Genome-wide analysis and identification of HAK potassium transporter gene family in maize (Zea mays L.)

The high-affinity K(+) (HAK) transporter gene family constitutes the largest family that functions as potassium transporter in plant and is important for various cellular processes of plant life. In spite of their physiological importance, systematic analyses of ZmHAK genes have not yet been investigated. In this paper, we indicated the isolation and characterization of ZmHAK genes in whole-genome wide by using bioinformatics methods. A total of 27 members (ZmHAK1-ZmHAK27) of this family were identified in maize genome. ZmHAK genes were distributed in all the maize 10 chromosomes. These genes expanded in the maize genome partly due to tandem and segmental duplication events. Multiple alignment and motif display results revealed major maize ZmHAK proteins share all the three conserved domains. Phylogenetic analysis indicated ZmHAK family can be divided into six subfamilies. Putative cis-elements involved in Ca(2+) response, abiotic stress adaption, light and circadian rhythms regulation and seed development were observed in the promoters of ZmHAK genes. Expression data mining suggested maize ZmHAK genes have temporal and spatial expression pattern. In all, these results will provide molecular insights into the potassium transporter research in maize.     

Genome-wide isolation of resistance gene analogs in maize (Zea mays L.)

Conserved domains or motifs shared by most known resistance (R) genes have been extensively exploited to identify unknown R-gene analogs (RGAs). In an attempt to isolate all potential RGAs from the maize genome, we adopted the following three methods: modified amplified fragment length polymorphism (AFLP), modified rapid amplification of cDNA ends (RACE), and data mining. The first two methods involved PCR-based isolations of RGAs with degenerate primers designed based on the conserved NBS domain; while the third method involved mining of RGAs from the maize EST database using full-length R-gene sequences. A total of 23 and 12 RGAs were obtained from the modified AFLP and RACE methods, respectively; while, as many as 109 unigenes and 77 singletons with high homology to known R-genes were recovered via data-mining. Moreover, R-gene-like ESTs (or RGAs) identified from the data-mining method could cover all RACE-derived RGAs and nearly half AFLP-derived RGAs. Totally, the three methods resulted in 199 non-redundant RGAs. Of them, at least 186 were derived from putative expressed R-genes. RGA-tagged markers were developed for 55 unique RGAs, including 16 STS and 39 CAPS markers.     

Genome-wide association analysis of seedling root development in maize (Zea mays L.)

Background

Plants rely on the root system for anchorage to the ground and the acquisition and absorption of nutrients critical to sustaining productivity. A genome wide association analysis enables one to analyze allelic diversity of complex traits and identify superior alleles. 384 inbred lines from the Ames panel were genotyped with 681,257 single nucleotide polymorphism markers using Genotyping-by-Sequencing technology and 22 seedling root architecture traits were phenotyped.

Results

Utilizing both a general linear model and mixed linear model, a GWAS study was conducted identifying 268 marker trait associations (p ≤ 5.3×10^-7). Analysis of significant SNP markers for multiple traits showed that several were located within gene models with some SNP markers localized within regions of previously identified root quantitative trait loci. Gene model GRMZM2G153722 located on chromosome 4 contained nine significant markers. This predicted gene is expressed in roots and shoots.

Conclusion

This study identifies putatively associated SNP markers associated with root traits at the seedling stage. Some SNPs were located within or near (<1 kb) gene models. These gene models identify possible candidate genes involved in root development at the seedling stage. These and respective linked or functional markers could be targets for breeders for marker assisted selection of seedling root traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1226-9) contains supplementary material, which is available to authorized users.     

Genome-wide analysis and environmental response profiling of the FK506-binding protein gene family in maize (Zea mays L.)

The FK506-binding proteins (FKBPs) belong to the peptidyl-prolyl cis/trans isomerase (PPIase) superfamily, and have been implicated in a wide spectrum of biological processes, including protein folding, hormone signaling, plant growth, and stress responses. Genome-wide structural and evolutionary analyses of the entire FKBP gene family have been conducted in Arabidopsis and rice. In the present study, a genome-wide analysis was performed to identify all maize FKBP genes. The availability of complete maize genome sequences allowed for the identification of 24 FKBP genes. Chromosomal locations in the maize genome were determined and the protein domain and motif organization of ZmFKBPs analyzed. The phylogenetic relationships between maize FKBPs were also assessed. The expression profiles of ZmFKBP genes were measured under different environmental conditions and revealed distinct ZmFKBP gene expression patterns under heat, cold, salt, and drought stress. These data not only contribute to a better understanding of the complex regulation of the maize FKBP gene family, but also provide evidence supporting the role of FKBPs in multiple signaling pathways involved in stress responses. This investigation may provide valuable information for further research on stress tolerance in plants and potential strategies for enhancing maize survival under stressful conditions.     

Epistasis in maize (Zea mays L.)

