Recent advances in improving yield and immunity through transcription factor engineering

Abstract

Transcription factors (TFs) function as master regulators in multiple signaling pathways and govern diverse developmental and adaptive processes in plants. Some TFs identified in crop plants play critical roles in regulating yield through changes in plant architecture, including roots, stems, leaves, flowers, fruits, and grains. Although altering crop architecture can increase yields, the extent of yield enhancement is frequently hampered by diseases. Developing new crop varieties with improved yields and enhanced disease resistance remains challenging because immune system activation often impairs plant growth. Recently, approaches using TF engineering have made substantial progress in elevating both growth performance and disease resistance. However, most of these techniques rely on traditional transgenic methods. This review highlights discoveries in the last decade demonstrating improvements in growth performance, yield and immunity through TF engineering. We focus mainly on changes in plant architecture related to improved yield and disease resistance. We conclude with perspectives on the potential application of these discoveries for generating desirable crop traits by merging the most noteworthy biotechnology approaches, such as clustered regularly interspaced small palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated genome editing, with canonical molecular biology.

Keywords: CRISPR/Cas9; crop architecture; crop transcription factors; disease resistance; miRNA recognition site; uORF; yield improvement.

Figure 1

Engineered transcription factors (TFs) enhanced disease resistance with/without growth improvement (A–C) Representative engineered crop TFs that boost disease resistance without enhanced growth performance. (A) Transcriptional suppression of MADS26 through RNA interference (RNAi) promotes an immune response against Magnaporthe oryzae and Xanthomonas oryzae in rice plants. (B) The loss‐of‐function of mutation in the BBX20 elevates an immune response against Botrytis cinerea in tomato plants. (C) Transcriptionally upregulated WRKY100 resulting from gene transfer, enhances disease resistance against Colletotrichum gloeosporioides in apple seedlings. (D–F) Representative engineered crop TFs that boost disease resistance with enhanced growth performance. (D) Increasing both transcriptional and translational regulation of IPA1 via several techniques, including microRNA (miRNA) recognition site modification, overexpression and clustered regularly interspaced small palindromic repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9)‐mediated mutation in the promoter region, increases disease resistance and yield in rice. (E) Overexpressing MYB75 in tomato plants reduces susceptibility to B. cinerea. (F) Overexpressing NF‐YC4‐2 in soybean plants provides broad‐spectrum disease resistance and rapid flowering and podding. NG, normal growth; EY, enhanced yield; RY, reduced yield; LSL, long shelf life; EM, expedited maturity; R, resistance; S, susceptibility. The figure was created with www.BioRender.com.

Figure 2

Potential strategies to improve disease resistance without growth penalty (A) The main open reading frame (mORF) translation is regulated by the upstream ORF (uORF). Most uORFs suppress the translational activity of mORF. Modification of the uORF sequence (indel mutation or deletion) will allow us to enable the improvement of translation. (B–D) Potential strategies to enhance translational regulation of OsWRKY53, SlSRN1, GmNF‐YC4‐2, and MdWRKY100 by engineering uORFs. Predicted uORFs in Table 2 can be used to design clustered regularly interspaced small palindromic repeats (CRISPR)‐based genome editing to directly target these uORF sequences. Disruption of the uORFs function in the (B) OsWRKY53, (C) SlSRN1, and (D) GmNF‐YC4‐2 messenger RNAs (mRNAs) might enhance translation. (E) Canonical microRNA (miRNA) biogenesis pathway. A region of the miRNA binds to a complementary sequence in the target mRNA to direct the repression of an mRNA molecule via mRNA cleavage and degradation. Alteration of the miRNA recognition site abolishes miRNA binding activity, leading to increased post‐transcriptional regulation. (F) In the case of MdWRKY100, base editors such as adenine or cytosine deaminases can be fused with dead Cas9 (dCas9) or Cas9 nickase to promote A‐to‐G or C‐to‐T conversions at the genomic sites of the MdSPL13‐miR156a recognition element. The nucleotide changes in the miR156a recognition element further result in enhanced transcriptional activity of MdWRKY100. The figure was created with www.BioRender.com.