On February 25, 2021, David Jackson's team from Cold Spring Harbor Laboratory in the United States published a research paper entitled "Enhancing grain-yield-related traits by CRISPR–Cas9 promoter editing of maize CLE genes" online in the internationally renowned journal "Nature Plants". The study highlights two different ways in which genome editing can improve maize traits, one is CRISPR-based promoter editing and the other utilizes compensation and redundancy mechanisms, which may be applicable to different crops.
Background:
CEREAL CROPS SUCH AS MAIZE ARE OUR MAIN FOOD AND FEED SOURCES, MAIZE YIELD IS DETERMINED BY BOTH GRAIN NUMBER AND GRAIN WEIGHT, AND THE NUMBER OF GRAINS PER PANICLE DEPENDS ON INFLORESCENCE MERISTEM (IM) ACTIVITY, WHICH IS MAINTAINED BY THE CLAVATA (CLV)-WUSCHEL(WUS) FEEDBACK SIGNALING PATHWAY, WHICH WAS FIRST IDENTIFIED IN ARABIDOPSIS THALIANA BUT IS CONSERVED IN MAIZE AND OTHER SPECIES. In this pathway, the homologous transcription factor WUS is expressed at the center of the meristem and promotes the expression of CLV3, which binds to its receptor CLV1 and inhibits WUS expression. Mutations in the CLV gene lead to excessive proliferation of meristems, and the inflorescence stems and ears of maize become larger, resulting in more disorganized and shorter grain rows, resulting in lower yields.
The weakly coding sequence alleles of FASCIATED EAR 2 (fea2) and FASCIATED EAR 2 (fea3) produced by ethyl mesylate mutagenesis led to an increase in the number of grain rows. These weak alleles maintain meristem and spike length and have the potential to increase yield. Weakly coding allele method: (1) The weakly coding alleles of fasciated ear2 (fea2) and fea3 produced by EMS mutagenesis led to an increase in the number of grain rows. (2) Editing cis-regulated regions, such as the promoter used in tomatoes, was used using CRISPR-Cas9 to design the quantitative variation of inflorescence trajectories.
Findings:
1. The CRISPR-Cas9 system edits the promoters of ZmCLE7 and ZmFCP1 in maize
ATAC-seq and MNase-seq data were used to identify the promoter regions of ZmCLE7 and ZmFCP1 to effectively manipulate gene expression. Multiple weak alleles of the two genes were obtained, in which the expression of ZmCLE7 and ZmFCP1 was significantly reduced. Further observation showed that the alleles edited by ZmCLE7 and FCP1 promoters were able to maintain normal IM structure.
Figure 1: CRISPR-Cas9 mutant ZmCLE7 and ZmFCP1 promoters
2. Alleles edited by ZmCLE7 and FCP1 promoters can improve maize yield
The alleles edited by the ZmCLE7 and ZmFCP1 promoters significantly increased most yield-related traits, including spike diameter, spike diameter, grain row count, grain depth, spike weight, and yield per spike. They can significantly increase yield in both inbred and hybrid backgrounds.
Figure 2: Alleles edited by the ZmCLE7 and ZmFCP1 promoters can increase grain yields
3. ZmCLE1E5 can partially complement the functions of ZmCLE7
In addition to ZmCLE7 and ZmFCP1, 47 CLE genes were annotated in maize, and ZmCLE1E5 was also found to be upregulated in addition to ZmFCP1 in the Zmcle7 mutant. This gene exhibits compensatory upregulation in the Zmcle7 mutant. ZmCLE1E5 exhibits a similar effect to the weak allele of the ZmCLE7 promoter.
Figure 3: Invalid allele with deletion of ZmCLE1E5 increases meristem size and grain yield-related traits.
Figure 4: Two strategies edit three CLV3 orthologs in the CLV-WUS pathway to quantitatively increase maize yields
Quantitative variants of yield-related traits in maize were designed by editing the promoter weak allele of the CLE gene and the invalid allele of the partially redundant compensating CLE gene by using the CRISPR-Cas9 system. These strategies have improved a variety of traits associated with maize yields, demonstrating the great potential of genome editing in crop improvement.
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