Wheat seed transcriptome reveals genes controlling key traits for human preference and crop adaptation

RNA-Seq transcriptome profiling of immature grain wheat is a technique for understanding comparative modeling of baking quality

Improving the baking quality is a primary challenge in the wheat flour production value chain, as baking quality represents a crucial factor in determining its overall value. In the present study, we conducted a comparative RNA-Seq analysis on the high baking quality mutant "O-64.1.10" genotype and its low baking quality wild type "Omid" cultivar to recognize potential genes associated with bread quality. The cDNA libraries were constructed from immature grains that were 15 days post-anthesis, with an average of 16.24 and 18.97 million paired-end short-read sequences in the mutant and wild-type, respectively. A total number of 733 transcripts with differential expression were identified, 585 genes up-regulated and 188 genes down-regulated in the "O-64.1.10" genotype compared to the "Omid". In addition, the families of HSF, bZIP, C2C2-Dof, B3-ARF, BES1, C3H, GRF, HB-HD-ZIP, PLATZ, MADS-MIKC, GARP-G2-like, NAC, OFP and TUB were appeared as the key transcription factors with specific expression in the "O-64.1.10" genotype. At the same time, pathways related to baking quality were identified through Kyoto Encyclopedia of Genes and Genomes. Collectively, we found that the endoplasmic network, metabolic pathways, secondary metabolite biosynthesis, hormone signaling pathway, B group vitamins, protein pathways, pathways associated with carbohydrate and fat metabolism, as well as the biosynthesis and metabolism of various amino acids, have a great deal of potential to play a significant role in the baking quality. Ultimately, the RNA-seq results were confirmed using quantitative Reverse Transcription PCR for some hub genes such as alpha-gliadin, low molecular weight glutenin subunit and terpene synthase (gibberellin) and as a resource for future study, 127 EST-SSR primers were generated using RNA-seq data.

Transcriptome Analysis of Roots from Wheat (Triticum aestivum L.) Varieties in Response to Drought Stress

Under climate change, drought is one of the most limiting factors that influences wheat (Triticum aestivum L.) production. Exploring stress-related genes is vital for wheat breeding. To identify genes related to the drought tolerance response, two common wheat cultivars, Zhengmai 366 (ZM366) and Chuanmai 42 (CM42), were selected based on their obvious difference in root length under 15% PEG-6000 treatment. The root length of the ZM366 cultivar was significantly longer than that of CM42. Stress-related genes were identified by RNA-seq in samples treated with 15% PEG-6000 for 7 days. In total, 11,083 differentially expressed genes (DEGs) and numerous single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) were identified. GO enrichment analysis revealed that the upregulated genes were mainly related to the response to water, acidic chemicals, oxygen-containing compounds, inorganic substances, and abiotic stimuli. Among the DEGs, the expression levels of 16 genes in ZM366 were higher than those in CM42 after the 15% PEG-6000 treatment based on RT-qPCR. Furthermore, EMS-induced mutants in Kronos (T. turgidum L.) of 4 representative DEGs possessed longer roots than the WT after the 15% PEG-6000 treatment. Altogether, the drought stress genes identified in this study represent useful gene resources for wheat breeding.

A pleiotropic QTL increased economic water use efficiency in bread wheat (Triticum aestivum L.)

Wheat is one of the most important food crops in the world and drought can severely impact on wheat productivity. The identification and deployment of genes for improved water use efficiency (WUE) can help alleviate yield loss under water limitation. In this study, a high-density genetic linkage map of wheat recombinant inbred lines (Ningchun 4 x Ningchun 27) containing 8751 specific locus amplified fragment (SLAF) tags (including 14757 SNPs), with a total map distance of 1685 cM and an average inter-marker map distance of 0.19 cM was constructed by SLAF-seq technology. The economic yield WUE and nine related traits under three water treatments was monitored over four years. The results showed that loci conditioning WUE were also associated with grain carbon isotope discrimination (CID), flag leaf chlorophyll content, plant height, 1000-grain weight, grain weight per spike and grain number per spike. One locus on chromosome 2B explained 26.3% WUE variation in multiple environments. Under good soil moisture conditions before flowering, the high CID genotype QWue.acn-2B ^{Ningchun 27}, was associated with WUE, high grain weight per spike, and kilo-grain weight. Under rain-fed conditions, the low CID genotype QWue.acn-2B ^{Ningchun 4} tended to maintain more spike number and was associated with improved WUE and yield. The introduction of good chromosome fragments of QWue.acn-2B into elite lines by molecular marker assisted selection will boost up the cultivation of high-yield and water-saving wheat varieties.

