Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance

Abstract

Rice is the main food crop for people in low- and lower-middle-income countries in Asia and sub-Saharan Africa (SSA). Since 1982, there has been a significant increase in the demand for rice in SSA, and its growing importance is reflected in the national strategic food security plans of several countries in the region. However, several abiotic and biotic factors undermine efforts to meet this demand. Rice yellow mottle virus (RYMV) caused by Solemoviridae is a major biotic factor affecting rice production and continues to be an important pathogen in SSA. To date, six pathogenic strains have been reported. RYMV infects rice plants through wounds and rice feeding vectors. Once inside the plant cells, viral genome-linked protein is required to bind to the rice translation initiation factor [eIF(iso)4G1] for a compatible interaction. The development of resistant cultivars that can interrupt this interaction is the most effective method to manage this disease. Three resistance genes are recognized to limit RYMV virulence in rice, some of which have nonsynonymous single mutations or short deletions in the core domain of eIF(iso)4G1 that impair viral host interaction. However, deployment of these resistance genes using conventional methods has proved slow and tedious. Molecular approaches are expected to be an alternative to facilitate gene introgression and/or pyramiding and rapid deployment of these resistance genes into elite cultivars. In this review, we summarize the knowledge on molecular genetics of RYMV-rice interaction, with emphasis on host plant resistance. In addition, we provide strategies for sustainable utilization of the novel resistant sources. This knowledge is expected to guide breeding programs in the development and deployment of RYMV resistant rice varieties.

Rice Yellow Mottle Virusresistance by genome editing of theOryza sativaL. ssp. japonica nucleoporin geneOsCPR5.1but notOsCPR5.2

“…To evaluate whether genome editing of the two rice CPR5 homologs can be used to confer resistance to RYMV, a major biotic constraint affecting rice production in sSA (Odongo et al ., 2021), two nucleoporin paralogs were edited in the japonica rice variety Kitaake (Fig. S12).…”

“…Three major resistance genes have been identified to date: RYMV1 (eIF(iso)4G1), RYMV2 ( CPR5 . 1 ), and RYMV3 (NB-LRR) (Albar et al ., 2006; Bonnamy et al ., 2023; Odongo et al ., 2021; Orjuela et al ., 2013; Pidon et al ., 2017). Interspecific sterility barriers hamper the introgression of interesting traits from O. glaberrima to O. sativa (Garavito et al ., 2010).…”

“…High resistance has been observed in about 7% of accessions of O. glaberrima, a domesticated African rice species, but is very rare in O. sativa, which is by far the most cultivated rice species around the world and in Africa (Pidon et al, 2020;Thiémélé et al, 2010). Three major resistance genes have been identified to date: RYMV1 (eIF(iso)4G1), RYMV2 (CPR5.1), and RYMV3 (NB-LRR) (Albar et al, 2006;Bonnamy et al, 2023;Odongo et al, 2021;Orjuela et al, 2013;Pidon et al, 2017). Interspecific sterility barriers hamper the introgression of interesting traits from O. glaberrima to O. sativa (Garavito et al, 2010).…”

A Review of Vector-Borne Rice Viruses

“…Using genome-wide association study (GWAS), linkage disequilibrium (LD) decay analyses, RNA-sequencing, and genome editing, a highly RBSDV-resistant variety and its first functional gene, Hap1, was identified [ 140 ]. Besides, multiple recessive resistance loci to RYMV have been mapped [ 141 , 142 ]. For example, mutations in the eIF(iso)4G translation initiation factor confer high resistance of rice to RYMV [ 109 ].…”

Genome editing of an African elite rice variety confers resistance against endemic and emergingXanthomonas oryzaepv.oryzaestrains

“…Rice is one of the most important staple foods for developing countries in Asia and Africa (Odongo et al, 2021). African consumers increasingly replace the traditional staples of sorghum, millet and maize with rice.…”