Working group session:
Breeding and Applied Genomics
Presentation type:
oral
Authors:
Peterson, Daniel G.; Sanders, Williams S.; Showmaker, Kurt C.; Arick II, Mark A.; Ganji, Satish; Jenkins, Johnie N.; Wubben, Martin J.
Presenter:
Peterson, Daniel G.
Correspondent:
Peterson, Daniel G.
Abstract:
Reniform nematode (Rotylenchulus reniformis) currently accounts for $130M in annual losses to the U.S. cotton industry and has supplanted root-knot nematode (Meloidogyne incognita) as the major nematode pest of cotton in Mississippi, Louisiana, and Alabama. Moreover, in other cotton-producing areas throughout the world the range and influence of reniform nematode is growing rapidly. As there is no natural resistance to reniform nematode in Gossypium hirsutum germplasm, plant breeders have been working to introgress resistance from other cotton species (e.g., G. longicalyx, G. barbadense, and G. arboreum) into upland cotton lines. Recently, these breeding programs have begun to yield tenable results, and resistant G. hirsutum cultivars adapted for growth in the southern U.S. will be available within the next 1 to 2 years. However, natural R. reniformis populations possess considerable genetic variability, and thus it is probable that resistance-breaking nematode populations/races will not take long to emerge/evolve. Genomics affords a means of investigating genes and their expression patterns in pests/pathogens at unprecedented resolution and scale. Of note, the genome and/or transcriptome of a pest can be used to develop strategies that selectively disrupt key pest metabolic/developmental pathways. Towards this end, we have sequenced and assembled both the genome and the transcriptome of R. reniformis as means to better understand this major cotton parasite and develop strategies for limiting the damage it causes. Using flow cytometry, we found the R. reniformis genome to have a 1C value of 185 Mb. DNA isolated from a single unfertilized egg was amplified and sequenced using an Illumina MiSeq. Illumina HiSeq and Roche 454 reads from pooled egg (population) samples were combined with the single egg data to provide 116X coverage of the reniform nematode genome. Illumina mate pair data from pooled eggs is currently being produced, and it will be integrated with the other sequence types to produce a quality draft assembly of the R. reniformis genome. With regard to the transcriptome, mRNA was isolated from egg, J2, J3, vermiform adult (male and female), and sedentary female nematodes and sequenced using Illumina technologies. The RNA sequence data was pooled and a basic transcriptome was constructed for R. reniformis. Transcripts were annotated using GO terms. At present, RNA-Seq is being utilized to study lifestage differences in gene expression. The initial results of the R. rotylenchulus genome project, transcriptome analysis, and differential gene expression studies will be discussed.