“R genes: Identification and their utilization in resistance breeding”

  

The increasing global population, shrinking arable land, water scarcity, and climate change have raised serious concerns about food production worldwide. The conventional plant breeding has made substantial contributions by developing high-yielding varieties and hybrids, many of these cultivars have become genetically vulnerable to major diseases, leading to a global yield loss of 13-14% and increased reliance on pesticides for disease control. To address this issue, it is essential to understand plant-pathogen interaction and to develop new disease-resistant cultivars by identifying novel resistant sources and resistant (R) genes to be used in breeding programs.

Disease resistance is the inherent ability of a plant to prevent or restrict the establishment and subsequent activities of a potential pathogen. Plant disease resistance is classified based on stability and epidemiology of resistance into complete resistance governed by oligogenes in a gene-for-gene hypothesis manner and partial resistance is governed by QTLs (Quantitative Resistant Loci – QRL) with minor effects giving durable and broad-spectrum resistance (BSR). The mechanism of the plant immune system includes the framework of pattern recognition receptors (PRRs) mediated PAMP-triggered immunity (PTI) and nucleotide-binding leucine-rich repeat proteins (NLR) mediated effector-triggered immunity (ETI).1

However, the mere utilization of R genes/ QRLs is difficult and genetic vulnerability due to the monoculture of High yielding varieties (HYVs). This can be overcome by the identification of new resistant sources (germplasm sources) with novel R gene combinations that can pose BSR to diseases. The approaches to identifying new R genes include fine mapping, positional cloning, genome sequencing, bioinformatic technologies and engineered NLRs.1 Fang et al. (2019) identified two QTLs qPb11–1and qPb6–1and fine-mapped a panicle blast-resistant gene Pb-db1 encoding NBS-LRR region in rice landrace Bodao.2 These novel R genes can be utilized in breeding to develop new resistant sources through marker-assisted selection (MAS), gene pyramiding, and genome-wide association studies (GWAS). Mahesh et al. (2021) identified putative SNPs and candidate genes (MLO and RPW8.2) associated with powdery mildew resistance in horsegram.3 These identified novel genes can be validated using mutants developed through RNAi and CRISPR techniques.

Crop improvement for disease resistance necessitates the discovery of new R genes, a deep understanding of disease resistance, and insights into the underlying mechanisms. Fortunately, advances in genomic technologies have made studying broad-spectrum resistance (BSR) easier. These advancements provide a more comprehensive understanding of plant defense, which can be utilized to reduce disease-related losses, understand host-pathogen interactions, and uncover underlying mechanisms.

References: 

1 DENG, Y., NING, Y., YANG, D.L., ZHAI, K., WANG, G.L. AND HE, Z., 2020, Molecular basis of disease resistance and perspectives on breeding strategies for resistance improvement in crops. Mol. Plant, 13(10): 1402-1419.

2 FANG, N., WEI, X., SHEN, L., YU, Y., LI, M., YIN, C., HE, W., GUAN, C., CHEN, H., ZHANG, H. AND BAO, Y., 2019, Fine mapping of a panicle blast resistance gene Pb-bd1 in Japonica landrace Bodao and its application in rice breeding. Rice, 12: 1-12.

3 MAHESH, H.B., PRASANNAKUMAR, M.K., MANASA, K.G., PERUMAL, S., KHEDIKAR, Y., KAGALE, S., SOOLANAYAKANAHALLY, R.Y., LOHITHASWA, H.C., RAO, A.M. AND HITTALMANI, S., 2021, Genome, Transcriptome, and Germplasm Sequencing Uncovers Functional Variation in the Warm-Season Grain Legume Horsegram Macrotyloma uniflorum (Lam.) Verdc. Front. Plant Sci., 12: 758119.