Summary Three flint and three dent maize (Zea mays L.) inbred lines, their possible F₁ crosses, F₂ and backcross progenies, and all possible three-way crosses were evaluated in a three-year experiment for yield, ear moisture, and plant height. The purpose was to estimate genetic parameters in European breeding materials from (i) generation means analysis, (ii) diallel analysis of generation means, and (iii) analysis of F₁ and three-way cross hybrids. Method (i) was based on the F-metric model and methods (ii) and (iii) on the Eberhart-Gardner (1966) genetic model; both models extended for heterotic maternal effects.Differences among generation means for yield and plant height were mainly attributable to dominance effects. Epistatic effects were significantly different from zero in a few crosses and considerably reduced heterosis in both traits. Additive x additive and domiance x dominance effects for yield were consistently positive and negative, respectively. Significant maternal effects were established to the advantage of generations with a heterozygous seed parent. In the diallel analysis, mean squares for dominance effects were greater than for additive effects for yield and plant height but smaller for ear moisture. Though significant for yield and plant height, epistatic variation was small compared to additive and dominance variation. Estimates of additive x additive epistasis for yield were significantly negative in 11 of 15 crosses, suggesting that advantageous gene combinations in the lines had been disrupted by recombination in the segregating generations. The analysis of hybrids supported the above findings regarding the analysis of variance. However, the estimates of additive x additive epistasis for yield were considerably smaller and only minimally correlated with those from the diallel analysis. Use of noninbred materials as opposed to materials with different levels of inbreeding is considered the main reason for the discrepancies in the results.     

Genome-wide identification of Aux/IAA and ARF gene families in bread wheat (Triticum aestivum L.)

Protoplasma - Wheat (Triticum aestivum L.) is one of the most important food crops in the world. Somatic embryogenesis is an event that is triggered by the presence of auxin hormone for the...     

Proteomic analysis of shoot-borne root initiation in maize (Zea mays L.)

Postembryonically formed shoot-borne roots make up the major backbone of the adult maize root stock. In this study the abundant soluble proteins of the first node (coleoptilar node) of wild-type and mutant rtcs seedlings, which do not initiate crown roots, were compared at two early stages of crown root formation. In Coomassie Bluestained 2-D gels, representing soluble proteins of coleoptilar nodes 5 and 10 days after germination, 146 and 203 proteins were detected, respectively. Five differentially accumulated proteins (> two-fold change; t-test: 95% significance) were identified in 5-day-old and 14 differentially accumulated proteins in 10-day-old coleoptilar nodes of wild-type versus rtcs. All 19 differentially accumulated proteins were identified via ESI MS/MS mass spectrometry. Five differentially accumulated proteins, including a regulatory G-protein and a putative auxin-binding protein, were further analyzed at the RNA expression level. These experiments confirmed differential gene expression and revealed subtle developmental regulation of these genes during early coleoptilar node development. This study represents the first proteomic analysis of shoot-borne root initiation in cereals and will contribute to a better understanding of the molecular basis of this developmental process unique to cereals.     

Microsatellite megatracts in the maize (Zea mays L.) genome.

Long tracts (megatracts) of (CAG)n, (TAG)n, and (GAA)n microsatellite sequences capable of forming composite DNA segments were found in the maize (Zea mays L.) genome. Some of the (CAG)n and (TAG)n megatracts were organized in clusters of up to 1 Mb on several chromosomes, as detected by fluorescence in situ hybridization (FISH), as well as on extended DNA fibers. Extensive polymorphism was found among different maize inbred lines with respect to the number and size of microsatellite megatract clusters on the A chromosomes. Polymorphism was also common among B chromosomes of different nuclei in the inbred line Zapalote Chico. Different retrotransposable elements were often inserted into the microsatellite tracts. Size variation in some (TAG)n and (GAA)n megatracts was observed in consecutive generations among siblings of the inbred lines, indicating that these loci are highly unstable and predisposed to dynamic mutations similar to those described in mammalian systems.     

Biochemical composition of maize (Zea mays L.) pollen

Summary Pollen grains containing either the Wx, wx, Su ₁, su ₁, Sh ₂ or sh ₂ alleles were stored at 0, 1, 2, 3, 4 and 5 days at 2 °C. After each storage period, a portion of pollen from each genotype was analyzed for free amino acid content. Over all genotypes, storage significantly altered the content of all 16 amino acids measured. With increasing storage, a relatively consistent increase in aspartic acid, isoleucine, leucine, phenylalanine, ethanolanine, aminobutyric acid, NH₃ and lysine was found. A relatively consistent decrease in glutamic acid, proline, glycine and alanine occurred with increasing storage. No consistent response to storage was obtained with threonine-serine, valine, histidine and the unknown. Apparently, storage or stage of viability loss has a pronounced effect on amino acid metabolism in maize pollen grains. The experiment was designed so that comparisons free of genetic background effects could be made between alleles at each locus. Significant allele X storage interactions at each locus were found as follows: at the waxy locus, aspartic acid, glycine, alanine and ethanolanine; at the sugary locus, aspartic acid, alanine, ethanolanine and aminobutyric acid; and at the shrunken locus, aspartic acid, alanine, valine, leucine and ethanolanine. Amino acid metabolism is apparently influenced by the action of the alleles at these loci. The differences between the loci in the amino acids affected indicate the different areas of amino acid metabolism are influenced by each locus.Journal Series Paper No. 4425, Florida Agricultural Experiment Station.