Natural variation in a plant species is derived from spontaneous mutations in its wild progenitors, usually harboring signatures generated by long-term natural and artificial selection. To date, sequence variations in the coding region and transcription level polymorphisms caused by variations in the promoter have been prioritized in the search for candidate genes and causal variants. However, a large number of genetic mapping hits in plants are enriched in UTRs, which have elements affecting the gene translation efficiency or stability of messenger RNAs (mRNAs)4.

A primary regulatory element of gene expression at the translation or post-transcription level is the uORF, which lies upstream of the main open reading frame (mORF) in 18–57% of plant mRNAs. uORFs function either (i) by affecting (usually repressing) translation initiation of the mORF and/or inducing nonsense-mediated decay in a cis-acting manner or (ii) by encoding bioactive peptides with distinct biological functions beyond regulating mORF translation5.

A candidate gene HvDEP1 (encoding a γ-subunit of the heterotrimeric G-protein complex) and its uORF were found in a barley quantitative trait locus (QTL) controlling grain length. A 9-bp insertion/deletion variation in the HvDEP1 uORF was associated with grain length in DH population and a diversity panel1.

GWAS of phosphorus acquisition in soybean diversity panel identified candidate gene, GmPHF1, which encodes phosphate transporter traffic facilitator 1, a SEC12-like protein that facilitates the exit of phosphate transporters from the endoplasmic reticulum. Investigation of GmPHF1-based association mapping revealed a uORF in the 5′ UTR and a SNP introduced premature stop codon (TCA→TAA) that truncated the Uorf2.

PELAN (PETAL LOBE ANTHOCYANIN), encoding an anthocyanin-activating R2R3 MYB, was identified in a QTL for flower color in monkeyflower species. A SNP in the 5′ UTR was observed to create a start codon (AGG→ATG) and thus produced an uORF. The uORF represses PELAN translation, resulting in lower anthocyanin levels, and transforms the flower color from dark pink to pale pink3.

To completely decode the genetic basis of natural variation in plants, attention should be paid to the long-neglected uORF variation. Understanding of uORFs’ regulatory activities, the exploration of natural uORF variation, and CRISPR-based uORF engineering will mutually reinforce and collectively accelerate the dissection of the uORF-mediated genetic basis of phenotypic diversity and trait evolution, ultimately promoting the use of uORFs in plant breeding4.

Reference

1. Gage, J.L., Mali, S., McLoughlin, F., Khaipho-Burch, M., Monier, B., Bailey-Serres, J., Vierstra, R.D. and Buckler, E.S., 2022, Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance. Proc Natl Acad Sci.,119(14)

2. Guo, Z., Cao, H., Zhao, J., Bai, S., Peng, W., Li, J., Sun, L., Chen, L., Lin, Z., Shi, C. and Yang, Q., 2022, A natural uORF variant confers phosphorus acquisition diversity in soybean. Nat. Commun., 13(1), p.3796.

3. Liang, M., Foster, C.E. and Yuan, Y.W., 2022, Lost in translation: molecular basis of reduced flower coloration in a self-pollinated monkeyflower (Mimulus) species. Sci. Adv., 8(37), 1113.

4. Wang, J., Liu, J., & Guo, Z., 2024, Natural uORF variation in plants. Trends Plant Sci., 29(3), 290–302.

5. Watt, C., Zhou, G., Angessa, T.T., Moody, D. and Li, C., 2020, A novel polymorphism in the 5′ UTR of HvDEP1 is associated with grain length and 1000-grain weight in barley (Hordeum vulgare). Crop Pasture Sci. 71, 752–759.