Resilience response to yellow leaf curl disease and identification of resistance gene analogs (RGA) in pepper (Capsicum annuum)

Ayu DK, Maharijaya A, Syukur M, Hidayat SH. 2021. Resilience response to yellow leaf curl disease and identification of resistance gene analogs (RGA) in pepper (Capsicum annuum). Biodiversitas 22: 4731-4739. Pepper yellow leaf curl disease (PYLCD) caused by infection of Begomovirus is a serious threat to pepper production worldwide. Identification of the resistance gene analogs (RGA) and resilience response of pepper against PYLCD is needed especially for selection resistance genotype. Evaluation of resistance response involving 28 pepper genotypes was carried out through transmission of Begomovirus using whitefly (Bemisia tabaci) as vector. The result showed that IPB C12 and F4-012328-6-3 were potential resistance genotypes. A total of 15 R gene analogs (CaRGA) containing NBS motif, namely CARGA1 to CARGA15, were identified by degenerated PCR amplification and database mining. The alignment of deduced amino acid sequence revealed conservation of subdomains Ploop (GKTT), kinase2 (LVVLDDV), RNBSB/kinase3 (IILTTR) and GLPL. BLASTp analysis indicated that 15 RGA showed high homology at deduced amino acid level with R gene identified such as whitefly resistance protein Mi-1.2, Pvr 9 gene for potyvirus, Begomovirus resistance protein, TRGA15 and RGA 13 for putative late blight resistance. Phylogenetic analysis exhibited that isolated sequences distinguished into CNL-NBS groups. These pepper RGA could be considered as candidate sequences of resistance genes.

Characterization and selection of markers associated with resistance analogous genes as input for genetic analysis of Prosopis juliflora (Sw.) DC.

The characterization and selection of molecular markers are important for genetic pre-breeding programs since they make it possible to choose the most appropriate markers to be used in future research. Therefore, enabling the generation of subsidies for genetic-molecular studies in algabora (Prosopis juliflora (Sw.) DC). The amplification profile was characterized. It was generated from 17 pairs of RGA primers (Resistance Gene Analogs) in 20 samples of genomic DNA of P. juliflora extracted from specimens collected in the city of Itapetinga, Bahia. The amplifications were performed according to previously published laboratory routines and the amplification profiles analyzed from the photodocumentation of the electrophoresis results in 2% agarose gels. Based on the amplification profiles the primer pairs were classified as: Suitable: amplifications in the whole samples and with easy visualization; Reasonable: amplification in parts of the samples and/or difficult to visualize or Inadequate: absence of visible amplification products. Descriptive analyzes associated with the number of generated markers, percentage of polymorphism, expected heterozygosity (He) and the content of polymorphic information (PIC) were also performed. In a nutshell, 12 out of the 17 pairs of RGA primers generated amplification products with easy visualization and only two of these 12 pairs of primers were monomorphic. The percentage of polymorphism varied from 60% to 100%, He and PIC presented an average of 0.21 (ranging from 0 to 0.38) and 0.17 (ranging from 0 to 0.29), respectively. The results confirm that the RGA primers present adequate characteristics for genetic studies in P. juliflora, making it possible to prioritize 12 pairs of primers, which are subject to genetic improvement studies.

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

Mango is an economically important fruit crop largely cultivated in the (sub)tropics and thus, is constantly challenged by a myriad of insect pests and diseases. Here, we identified and characterized the resistance gene analogs (RGAs) of mango from de novo assembly of transcriptomic sequences. A core RGA database of mango with 747 protein models was established and classified based on conserved domains and motifs: 53 nucleotide binding site proteins (NBS); 27 nucleotide binding site-leucine rich repeat proteins (NBS-LRR); 17 coiled-coil NBS-LRR (CNL); 2 toll/interleukin-1 receptor NBS-LRR (TNL); 29 coiled-coil NBS (CN); 4 toll/interleukin-1 receptor NBS (TN); 17 toll/interleukin-1 receptor with unknown domain (TX); 158 receptor-like proteins (RLP); 362 receptor-like kinases (RLK); 72 transmembrane coiled-coil domain protein (TM-CC), and 6 NBS-encoding proteins with other domains. The various molecular functions, biological processes, and cellular localizations of these RGAs were functionally well-annotated through gene ontology (GO) analysis, and their expression profiles across different mango varieties were also determined. Phylogenetic analysis broadly clustered the core RGAs into 6 major clades based on their domain classification, while TM-CC proteins formed subclades all across the tree. The phylogenetic results suggest highly divergent functions of the RGAs which also provide insights into the mango-pest co-evolutionary arms race. From the mango RGA transcripts, 134 unique EST-SSR loci were identified, and primers were designed targeting these potential markers. To date, this is the most comprehensive analysis of mango RGAs which offer a trove of markers for utilization in resistance breeding of mango.

Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype

Background Resistance genes composing the two-layer immune system of plants are thought as important markers for breeding pathogen-resistant crops. Many have been the attempts to establish relationships between the genomic content of Resistance Gene Analogs (RGAs) of modern sugarcane cultivars to its degrees of resistance to diseases such as smut. However, due to the highly polyploid and heterozygous nature of sugarcane genome, large scale RGA predictions is challenging. Results We predicted, searched for orthologs, and investigated the genomic features of RGAs within a recently released sugarcane elite cultivar genome, alongside the genomes of sorghum, one sugarcane ancestor (Saccharum spontaneum), and a collection of de novo transcripts generated for six modern cultivars. In addition, transcriptomes from two sugarcane genotypes were obtained to investigate the roles of RGAs differentially expressed (RGADE) in their distinct degrees of resistance to smut. Sugarcane references lack RGAs from the TNL class (Toll-Interleukin receptor (TIR) domain associated to nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains) and harbor elevated content of membrane-associated RGAs. Up to 39% of RGAs were organized in clusters, and 40% of those clusters shared synteny. Basically, 79% of predicted NBS-encoding genes are located in a few chromosomes. S. spontaneum chromosome 5 harbors most RGADE orthologs responsive to smut in modern sugarcane. Resistant sugarcane had an increased number of RGAs differentially expressed from both classes of RLK (receptor-like kinase) and RLP (receptor-like protein) as compared to the smut-susceptible. Tandem duplications have largely contributed to the expansion of both RGA clusters and the predicted clades of RGADEs. Conclusions Most of smut-responsive RGAs in modern sugarcane were potentially originated in chromosome 5 of the ancestral S. spontaneum genotype. Smut resistant and susceptible genotypes of sugarcane have a distinct pattern of RGADE. TM-LRR (transmembrane domains followed by LRR) family was the most responsive to the early moment of pathogen infection in the resistant genotype, suggesting the relevance of an innate immune system. This work can help to outline strategies for further understanding of allele and paralog expression of RGAs in sugarcane, and the results should help to develop a more applied procedure for the selection of resistant plants in sugarcane.