Graduate Thesis Or Dissertation
 

Comparative Genomics of Different Races of Columbia Root-knot Nematode and Development of Molecular Markers Linked to Corky Ringspot Resistance in Potato

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  • On a global scale, potato (Solanum tuberosum L.) plays an important role in tackling the threat of food insecurity due to its high yield and broad global acceptance. However, pathogens threaten potato production, causing direct yield loss and rendering potatoes tubers unmarketable. Breeding new cultivars that carry multiple resistances is an efficient way for sustainable potato production. Columbia root-knot nematode (CRKN, Meloidogyne chitwoodi) parasitizes potato plants and causes small brown dots in the tuber flesh that dramatically reduce the market value of the crop. In the Pacific Northwest (PNW) two races of M. chitwoodi exist, Race 1 and Race 2; a pathotype of Race 1, Race 1Roza also occurs. The races of M. chitwoodi are primarily identified based on a differential host test. In order to understand the phylogeny of M. chitwoodi and develop molecular markers to identify the different races, we sequenced the genomes of M. chitwoodi Race 1, Race 2 and Race 1Roza using Illumina and PacBio sequencing. Each genome was assembled and annotated. Comparisons of syntenies and orthologs elucidate the complex evolutionary history of this species and facilitate molecular marker development and analysis of host plant resistance to these root-knot nematodes. Based on the genome comparisons of M. chitwoodi Race 1, Race 2 and Race 1Roza, we developed 36 pairs of PCR primers for SSR markers and 17 pairs of PCR primers for INDEL markers. Four of those molecular markers, HSINDEL8, HSINDEL5, HSINDEL9 and HSINDEL10, can successfully differentiate the three pathotypes of M. chitwoodi used in this study on agarose gel electrophoresis. These markers have application in plant disease diagnostics. Corky ringspot (CRS) disease caused by tobacco rattle virus (TRV) and vectored by stubby root nematodes, can render 6-55% of potatoes in an infested field unmarketable. Previous studies identified 22 SNP markers that are significantly associated with CRS resistance from ‘Castle Russet’ using a progeny of 48 seedlings. In this study we developed 44 pairs of PCR primers around previously identified significant SNPs. SNP marker PotVar0108448 on chromosome 9 shows polymorphisms on agarose gel electrophoresis and explains the highest percentage of phenotypic variance. Based on the initial marker screening, we developed 36 pairs of SSR primers, 72 pairs of primers for short INDELs and 36 pairs of primers for long INDELs on the upstream and downstream of SNP marker PotVar0108448. We screened them on 48 seedlings of progeny POR15V001 and 170 seedlings of progeny POR16V001. Markers INDEL20, INDEL490-7, Potvar008448 are linked to CRS resistance from ‘Castle Russet’. Of these, marker INDEL490-7 was robust and able to identify resistance from diverse germplasm. It has the potential for use in marker-assisted selection (MAS).
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