Genome-wide investigation of the ZF-HD gene family in Tartary buckwheat (Fagopyrum tataricum)

Abstract

Background ZF-HD is a family of genes that play an important role in plant growth, development, some studies have found that after overexpression AtZHD1 in Arabidopsis thaliana , florescence advance, the seeds get bigger and the life span of seeds is prolonged, moreover, ZF-HD genes are also participate in responding to adversity stress. The whole genome of the ZF-HD gene family has been studied in several model plants, such as Arabidopsis thaliana and rice. However, there has been little research on the ZF-HD genes in Tartary buckwheat ( Fagopyrum tataricum ), which is an important edible and medicinal crop. The recently published whole genome sequence of Tartary buckwheat allows us to study the tissue and expression profiles of the ZF-HD gene family in Tartary buckwheat on a genome-wide basis. Results In this study, the whole genome and expression profile of the ZF-HD gene family were analyzed for the first time in Tartary buckwheat. We identified 20 FtZF-HD genes and divided them into MIF and ZHD subfamilies according to phylogeny. The ZHD genes were divided into 5 subfamilies. Twenty FtZF-HD genes were distributed on 7 chromosomes, and almost all the genes had no introns. We detected seven pairs of chromosomes with fragment repeats, but no tandem repeats were detected. In different tissues and at different fruit development stages, the FtZF-HD genes obtained by a real-time quantitative PCR analysis showed obvious expression patterns. Conclusions In this study, 20 FtZF-HD genes were identified in Tartary buckwheat, and the structures, evolution and expression patterns of the proteins were studied. Our findings provide a valuable basis for further analysis of the biological function of the ZF-HD gene family. Our study also laid a foundation for the improvement of Tartary buckwheat crops. Electronic supplementary material The online version of this article (10.1186/s12870-019-1834-7) contains supplementary material, which is available to authorized users.

Zinc Finger-Homeodomain Transcriptional Factors (ZF-HDs) in Wheat (Triticum aestivum L.): Identification, Evolution, Expression Analysis and Response to Abiotic Stresses

“…The phylogenetic tree was constructed with TaZF-HD, AtZF-HD and OsZF-HD proteins ( Table S2 ). The results indicated that TaZF-HD proteins were divided into six groups ( Figure 1 and Figure 2 A), which were consistent with previous phylogenetic analyses of plant ZF-HD proteins [ 16 , 18 ]. Group II and MIF were the largest with 10 and 9 members, respectively.…”

“…In this study, we identified 37 TaZF-HD genes in wheat including 28 TaZF-HD genes and nine TaMIF genes ( Figure 1 and Table S1 ). The number of TaZF-HD genes was relatively higher than that identified in Arabidopsis (17) [ 11 ], tomato (22) [ 16 ], Chinese cabbage (31) [ 12 ] and Tartary buckwheat (20) [ 18 ] and the same as that in cotton (37) [ 17 ], suggesting that genome duplication events might have contributed to the expansion of TaZF-HD genes in wheat. Thirty-six paralogous gene pairs were identified in wheat, which all had undergone WGD or segmental duplication events and a strong purifying selection pressure ( Figure 4 and Table S3 ).…”

“…ZF-HD proteins were first identified in the C4 plant Flaveria as a potential regulator of the gene encoding C4 phosphoenolpyruvate carboxylase (PEPCase) [ 13 ]. Subsequently, ZF-HD genes were identified in several plant species such as Arabidopsis thaliana [ 11 ], tomato ( Solanum lycopersicum ) [ 16 ], cotton ( Gossypium hirsutum ) [ 17 ], Chinese cabbage [ 12 ] and Tartary buckwheat ( Fagopyrum tataricum ) [ 18 ]. In Arabidopsis , ZFHD10 recruits TANDEM ZINC-FINGER PLUS3 (TZP) to bind to light-regulated elements and regulate hypocotyl elongation [ 19 ].…”

Genome-wide identification, expression analysis and functional study of the GRAS gene family in Tartary buckwheat (Fagopyrum tataricum)

“…Tartary buckwheat is a dicotyledonous plant in the Polygonaceae family that contains a variety of nutrients, especially flavonoids such as rutin and quercetin [26]. Until now, transcription factor families such as ARF, MADS, AP2/ ERF, NAC, bZIP, ZF-HD have been identified in Tartary buckwheat [27–32]. More importantly, through in-depth research of ARF2 , it has been found that ARF2 plays an important role in determining the final size of Tartary buckwheat fruit [33].…”

Function analysis of ZmZHD9, a positive regulator in drought stress response in transgenic maize

“…Phylogenetic analyses showed that ZF-HD proteins were divided into two subfamilies, ZHD and MIF (Mini Zinc nger), and MIF genes only possess zinc nger structure but lacking HD domains at C-terminal, which similar with ZHD proteins without introns [6]. Since the rst ZF-HD TF was identi ed in the C4 plant Flaveria bidentis [7], a series of studies in plants have focused on ZF-HD TFs, including Arabidopsis thaliana [8], Oryza sativa L. [9], Solanum lycopersicum [10], Fagopyrum tataricum [11] and Glycine max [12]. ZF-HD genes play pivotal roles including the regulation of plant growth and development, hormone conduction and various environmental stresses [12,13].…”