Genome-wide identification and expression analysis of the GSK gene family in wheat (Triticum aestivum L.)

BACKGROUND

Plant glycogen synthase kinase 3/shaggy kinase (GSK3) proteins contain the conserved kinase domain and play a pivotal role in the regulation of plant growth and abiotic stress responses. Nonetheless, genome-wide analysis of the GSK gene family in wheat (Triticum aestivum L.) has not been reported.

METHODS AND RESULTS

Using high-quality wheat genome sequences, a comprehensive genome-wide characterization of the GSK gene family in wheat was conducted. Their phylogenetics, chromosome location, gene structure, conserved domains, promoter cis-elements, gene duplications, and network interactions were systematically analyzed. In this study, we identified 22 GSK genes in wheat genome that were unevenly distributed on nine wheat chromosomes. Based on phylogenetic analysis, the GSK genes from Arabidopsis, rice, barley, and wheat were clustered into four subfamilies. Gene structure and conserved protein motif analysis revealed that GSK proteins in the same subfamily share similar motif structures and exon/intron organization. Results from gene duplication analysis indicate that four segmental duplications events contribute to the expansion of the wheat GSK gene family. Promoter analysis indicated the participation of TaSK genes in response to the hormone, light and abiotic stress, and plant growth and development. Furthermore, gene network analysis found that five TaSKs were involved in the regulatory network and 130 gene pairs of network interactions were identified. The heat map generated from the available transcriptomic data revealed that the TaSKs exhibited preferential expression in specific tissues and different expression patterns under abiotic stress conditions. Moreover, results from qRT-PCR analysis revealed that the randomly selected TaSK genes were abundantly expressed in spikes and grains at one specific developmental stage, as well as in responding to drought and salt stress.

CONCLUSIONS

These findings clearly depicted the evolutionary processes and the characteristics, and expression profiles of the GSK gene family in wheat, revealed their role in wheat development and response to abiotic stress responses.

Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

Background

DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat. The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family.

Results

Using the recently released wheat genome database (IWGSC RefSeq v1.0), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. Gene duplication analysis revealed a broad and heterogeneous distribution of TaDofs on the chromosome groups 1 to 7, and obvious tandem duplication genes were present on chromosomes 2 and 3.Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences. Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31 T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and qRT-PCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses.

Conclusions

The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family.

Genome-Wide Identification and Analysis of the AP2 Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

The AP2 transcription factors play important roles in regulating plant growth and development. However, limited data are available on the contributions of AP2 transcription factors in wheat (Triticum aestivum L.). In the present study, a total of 62 AP2 genes were identified in wheat from a genome-wide search against the latest wheat genome data. Phylogenetic and sequence alignment analyses divided the wheat AP2 genes into 3 clusters, euAP2, euANT, and basalANT. Chromosomal distribution, gene structure and duplication, and motif composition were subsequently investigated. The 62 TaAP2 genes were unevenly distributed on 21 chromosomes. Twenty-four homologous gene sets among A, B, and D sub-genomes were detected, which contributed to the expansion of the wheat AP2 gene family. The expression levels of TaAP2 genes were examined using the WheatExp database; most detected genes exhibited tissue-specific expression patterns. The transcript levels of 9 randomly selected TaAP2 genes were validated through qPCR analyses. Overexpression of TaAP2-10-5D, the most likely homolog of Arabidopsis ANT gene, increased organ sizes in Arabidopsis. Our results extend our knowledge of the AP2 gene family in wheat, and contribute to further functional characterization of AP2s during wheat development with the ultimate goal of improving crop production.

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense

Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete^1-4. Here we report reference-grade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3-79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques. Compared with previous assembled draft genomes^1,3, these genome sequences show considerable improvements in contiguity and completeness for regions with high content of repeats such as centromeres. Comparative genomics analyses identify extensive structural variations that probably occurred after polyploidization, highlighted by large paracentric/pericentric inversions in 14 chromosomes. We constructed an introgression line population to introduce favorable chromosome segments from G. barbadense to G. hirsutum, allowing us to identify 13 quantitative trait loci associated with superior fiber quality. These resources will accelerate evolutionary and functional genomic studies in cotton and inform future breeding programs for fiber improvement.

A 55 K SNP array-based genetic map and its utilization in QTL mapping for productive tiller number in common wheat

A high-density genetic map constructed with a wheat 55 K SNP array was highly consistent with the physical map of this species and it facilitated the identification of a novel major QTL for productive tiller number. Productive tiller number (PTN) plays a key role in wheat grain yield. In this study, a recombinant inbred line population with 199 lines derived from a cross between '20828' and 'Chuannong16' was used to construct a high-density genetic map using wheat 55 K single nucleotide polymorphism (SNP) array. The constructed genetic map contains 12,109 SNP markers spanning 3021.04 cM across the 21 wheat chromosomes. The orders of the genetic and physical positions of these markers are generally in agreement, and they also match well with those based on the 660 K SNP array from which the one used in this study was derived. The ratios of SNPs located in each of the wheat deletion bins were similar among the wheat 9 K, 55 K, 90 K, 660 K and 820 K SNP arrays. Based on the constructed maps, a novel major quantitative trait locus QPtn.sau-4B for PTN was detected across multi-environments in a 0.55 cM interval on 4B and it explained 17.23-45.46% of the phenotypic variance. Twenty common genes in the physical interval between the flanking markers were identified on chromosome 4B of 'Chinese Spring' and wild emmer. These results indicate that wheat 55 K SNP array could be an ideal tool in primary mapping of target genes and the identification of QPtn.sau-4B laid a foundation for the following fine mapping and cloning work.

Variation and diversity of the breakpoint sequences on 4AL for the 4AL/5AL translocation in Triticum

The translocation of 4AL/5AL in Triticum, which occurred before the differentiation of T. urartu and einkorn, is an important chromosomal rearrangement. Recently, the first identification of breakpoint sequence on 4AL for this translocation provides the opportunity to analyze the variation and diversity of breakpoints in Triticum. In this study, the breakpoint regions of 52 accessions from 21 species were isolated and further characterized. The sequences were divided into 12 types based on their lengths, which ranged from 2009 to 2552 bp. Cluster analysis showed that they were further divided into three groups. Interesting evolutionary relationships among a few of the species were observed and discussed. Multiple sequence alignment of the 52 sequences made it possible to detect 13 insertion and deletion length polymorphisms (InDels) and 101 single nucleotide polymorphisms (SNPs). Furthermore, several species- or accession-specific SNPs or InDels were also identified. Based on BLAST analysis of the conserved sequences, the breakpoint was narrowed down to a 125 bp fragment. Taken together, the results obtained in this study enrich our understanding of chromosomal breakpoints and will be useful for the identification of other breakpoints in wheat.