Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

Abstract

10Plants have developed mechanisms to recognize pathogen and insect attacks and to 11 activate defense response against them through the action of resistance genes (R genes). 12Hence, R gene analogs (RGAs) have been widely studied and efficiently used for breeding of 13 resistant crops. Mango is an economic fruit crop largely cultivated in the (sub)tropics and thus, 14 is constantly challenged by a myriad of insect pests and diseases. RGAs of mango from 15 different varieties were identified and characterized via de novo assembly of raw transcriptome 16 sequences currently available in biological repositories. Using bioinformatics pipelines, a core 17 RGA database of mango with 747 protein models was established and were classified based 18 on their conserved domains and motifs: 53 nucleotide binding site protein (NBS); 27 nucleotide 19 binding site-leucine rich repeat proteins (NBS-LRR); 17 coiled-coil NBS-LRR (CNL); 2 20 toll/interleukin-1 receptor NBS-LRR (TNL); 29 coiled-coil NBS (CN); 4 toll/interleukin-1 21 receptor NBS (TN); 17 toll/interleukin-1 receptor with unknown domain (TX); 158 receptor-like 22 proteins (RLP); 362 receptor-like kinases (RLK); 72 transmembrane coiled-coil domain protein 23 (TM-CC), and 6 NBS-encoding proteins with other domains. Phylogenetic analysis broadly 24 clustered the core RGAs into 6 major clades based on their domain classification, while TM- 25CC formed subclades all across the tree. The phylogenetic results suggest highly divergent 26 functions of the RGAs which also provide insights into the mango-pest co-evolutionary arms 27 race. The various molecular functions, biological processes, and cellular localizations of these RGAs were functionally well-annotated through gene ontology (GO) analysis, and their 29 expression profiles across different mango varieties were also determined. From the mango 30 RGA transcripts, 134 unique EST-SSRs loci were identified, and primers were designed 31 targeting these potential markers. To date, this is the most comprehensive analysis of mango 32 RGAs which offer a trove of markers for direct utilization in resistance breeding of mango. 33 34 35 36 Introduction 37 Mango (Mangifera indica L.) is a globally popular fruit crop with economical and 38 agricultural significance, especially in the (sub)tropics where it is largely cultivated. One of the 39 constraints in mango production worldwide include a myriad of insect pests (e.g., oriental fruit 40 fly, mango hopper, cecid fly, etc.) and diseases, (e.g., anthracnose, stem-end rot, scab, etc.) 41 which can affect mango at different life stages thus significantly reducing fruit quality and yield 42 (Bally, 2006). These are major barriers to the export market and can impede international 43 trade as many pests and diseases in mango are important quarantine considerations. 44 Along the course of evolution, plants have generally developed mechanisms to 45 recognize pathogen and insect attacks and to activate defense response against them (Dangl 46 and Jones., 2001; Acevedo et al., 2015). The mole...