Genome-wide identification and expression pattern analysis of quinoa BBX family

Transcript-Wide Identification and Characterization of the BBX Gene Family in Trichosanthes kirilowii and Its Potential Roles in Development and Abiotic Stress

The B-box (BBX) protein has an impact on flowering physiology, photomorphogenesis, shade effects, and responses to both biotic and abiotic stresses. Although recent research described the BBX gene family in numerous plants, knowledge of the BBX gene in Trichosanthes kirilowii was sparse. In this study, we identified a total of 25 TkBBX genes, and phylogenetic analysis showed that these genes were divided into five subfamilies. Analyses of gene structure and motifs for each group found relative conservation. Ka/Ks values showed that most TkBBX genes have undergone negative selection. qRT-PCR analyses revealed that TkBBX1, TkBB4, TkBBX5, TkBBX7, TkBBX15, TkBBX16, TkBBX17, TkBBX19, and TkBBX21 genes respond to salt and drought treatment. Furthermore, we cloned TkBBX7 and TkBBX17 genes and performed a subcellular localization experiment, which revealed that these two genes were both located in the nucleus. Transgenic yeast experiments demonstrated that TkBBX7 and TkBBX17 enhanced yeast tolerance to both salt and drought stresses. These findings provide a theoretical foundation for further investigation on the functions of TkBBX genes in Trichosanthes kirilowii.

Identification of the Valine-Glutamine gene family in Chenopodium quinoa Willd and analysis of its expression pattern and subcellular localization under drought stress

BACKGROUND

Chenopodium quinoa Willd (Quinoa) is highly tolerant to drought, cold, and salt stress. Gene editing technology development, and research on quinoa's drought resistance have attracted much attention. The transcriptional cofactor VQ plays an important role in the drought response in plants, but its role in quinoa has not been reported.

RESULTS

Bioinformatics identified 23 members of the quinoa VQ gene family, mainly located in the nucleus and unevenly distributed on 10 chromosomes. Gene structure and phylogenetic analysis indicated that the VQ genes were closely related and highly conserved, forming three subfamilies. The cis-acting elements of the promoter reveal its involvement in the response to light and hormonal stress. qRT-PCR analysis showed that all VQ genes were differentially expressed under drought stress, among which CqVQ13 was significantly up-regulated, and subcellular localization indicated that it was localized to the nucleus.

CONCLUSION

This study conducted a systematic bioinformatics analysis of the basic physicochemical properties and chromosome localization of 23 members of the CqVQ gene family. Combined with transcriptome gene expression profiling and qRT-PCR, we found that CqVQ13 was significantly up-regulated under drought stress and localized in the nucleus. This discovery provides an important candidate gene for drought response studies in quinoa and lays the foundation for further exploration of the molecular mechanisms of the VQ gene family in response to drought stress.

A tomato B-box protein regulates plant development and fruit quality through the interaction with PIF4, HY5, and RIN transcription factors

During the last decade, knowledge about BBX proteins has greatly increased. Genome-wide studies identified the BBX gene family in several ornamental, industry, and food crops; however, reports regarding the role of these genes as regulators of agronomically important traits are scarce. Here, by phenotyping a knockout mutant, we performed a comprehensive functional characterization of the tomato locus Solyc12g089240, hereafter called SlBBX20. The data revealed the encoded protein as a positive regulator of light signaling affecting several physiological processes during the life span of plants. Through inhibition of PHYTOCHROME INTERACTING FACTOR 4 (SlPIF4)-auxin crosstalk, SlBBX20 regulates photomorphogenesis. Later in development, it controls the balance between cell division and expansion to guarantee correct vegetative and reproductive development. In fruits, SlBBX20 is transcriptionally induced by the master transcription factor RIPENING INHIBITOR (SlRIN) and, together with ELONGATED HYPOCOTYL 5 (SlHY5), up-regulates flavonoid biosynthetic genes. Finally, SlBBX20 promotes the accumulation of steroidal glycoalkaloids and attenuates Botrytis cinerea infection. This work clearly demonstrates that BBX proteins are multilayer regulators of plant physiology because they affect not only multiple processes during plant development but they also regulate other genes at the transcriptional and post-translational levels.

Molecular Characterization and Expression Analysis of YABBY Genes in Chenopodium quinoa

Plant-specific YABBY transcription factors play an important role in lateral organ development and abiotic stress responses. However, the functions of the YABBY genes in quinoa remain elusive. In this study, twelve YABBY (CqYAB) genes were identified in the quinoa genome, and they were distributed on nine chromosomes. They were classified into FIL/YAB3, YAB2, YAB5, INO, and CRC clades. All CqYAB genes consist of six or seven exons, and their proteins contain both N-terminal C2C2 zinc finger motifs and C-terminal YABBY domains. Ninety-three cis-regulatory elements were revealed in CqYAB gene promoters, and they were divided into six groups, such as cis-elements involved in light response, hormone response, development, and stress response. Six CqYAB genes were significantly upregulated by salt stress, while one was downregulated. Nine CqYAB genes were upregulated under drought stress, whereas six CqYAB genes were downregulated under cadmium treatment. Tissue expression profiles showed that nine CqYAB genes were expressed in seedlings, leaves, and flowers, seven in seeds, and two specifically in flowers, but no CqYAB expression was detected in roots. Furthermore, CqYAB4 could rescue the ino mutant phenotype in Arabidopsis but not CqYAB10, a paralog of CqYAB4, indicative of functional conservation and divergence among these YABBY genes. Taken together, these results lay a foundation for further functional analysis of CqYAB genes in quinoa growth, development, and abiotic stress responses.