Engineering high yield basmati rice by editing multiple negative regulators of yield

Yield improvement in Basmati rice is important to meet the growing demand of Basmati and pivotal to world food security. Yield in rice is a complex quantitative trait controlled by many genes and yield-determining factors. Although dominant genes introgression through breeding have been extensively used but it is a laborious and time-consuming process. Yield genes OsD27, OsGW2, OsTGW6 and OsGN1a have been shown to negatively regulate an increase in the number of tillers, grain width, grain weight, and number of grains per panicle respectively in different genetic backgrounds of rice separately. The aim of our study is to establish a multiplex system in Super Basmati to check if it acts similarly and what is their combinatorial effect on yield enhancement.

Here we generated Super Basmati quadruple edited lines for all four genes OsD27, OsGW2, OsTGW6 and OsGN1a through CRISPR-Cas9 polycistronic tRNA-gRNA (PTG) endogenous processing efficient multiplex editing system. Quadruple edited lines were characterized for key yield parameters such as number of tillers, number of grains, grain weight, overall yield increase, lodging resistance and cooking quality related traits.

We found that all quadruple edited plants produced more tillers, a greater number of grains with high grain weight in field evaluations along with decreased plant height. Overall, the contribution of all four genes was additive resulting in boosting the yield in Super Basmati remarkably. Our data hence demonstrated a promising multiplex genome editing approach for rapid generation of superior alleles for all four yield contributing factor genes in elite Basmati variety with 30% co-editing efficiency.

We conclude that multiplex CRISPR-Cas9 genome editing of yield-negative regulators may boost the yield of elite Basmati rice in a short time without causing any drastic effect on other agronomic and quality traits such as aroma, chalkiness, and cooking qualities. Data suggests that the tRNA-gRNA multiplexing CRISPR-Cas9 system is efficient in the Basmati rice background for simultaneously editing multiple genes. Due to its capability of rapid generation of beneficial alleles, this multiplex system is well suited for pyramiding of multiple alleles in Basmati rice and may prove a promising approach to enhance yield in Basmati rice while it may provide useful germplasm resource for high-yielding future rice breeding programs.