Genome-Wide Analysis of the LRR-RLP Gene Family in a Wild Banana (Musa acuminata ssp. malaccensis) Uncovers Multiple Fusarium Wilt Resistance Gene Candidates

Abstract

Banana is the most popular fruit in the world, with a relevant role in food security for more than 400 million people. However, fungal diseases cause substantial losses every year. A better understanding of the banana immune system should facilitate the development of new disease-resistant cultivars. In this study, we performed a genome-wide analysis of the leucine-rich repeat receptor-like protein (LRR-RLP) disease resistance gene family in a wild banana. We identified 78 LRR-RLP genes in the banana genome. Remarkably, seven MaLRR-RLPs formed a gene cluster in the distal part of chromosome 10, where resistance to Fusarium wilt caused by Foc race 1 has been previously mapped. Hence, we proposed these seven MaLRR-RLPs as resistance gene candidates (RGCs) for Fusarium wilt. We also identified seven other banana RGCs based on their close phylogenetic relationships with known LRR-RLP proteins. Moreover, phylogenetic analysis of the banana, rice, and Arabidopsis LRR-RLP families revealed five major phylogenetic clades shared by these plant species. Finally, transcriptomic analysis of the MaLRR-RLP gene family in plants treated with Foc race 1 or Foc TR4 showed the expression of several members of this family, and some of them were upregulated in response to these Foc races. Our study provides novel insights into the structure, distribution, evolution, and expression of the LRR-RLP gene family in bananas as well as valuable RGCs that will facilitate the identification of disease resistance genes for the genetic improvement of this crop.

Keywords: Fusarium wilt; LRR-RLP; banana; disease resistance; genetic improvement; genome-wide analysis.

Figure 1

Gene structure of banana LRR-RLP genes. Yellow boxes indicate exons, blue boxes indicate untranslated regions and black lines represent introns.

Figure 2

Conserved motifs of banana LRR-RLP proteins. The number of conserved motifs identified by the MEME program was set to 10.

Figure 3

Chromosomal distribution of banana LRR-RLP genes. The chromosome number is shown above each chromosome. The left scale represents the length of chromosomes in megabases.

Figure 4

Cartoon view of the predicted LRR structures of I-7, I, MaLRR-RLP74 and MaLRR-RLP75. I-7 and I confer resistance to Fusarium wilt in tomato, and RGCs MaLRR-RLP74 and MaLRR-RLP75 clustered in the distal part of chromosome 10, where resistance to Foc race 1 has been mapped [48]. Crystal structure data of Arabidopsis FLS2 (PDB Acc. No. 4mn8.1) were used for the model constructions. The structure of FLS2 LRR is superhelical [50].

Figure 5

Maximum likelihood phylogenetic tree of the banana LRR-RLP family and LRR-RLPs from different plant species involved in disease resistance or development. The names and accession numbers (in parentheses) of LRR-RLPs involved in plant immunity or development are highlighted in blue or green, respectively. Banana LRR-RLP resistance gene candidates or with a potential role in development are highlighted in red or orange, respectively. Clades containing MaLRR-RLP RGCs are highlighted in blue. Numbers on the branches indicate the percentage of 100 bootstrap replications supporting the particular nodes, and only those ≥50% are shown. The C3-F region of LRR-RLP proteins was used for phylogenetic tree construction.

Figure 6

Maximum likelihood phylogenetic tree of banana, rice, and Arabidopsis LRR-RLP families. Banana, rice, and Arabidopsis LRR-RLP members are highlighted in blue, red, and black, respectively. The names and accession numbers (in parentheses) of LRR-RLPs involved in plant immunity or development are highlighted in gray or green, respectively. Numbers on the branches indicate the percentage of 100 bootstrap replications supporting the particular nodes, and only those ≥50% are shown. The C3-F region of LRR-RLP proteins was used for phylogenetic tree construction.

Figure 7

Expression profiles of banana LRR-RLP genes. (a) Expression profiles of MaLRR-RLP genes in response to Foc race 1 or Foc TR4 at 51 h postinoculation. The color scale reflects gene expression levels. Expression data reported by Li et al. [45] were used to obtain information about the expression levels of MaLRR-RLPs in response to Foc race 1 or Foc TR4. (b) RT–qPCR of MaLRR-RLP RGCs MaLRR-RLP58, MaLRR-RLP74, and MaLRR-RLP78 in leaf and root tissues of a M. acuminata ssp. burmannica in vitro. The relative expression of genes was calculated by the 2^−ΔΔCT method [47]. The mean ± S.D. of three biological replicates is presented. Asterisks indicate p ≤ 0.05 (t test).