A community resource to mass explore the wheat grain proteome and its application to the late-maturity alpha-amylase (LMA) problem

BACKGROUND

Late-maturity alpha-amylase (LMA) is a wheat genetic defect causing the synthesis of high isoelectric point alpha-amylase following a temperature shock during mid-grain development or prolonged cold throughout grain development, both leading to starch degradation. While the physiology is well understood, the biochemical mechanisms involved in grain LMA response remain unclear. We have applied high-throughput proteomics to 4,061 wheat flours displaying a range of LMA activities. Using an array of statistical analyses to select LMA-responsive biomarkers, we have mined them using a suite of tools applicable to wheat proteins.

RESULTS

We observed that LMA-affected grains activated their primary metabolisms such as glycolysis and gluconeogenesis; TCA cycle, along with DNA- and RNA- binding mechanisms; and protein translation. This logically transitioned to protein folding activities driven by chaperones and protein disulfide isomerase, as well as protein assembly via dimerisation and complexing. The secondary metabolism was also mobilized with the upregulation of phytohormones and chemical and defence responses. LMA further invoked cellular structures, including ribosomes, microtubules, and chromatin. Finally, and unsurprisingly, LMA expression greatly impacted grain storage proteins, as well as starch and other carbohydrates, with the upregulation of alpha-gliadins and starch metabolism, whereas LMW glutenin, stachyose, sucrose, UDP-galactose, and UDP-glucose were downregulated.

CONCLUSIONS

To our knowledge, this is not only the first proteomics study tackling the wheat LMA issue but also the largest plant-based proteomics study published to date. Logistics, technicalities, requirements, and bottlenecks of such an ambitious large-scale high-throughput proteomics experiment along with the challenges associated with big data analyses are discussed.

Pleiotropic effect analysis and marker development for grain zinc and iron concentrations in spring wheat

Wheat (Triticum aestivum L.) is one of the main food crops in the world and a primary source of zinc (Zn) and iron (Fe) in the human body. The genetic mechanisms underlying related traits have been clarified, thereby providing a molecular theoretical foundation for the development of germplasm resources. In this study, a total of 23,536 high-quality DArT markers was used to map quantitative trait loci (QTL) of grain Zn (GZn) and grain Fe (GFe) concentrations in recombinant inbred lines crossed by Avocet/Chilero. A total of 17 QTLs was located on chromosomes 1BL, 2BL, 3BL, 4AL, 4BS, 5AL, 5DL, 6AS, 6BS, 6DS, and 7AS accounting for 0.38-16.62% of the phenotypic variance. QGZn.haust-4AL, QGZn.haust-7AS.1, and QGFe.haust-6BS were detected on chromosomes 4AL, 6BS, and 7AS, accounting for 10.63-16.62% of the phenotypic variance. Four stable QTLs, QGZn.haust-4AL, QGFe.haust-1BL, QGFe.haust-4AL, and QGFe.haust-5DL, were located on chromosomes 1BL, 4AL, and 5DL. Three pleiotropic effects loci for GZn and GFe concentrations were located on chromosomes 1BL, 4AL, and 5DL. Two high-throughput Kompetitive Allele Specific PCR markers were developed by closely linking single-nucleotide polymorphisms on chromosomes 4AL and 5DL, which were validated by a germplasm panel. Therefore, it is the most important that quantitative trait loci and KASP marker for grain zinc and iron concentrations were developed for utilizing in marker-assisted breeding and biofortification of wheat grain in breeding programs.

