Genome-Wide Identification and Expression Analysis of NBS-Encoding Genes in Malus x domestica and Expansion of NBS Genes Family in Rosaceae

Abstract

Nucleotide binding site leucine-rich repeats (NBS-LRR) disease resistance proteins play an important role in plant defense against pathogen attack. A number of recent studies have been carried out to identify and characterize NBS-LRR gene families in many important plant species. In this study, we identified NBS-LRR gene family comprising of 1015 NBS-LRRs using highly stringent computational methods. These NBS-LRRs were characterized on the basis of conserved protein motifs, gene duplication events, chromosomal locations, phylogenetic relationships and digital gene expression analysis. Surprisingly, equal distribution of Toll/interleukin-1 receptor (TIR) and coiled coil (CC) (1∶1) was detected in apple while the unequal distribution was reported in majority of all other known plant genome studies. Prediction of gene duplication events intriguingly revealed that not only tandem duplication but also segmental duplication may equally be responsible for the expansion of the apple NBS-LRR gene family. Gene expression profiling using expressed sequence tags database of apple and quantitative real-time PCR (qRT-PCR) revealed the expression of these genes in wide range of tissues and disease conditions, respectively. Taken together, this study will provide a blueprint for future efforts towards improvement of disease resistance in apple.

Genetic Analysis of NBS-LRR Gene Family in Chickpea and Their Expression Profiles in Response to Ascochyta Blight Infection

“…Most studies identified variable numbers of NBS-LRR genes ranging from 50 in papaya (Porter et al, 2009) to 1,015 in apple (Arya et al, 2014). The NBS-LRR genes are unevenly distributed in plant genomes and are often found in clusters.…”

Analysis of structure and differential expression of Pseudomonas syringae 5-like(RPS5-like) genes in pathogen-infected Vitis flexuosa

“…This ATP-bound form of RPS5 engages in downstream signaling molecules that activate the defense response (Ade et al, 2007;Qi et al, 2012). More than 50 NBS-LRR R-genes, including the almost 40 CC-NBS-LRR, conferred resistance against several pathogens in plants such as Arabidopsis, tomato, potato, barley, rice, maize, apple, grape, lettuce, pepper, sunflower, melon, and soybean (Kortekamp et al, 2008;Joshi and Nayak, 2011;Kar et al, 2013;Arya et al, 2014).…”

“…Tritici, the pathogen of powdery mildew disease. Arya et al (2014) reported that expression of 18 out of 26 Malus × domestica NBS genes (MdNBS gene) was induced, while expression of other MdNBS genes was not observed under attacks of several pathogens and insects. Kortekamp et al (2008) also reported that the CC-NBS-LRR family gene, VRP1, was induced during pathogen attack in the resistant grapevine cultivar 'Gloire de Montpellier' .…”

“…More than 50 novel NBS-LRR class resistance genes have been isolated and characterized in different plant species (Joshi and Nayak, 2011). For example, the Arabidopsis genome sequence contains 149 NBS-LRR genes (Meyers et al, 2003), the rice genome contains more than 500 NBS coding sequences (Bai et al, 2002;Meyers et al, 2002;Zhou et al, 2004), and the apple genome contains 1015 NBS-LRR genes (Arya et al, 2014). Furthermore, NBS-LRR class R-genes have been categorized into three major classes based on the N-terminus motif: TIR-NBS-LRR (TNL), which contains a domain resembling the drosophila toll and mammalian interleukin-1 receptors (TIR); CC-NBS-LRR (CNL), which contains a coiled-coil (CC) or a leucinezipper (LZ) motif; and the nonmotif group (Meyers et al, 1999;Pan et al, 2000;Liu et al, 2007;Joshi and Nayak, 2011).…”

Sorbitol Modulates Resistance to Alternaria alternata by Regulating the Expression of an NLR Resistance Gene in Apple

“…PR proteins include enzymes and antimicrobial peptides that play important roles in plant disease resistance, but they act at the later stages of plant defense responses. In effector-triggered immunity (ETI), plants deploy disease resistance proteins (R proteins) to interact with pathogenproduced effector proteins in a gene-for-gene manner at the early stage to mount a rapid and robust defense response (Martin et al, 2003;Jones and Dangl, 2006;Cui et al, 2015).The largest group of R genes encode intracellular nucleotide binding domain and leucine-rich repeat (NLR) receptors and these NLRs are highly amplified in plants (McHale et al, 2006;Arya et al, 2014;Zhong et al, 2015), but it is not known whether any of these R genes is regulated by sugars.…”