Small RNA Analysis of Resistant and Susceptible Cotton Roots Infested with Reniform Nematodes

Comparative Genomics and Bioinformatics

N/A

Li, Ruijuan; Hu, Hongtao; Sikkens, Roelof; Weaver, David; Singh, Narendra; Locy, Robert; Li, Ruijuan; Hu, Hongtao; Sikkens, Roelof; Weaver, David; Singh, Narendra; Locy, Robert

Li, Ruijuan; Li, Ruijuan

Locy, Robert; Locy, Robert

Cotton (Gossypium hirsutum L.) is an important crop plant that is susceptible to multiple species of parasitic nematodes including Rotylenchulus reniformis, reniform nematode (RN). There is much emphasis on breeding resistance to RN into commercially viable cotton varieties, and in 2007 LONREN-1 (LR1) and LONREN-2 (LR2), putative RN-resistant germplasm derived from Gossypium longicalyx was released. More recently Implementation of these materials in commercially useful germplasm has proven problematic. A resistant line BARBAREN-713 (B-713) has been developed with RN resistance based on Gossypium barbadense, which shows promise. To facilitate this implementation, the gene regulatory networks involved in RN-resistant and susceptible genotypes are under investigation particularly focusing on miRNAs. Initially, the role of small regulatory RNAs (srRNAs) in these regulatory networks is under investigation. In this study, LR1, LR2, and B-713 were selected as nematode resistant genotypes, and DeltaPine 90 & Suregrow 747 were susceptible lines. Small RNA libraries were prepared from greenhouse grown plants of each of these 4 genotypes either pre- or post-infection with reniform nematodes. RNA-seq was conducted on these small RNA libraries using the ABI Solid platform with single-end sequencing, and the resulting sequence libraries were submitted to a small RNA library pipeline that we have developed. Abundance of each small RNA found in each library was determined. We found a total of 2,976 putative small RNAs (2,263 identical to Viridiplantae miRNA sequences in miRBase18, and 713 novel unique miRNAs) in the datasets. All of these putative microRNAs fall into 181 existing (miRBase18) miRNA families. Of these 72 families (involving 1286 individual putative mature miRNA sequences) are up-regulated by nematode infection by more than 3-fold in at least 1 genotype, while 54 families (involving 1216 individual putative mature miRNA sequences) are down-regulated by more than 3-fold by nematode infection. Further analysis and characterization of these changes in the 5 genotypes will be utilized to to define regulatory networks that are involved in gene regulation during reniform nematode infestation of cotton roots.