Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains

Abstract

Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.

The mystery of an unprecedented plant disease in Africa

“…The international team of scientists sent members in Africa to collect samples of the blight and ran genetic and genomic analyses to determine the causative Xoo strain: “Together, our data showed that representative Tanzanian strains collected in 2019–2021 are phylogenetically related to Asian Xoo strains and have both iTALe and PthXo1 homologs unique to Asian Xoo isolates” (Schepler‐Luu et al , 2023). But the findings created new mysteries as “this outbreak can be ascribed to a recent colonization event by Xoo strains that are most similar to Asian strains, specifically from Yunnan province.” Yunnan Province in southwestern China is famed for its high‐yield hybrid rice and its neatly terraced farming system.…”

“…The international research consortium that analyzed the Xoo outbreak in Dakawa also used gene editing to develop a resistant rice strain (Schepler‐Luu et al , 2023). The science may have been the easy part.…”

“…Further analysis by the international Healthy Crops team (http://healthycrops.org) that is developing strategies for controlling rice diseases revealed that the plants were afflicted with bacterial blight, a major plant disease caused by the bacterium Xanthomonas oryzae and a special concern for Tanzania, which is dependent on rice to feed its booming population. The coalition of researchers from Africa, Europe, Asia, and North America reported their findings in a preprint (Schepler‐Luu et al , 2023). None of the co‐authors directly involved with Healthy Crops were available for comment.…”

Loss-of-function mutation in the polyamine transporter geneOsLAT5as a selectable marker for genome editing

“…Genome editing is widely used in both model plant and crop species for research and biotechnology [1,2]. Combinations of CRISPR/Cas9/Cpf1 and prime editing has successfully generated elite rice varieties with broad-spectrum resistance to bacterial blight and other diseases [3][4][5][6][7][8][9]. Major advantages of genome editing over classical breeding include the precision of prime editing, speed, and the ability to target multiple traits simultaneously without linkage drag.…”