Resistance Genes in Piper colubrinum: In Silico Survey From Leaf Transcriptome and Expression Studies Upon Challenge Inoculation with Phytophthora capsici

Abstract

The oomycetes, Phytophthora capsici, cause foot rot disease in black pepper. Piper colubrinum Link, a distant relative of cultivated black pepper, is highly resistant to this destructive pathogen. Identification of resistance (R) genes in P. colubrinum and the study of its expression profile during interaction with the pathogen can help in understanding the resistance mechanism involved. In the present study, 1289 R gene-related transcripts were mined from P. colubrinum transcriptome, clustered, and classified according to the conserved motifs and domains. Transcripts belonging to four major R gene classes were identified in P. colubrinum, but TIR-NBS-LRR-type R genes were absent. The relative expression of 12 selected R genes was studied using two virulent isolates of P. capsici, and these were found to be upregulated in the initial hours of plant pathogen interaction. The R genes studied were expressed even in aseptically maintained tissue-cultured plants and uninoculated greenhouse-grown plants at basal level suggesting that the plants are geared up with the R gene all the time and are under continuous surveillance for the pathogen and basal level of R gene expression do not require a pathogen trigger. ACT, ATUB, and EIF3E were identified as the most stable reference genes that can be used for real-time PCR study. The present study identified promising R genes in P. colubrinum which can be used in developing Phytophthora-resistant black pepper.

Identification of stable genes in the corpus luteum of lactating Holstein cows in pregnancy and luteolysis: Implications for selection of reverse-transcription quantitative PCR reference genes

“…Stable genes were identified through transcriptomic analysis, rather than consideration of gene function or historic use in normalization. Despite this, of the 13 genes evaluated for stability via RTq-PCR, 69% had previously been evaluated as candidate reference genes for RT-qPCR in diverse species from zebra fish to rats with 4 of these genes having been identified through RNA-seq or microarray (Nygard et al, 2007;Hoogewijs et al, 2008;Popovici et al, 2009;Too and Ling, 2011;Mossberg et al, 2016;Xu et al, 2016;Samiullah et al, 2017;Malik and George, 2018;Shaydurov et al, 2018). Additionally, COX4I1 has been evaluated for use as a control in western blots (Lee et al, 2016) and HIF1A has a housekeeping-like promoter noted in data from adult mouse tissues (Wenger et al, 1998).…”