Impact of Pseudomonas putida RRF3 on the root transcriptome of rice plants: Insights into defense response, secondary metabolism and root exudation

Kandaswamy, Rekha; Ramasamy, Mohan Kumar; Palanivel, Rameshthangam; Balasundaram, Usha

Impact of Pseudomonas putida RRF3 on the root transcriptome of rice plants: Insights into defense response, secondary metabolism and root exudation

Date

2019-09

Authors

Kandaswamy, Rekha

Ramasamy, Mohan Kumar

Palanivel, Rameshthangam

Balasundaram, Usha

Publisher

Indian Academy of Sciences

Abstract

The parasitic nematode Haemonchus contortus is one of the world’s most important parasites of small ruminants that causessignificant economic losses to the livestock sector. The population structure and selection in its various strains are poorlyunderstood. No study so far compared its different populations using genome-wide data. Here, we focused on differentgeographic populations of H. contours from China (Tibet, TB; Hubei, HB; Inner Mongolia, IM; Sichuan, SC), UK andAustralia (AS), using genome-wide population-genomic approaches, to explore genetic diversity, population structure andselection. We first performed next-generation high-throughput 2b RAD pool sequencing using Illumina technology, andidentified single-nucleotide polymorphisms (SNPs) in all the strains. We identified 75,187 SNPs for TB, 82,271 for HB,82,420 for IM, 79,803 for SC, 83,504 for AS and 78,747 for UK strain. The SNPs revealed low-nucleotide diversity (p =0.0092–0.0133) within each strain, and a significant differentiation level (average Fst = 0.34264) among them. Chinesepopulations TB and SC, along with the UK strain, were more divergent populations. Chinese populations IM and HBshowed affinities to the Australian strain. We then analysed signature of selection and detected 44 (UK) and 03 (AS) privateselective sweeps containing 49 and 05 genes, respectively. Finally, we performed the functional annotation of selectivesweeps and proposed biological significance to signature of selection. Our data suggest that 2b-RAD pool sequencing canbe used to assess the signature of selection in H. contortus.

Keywords

Defense, Pseudomonas putida, rice, root exudation, salicylic acid, secondary metabolism

Citation

Kandaswamy Rekha, Ramasamy Mohan Kumar, Palanivel Rameshthangam, Balasundaram Usha. Impact of Pseudomonas putida RRF3 on the root transcriptome of rice plants: Insights into defense response, secondary metabolism and root exudation. Journal of Biosciences. 2019 Sep; 44(4): 1-13