Genome-Wide Investigation of the Auxin Response Factor Gene Family in Tartary Buckwheat (Fagopyrum tataricum)

Abstract

Auxin signaling plays an important role in plant growth and development. It responds to various developmental and environmental events, such as embryogenesis, organogenesis, shoot elongation, tropical growth, lateral root formation, flower and fruit development, tissue and organ architecture, and vascular differentiation. However, there has been little research on the Auxin Response Factor (ARF) genes of tartary buckwheat (Fagopyrum tataricum), an important edible and medicinal crop. The recent publication of the whole-genome sequence of tartary buckwheat enables us to study the tissue and expression profile of the FtARF gene on a genome-wide basis. In this study, 20 ARF (FtARF) genes were identified and renamed according to the chromosomal distribution of the FtARF genes. The results showed that the FtARF genes belonged to the related sister pair, and the chromosomal map showed that the duplication of FtARFs was related to the duplication of the chromosome blocks. The duplication of some FtARF genes shows conserved intron/exon structure, which is different from other genes, suggesting that the function of these genes may be diverse. Real-time quantitative PCR analysis exhibited distinct expression patterns of FtARF genes in various tissues and in response to exogenous auxin during fruit development. In this study, 20 FtARF genes were identified, and the structure, evolution, and expression patterns of the proteins were studied. This systematic analysis laid a foundation for the further study of the functional characteristics of the ARF genes and for the improvement of tartary buckwheat crops.

Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum)

“…The FtNAC genes were obtained using two BLASTP methods. First, all AtNACs were used to search possible FtNACs on the TBGP website, and further identified using BLASTP [84] (score value ≥100 and e-value ≤1e − 10 ) [53]. Second, we downloaded the hidden Markov model (HMM) file of the NAC domain (PF 02365) through Pfam (http://pfam.xfam.org/).…”

“…We used the GSDS (Gene Structure Display Server) analysis to analyze the constituents of the exons/introns of the FtNAC genes. We used MEME to analyze the motifs of FtNAC proteins, (http://meme-suite.org/tools/meme), with the parameters as follows: motif width set to 6–200 and number set to 10 [53, 89].…”

“…The selected gene expression analysis used qPCR, and primers were designed by Primer3 (Additional file 4: Table S4). We used the FtH3 gene, which was stably expressed at each growth stage in almost all tissues, as an internal control [53]. The qPCR with SYBR Premix Ex Taq II (TaKaRa) was repeated at least three times and the data were analyzed using the 2 −(∆∆Ct) method [91].…”

“…The recent completion of Tartary buckwheat genome sequencing allowed us to study the NAC gene family of Tartary buckwheat at the genome level [52]. To date, only the ARF and MADS gene families have been systematically analyzed in Tartary buckwheat [53, 54]. In this article, we report the gene structure, chromosomal location, duplication, global expression and potential developmental roles of Tartary buckwheat NAC genes.…”

Genome-wide investigation of the AP2/ERF gene family in tartary buckwheat (Fagopyum Tataricum)

“…Alignment of FtAP2/ERF protein sequences with ClustalW default parameters. The exon-intron structure of the FtAP2/ERF genes were determined by Gene Structure Display Server (GSDS: http://gsds.cbi.pku.edu.cn/) and the conserved motifs of AP2/ERF proteins were evaluated by MEME online program (http:/meme.nbcr.net/meme/intro.html) [36].…”