is tightly linked to the hosts from which the strains were derived. Together, SNP and SSR marker systems appear to be useful tools for pathogen detection and population genetic analyses. INTRODUCTION Host plant resistance is a critical component of integrated crop management. However, durability of resistant grape plants depends upon the variability and adaptability of the pathogen population as well as disease resistance gene(s). Population genetics research demonstrates that the evolutionary potential of a pathogen is reflected in its genetic diversity and its genetic structure. Pathogen populations with higher evolutionary potential are more likely to overcome host resistance than pathogen populations with a lower evolutionary potential (MacDonald and Linde, 2002). The resulting changes in population structure or virulence can lead to host resistance breakdown. Therefore, understanding pathogen genetic diversity is critical in developing an effective disease control strategy. To characterize population structures of Xylella fastidiosa (Xf) and to understand genetic diversity of Xf in agricultural systems, sensitive and accurate marker system(s) are required. The goal of this project is to develop a reliable marker system(s) that unambiguously identifies Xf strains from various geographic locations and host plants and further to understand the pathogen dynamics. Previously, we reported the development of multilocus simple sequence repeats (SSR) markers for Xf population genetic analysis (Lin et al., 2005). This marker system appeared to be sensitive in detection and powerful in discriminating Xf genotypes. This marker system also provides high throughput capability for a large scale population sample analyses. Recently, we developed a new marker system; single nucleotide polymorphism (SNP). We performed whole-genome sequence analysis of CVC, PD, ALS and OLS strains and identified potential SNP loci in both coding and non-coding regions (Doddapaneni et al., 2006). This marker system has proven to be powerful and reliable for distinguishing genetic relatedness. This marker system is very sensitive, has a high degree of specificity, and is quite powerful in detecting genetic polymorphism. Further, adaptability to high a through-put diagnostic platform makes this system an ideal tool for large scale studies of Xf population genetics and epidemiological risk assessment analyses. OBJECTIVES 1. Analyze Xf seasonal population dynamics; spatial and temporal disease development and genetic diversity. 2. Comparative whole genome analyses of the X. fastidiosa strains to identify SNP loci and develop SNP based marker system for fingerprinting Xf strains. RESULTS AND DISCUSSION Objective 1. Previously, we analyzed genetic diversities and geographic population structures of Xf in California vineyards (Napa, Sonoma and Kern and Riverside counties). Results based on multi-locus SSR marker systems and hierarchical sampling |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | https://static.cdfa.ca.gov/PiercesDisease/proceedings/2006/2006_169-173.pdf |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
