Multiplex CRISPR-Cas9 editing of chlorophyll biosynthesis genes in chickpea via protoplast and Agrobacterium-mediated transformation

Abstract

Chickpea is an important legume consumed worldwide and a rich source of protein. Chickpea is less amenable to recent gene editing techniques despite its economic significance. Accelerating the improvement process and enabling novel trait development in chickpea will require new approaches for genetic intervention. The CRISPR system has been used in different plant species to generate genetic variation and manipulate gene functions, facilitating studies on gene function and crop improvement. To implement genome editing in chickpea, genes involved in the chlorophyll biosynthesis pathway were selected as targets for gene editing. A construct (pTrans_100-Chbio) carrying gRNAs for chlorophyllide a oxygenase (CAO) and chlorophyll synthase (CHLG), along with the Cas9 protein, was introduced into chickpea protoplasts via PEG-mediated transformation. Multiple edits containing deletions and base insertions were identified after protoplast transformation, as confirmed by Sanger sequencing. Afterward, Agrobacterium transformation of explants was performed, resulting in the successful regeneration of pale and chimeric yellow tissues, subsequently confirmed as containing largely substitutions, as detected through deep amplicon sequencing. Edited plants showed yellowish leaves and lower chlorophyll content. Our results indicated that chlorophyll biosynthesis pathway genes played an essential role in chlorophyll degradation and ROS scavenging to regulate both natural and induced chickpea senescence. We established an efficient and feasible CRISPR/Cas9-based editing system in chickpea that successfully generates allelic mutations and phenotypic variation. The established platform can be a foundation for future functional studies and precise genome editing of additional agronomic traits, ultimately contributing to chickpea crop improvement and sustainable agriculture.