Soybean hypocotyl elongation is regulated by a MYB33-SWEET11/21-GA2ox8c module involving long-distance sucrose transport.

The length of hypocotyl affects the height of soybean and lodging resistance, thus determining the final grain yield. However, research on soybean hypocotyl length is scarce, and the regulatory mechanisms are not fully understood. Here, we identified a module controlling the transport of sucrose, where sucrose acts as a messenger moved from cotyledon to hypocotyl, regulating hypocotyl elongation. This module comprises four key genes, namely MYB33, SWEET11, SWEET21 and GA2ox8c in soybean. In cotyledon, MYB33 is responsive to sucrose and promotes the expression of SWEET11 and SWEET21, thereby facilitating sucrose transport from the cotyledon to the hypocotyl. Subsequently, sucrose transported from the cotyledon up-regulates the expression of GA2ox8c in the hypocotyl, which ultimately affects the length of the hypocotyl. During the domestication and improvement of soybean, an allele of MYB33 with enhanced abilities to promote SWEET11 and SWEET21 has gradually become enriched in landraces and cultivated varieties, SWEET11 and SWEET21 exhibit high conservation and have undergone a strong purified selection and GA2ox8c is under a strong artificial selection. Our findings identify a new molecular pathway in controlling soybean hypocotyl elongation and provide new insights into the molecular mechanism of sugar transport in soybean.

ABI5 acts downstream of miR159 to delay vegetative phase change in Arabidopsis.

Vegetative development constitutes a critical phase in plant development, and it is regulated by an evolutionarily conserved miR156-SPL pathway. Previous studies have shown that miR159 acts to prevent the hyperactivation of miR156 to regulate the timing of vegetative phase change in Arabidopsis. However, whether miR159 integrates into the abscisic acid (ABA) signaling pathway to control vegetative phase change remains unexplored, since miR159 also plays an important regulatory role in ABA response. Here, we show that the expression of ABI5 (ABA INSENSITIVE5), a crucial regulator in the ABA signaling pathway, is significantly elevated in the loss-of-function mutant of miR159 (mir159ab). Loss of function in ABI5 (abi5) promotes juvenile-to-adult transition, whereas overexpression of ABI5 delays this transition under short-day conditions. Genetic analyses indicated that the effect of mir159ab on vegetative phase change is ABI5 dependent. Further analysis confirmed that MYB33, a major target of miR159, promotes the transcription of ABI5 by directly binding to its promoter. ABI5 functions upstream of miR156 to promote juvenile development by affecting the expression of genes in the miR156-SPL pathway. Therefore, our study uncovers a new role of ABI5 in vegetative development in plants, and implies a role of ABA signaling in vegetative development in Arabidopsis.

Comparative genomics reveals origin of MIR159A-MIR159B paralogy, and complexities of PTGS interaction between miR159 and target GA-MYBs in Brassicaceae.

Whole-genome and segmental duplications coupled with sequence and functional diversification are responsible for gene family expansion, and morphological and adaptive diversity. Although broad contours of such processes are understood, detailed investigations on regulatory elements, such as miRNA-transcription factor modules, especially in non-model crop plants with complex genomes, are few. The present study was performed to understand evolutionary history of MIR159 family, and changes in the miRNA-binding site (MBS) of the targets MYB33, MYB65, and MYB101 that may affect post-transcriptional gene silencing. We established orthology and paralogy between members of MIR159 family by reconstructing the phylogeny based on 240 precursor sequences sampled across green plants. An unambiguous paralogous relationship between MIR159A and MIR159B was observed only in Brassicaceae which prompted us to analyze the origin of this paralogy. Comparative micro-synteny of ca. 100 kb genomic segments surrounding MIR159A, MIR159B, and MIR159C loci across 15 genomes of Brassicaceae revealed segmental duplication that occurred in the common ancestor of Brassicaceae to be responsible for origin of MIR159A-MIR159B paralogy; extensive gene loss and rearrangements were also encountered. The impact of polyploidy was revealed when the three sub-genomes-least fractionated (LF), moderately fractionated (MF1), and most fractionated (MF2) sub-genomes of Brassica and Camelina sativa-were analyzed. Extensive gene loss was observed among sub-genomes of Brassica, whereas those in Camelina were largely conserved. Analysis of the target MYBs revealed the complete loss of MYB33 homologs in a Brassica lineage-specific manner. Our findings suggest that mature miR159a/b /c are capable of targeting MYB65 across Brassicaceae, MYB33 in all species except Brassica, and MYB101 only in Arabidopsis thaliana. Comparative analysis of the mature miRNA sequence and the miRNA-binding site (MBS) in MYB33, MYB65, and MYB101 showed the complexity of regulatory network that is dependent on strict sequence complementarity potentially leading to regulatory diversity.

MicroRNAs with analogous target complementarities perform with highly variable efficacies in Arabidopsis.

In plants, the silencing efficacy of microRNAs (miRNAs) is thought to be predominantly determined by the degree of complementarity to their target genes. Here, silencing efficacy was determined for Arabidopsis miR159 and four artificial miRNAs (amiRNAs) that all target MYB33/MYB65 with analogous complementarities. As determined through complementation of a loss-of-function mir159 mutant, the amiRNAs displayed highly variable efficacies, none of which was as strong as endogenous miR159. This was despite amiRNA expression levels being many fold-higher than miR159 in wild-type. The results highlight the variable nature of miRNA silencing efficacy in plants, where it appears that factors additional to complementarity strongly impact silencing.