Novel disease resistance gene paralogs created by CRISPR/Cas9 in soy

Abstract

Key message Novel disease resistance gene paralogues are generated by targeted chromosome cleavage of tandem duplicated NBS-LRR gene complexes and subsequent DNA repair in soybean. This study demonstrates accelerated diversification of innate immunity of plants using CRISPR. Abstract Nucleotide-binding-site-leucine-rich-repeat (NBS-LRR) gene families are key components of effector-triggered immunity. They are often arranged in tandem duplicated arrays in the genome, a configuration that is conducive to recombinations that will lead to new, chimeric genes. These rearrangements have been recognized as major sources of novel disease resistance phenotypes. Targeted chromosome cleavage by CRISPR/Cas9 can conceivably induce rearrangements and thus emergence of new resistance gene paralogues. Two NBS-LRR families of soy have been selected to demonstrate this concept: a four-copy family in the Rpp1 region (Rpp1L) and a large, complex locus, Rps1 with 22 copies. Copy-number variations suggesting large-scale, CRISPR/Cas9-mediated chromosome rearrangements in the Rpp1L and Rps1 complexes were detected in up to 58.8% of progenies of primary transformants using droplet-digital PCR. Sequencing confirmed development of novel, chimeric paralogs with intact open reading frames. These novel paralogs may confer new disease resistance specificities. This method to diversify innate immunity of plants by genome editing is readily applicable to other disease resistance genes or other repetitive loci.

A Critical Review: Recent Advancements in the Use of CRISPR/Cas9 Technology to Enhance Crops and Alleviate Global Food Crises

“…A novel diseases resistance paralog using Cas9 has been created in soybean. These novel paralogs confer diseases resistance [170]. Tobacco, an important cash crop, is severely affected by potato virus Y, which is due to the susceptibility of gene Ntab0942120.…”

Plant and Fungal Genome Editing to Enhance Plant Disease Resistance Using the CRISPR/Cas9 System

“…In grape, the CRISPR/Cas9-mediated targeted mutagenesis of the transcription factor VvWRKY52 generated biallelic mutation mutant lines and knock-out of VvWRKY52 enhanced resistance to gray mold disease caused by Botrytis cinerea ( Wang et al, 2018 ). In soybean, the novel chromosome rearrangement technique using CRISPR/Cas9 was reported ( Nagy et al, 2021 ). This study engineered two NLR gene clusters called Rpp1-like and Rps1, which related with the resistance for Phakopsora pachyrhizi and P. sojae , respectively, and showed a possible advanced approach for managing plant disease through artificially creating chimeric paralogs.…”

“…One concept that can be demonstrated by combined genome editing is the interaction between a pathogen effector and host plant resistance gene. For example, editing of the P. sojae effector Avr genes ( Fang and Tyler, 2016 ) and the soybean Rps genes ( Nagy et al, 2021 ) can be combined and applied for controlling Phytophthora root and stem rot in soybean. Also, one example that can be applied to plant disease control is eradicating malaria vector mosquitoes by the targeted disruption of the doublesex gene using the CRISPR/Cas9 gene drive system ( Kyrou et al, 2018 ).…”

Genome editing: propelling the next generation of crop improvement

“…In soybean, a CRISPR-Cas-based strategy was used to diversify plant innate immune system, enhancing disease resistance. This technique consisted of generating diversity on loci of the key defense family genes from the nucleotidebinding-site-leucine-rich-repeat (NBS-LRR) class, through gene rearrangements, resulting in new positive variants (NAGY et al, 2021). Another new emerging approach is based on engineering plant-associated microbiome not only to improve crop growth but also to increase pathogen resistance.…”