Impacts of Nitrogen Deficiency on Wheat (Triticum aestivum L.) Grain During the Medium Filling Stage: Transcriptomic and Metabolomic Comparisons

Nitrogen (N) supplementation is essential to the yield and quality of bread wheat (Triticum aestivum L.). The impact of N-deficiency on wheat at the seedling stage has been previously reported, but the impact of distinct N regimes applied at the seedling stage with continuous application on filling and maturing wheat grains is lesser known, despite the filling stage being critical for final grain yield and flour quality. Here, we compared phenotype characteristics such as grain yield, grain protein and sugar quality, plant growth, leaf photosynthesis of wheat under N-deficient and N-sufficient conditions imposed prior to sowing (120 kg/hm²) and in the jointing stage (120 kg/hm²), and then evaluated the effects of this continued stress through RNA-seq and GC-MS metabolomics profiling of grain at the mid-filling stage. The results showed that except for an increase in grain size and weight, and in the content of total sugar, starch, and fiber in bran fraction and white flour, the other metrics were all decreased under N-deficiency conditions. A total of 761 differentially expressed genes (DEGs) and 77 differentially accumulated metabolites (DAMs) were identified. Under N-deficiency, 51 down-regulated DEGs were involved in the process of impeding chlorophyll synthesis, chloroplast development, light harvesting, and electron transfer functions of photosystem, which resulted in the SPAD and Pn value decreased by 32 and 15.2% compared with N-sufficiency, inhibited photosynthesis. Twenty-four DEGs implicated the inhibition of amino acids synthesis and protein transport, in agreement with a 17-42% reduction in ornithine, cysteine, aspartate, and tyrosine from metabolome, and an 18.6% reduction in grain protein content. However, 14 DEGs were implicated in promoting sugar accumulation in the cell wall and another six DEGs also enhanced cell wall synthesis, which significantly increased fiber content in the endosperm and likely contributed to increasing the thousands-grain weight (TGW). Moreover, RNA-seq profiling suggested that wheat grain can improve the capacity of DNA repair, iron uptake, disease and abiotic stress resistance, and oxidative stress scavenging through increasing the content levels of anthocyanin, flavonoid, GABA, galactose, and glucose under N-deficiency condition. This study identified candidate genes and metabolites related to low N adaption and tolerance that may provide new insights into a comprehensive understanding of the genotype-specific differences in performance under N-deficiency conditions.

Dissection of Molecular Processes and Genetic Architecture Underlying Iron and Zinc Homeostasis for Biofortification: From Model Plants to Common Wheat

The micronutrients iron (Fe) and zinc (Zn) are not only essential for plant survival and proliferation but are crucial for human health. Increasing Fe and Zn levels in edible parts of plants, known as biofortification, is seen a sustainable approach to alleviate micronutrient deficiency in humans. Wheat, as one of the leading staple foods worldwide, is recognized as a prioritized choice for Fe and Zn biofortification. However, to date, limited molecular and physiological mechanisms have been elucidated for Fe and Zn homeostasis in wheat. The expanding molecular understanding of Fe and Zn homeostasis in model plants is providing invaluable resources to biofortify wheat. Recent advancements in NGS (next generation sequencing) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms have initiated a revolution in resources and approaches for wheat genetic investigations and breeding. Here, we summarize molecular processes and genes involved in Fe and Zn homeostasis in the model plants Arabidopsis and rice, identify their orthologs in the wheat genome, and relate them to known wheat Fe/Zn QTL (quantitative trait locus/loci) based on physical positions. The current study provides the first inventory of the genes regulating grain Fe and Zn homeostasis in wheat, which will benefit gene discovery and breeding, and thereby accelerate the release of Fe- and Zn-enriched wheats.

Pathways of Photosynthesis in Non-Leaf Tissues

Plants have leaves as specialised organs that capture light energy by photosynthesis. However, photosynthesis is also found in other plant organs. Photosynthesis may be found in the petiole, stems, flowers, fruits, and seeds. All photosynthesis can contribute to the capture of carbon and growth of the plant. The benefit to the plant of photosynthesis in these other tissues or organs may often be associated with the need to re-capture carbon especially in storage organs that have high respiration rates. Some plants that conduct C3 photosynthesis in the leaves have been reported to use C4 photosynthesis in petioles, stems, flowers, fruits, or seeds. These pathways of non-leaf photosynthesis may be especially important in supporting plant growth under stress and may be a key contributor to plant growth and survival. Pathways of photosynthesis have directionally evolved many times in different plant lineages in response to environmental selection and may also have differentiated in specific parts of the plant. This consideration may be useful in the breeding of crop plants with enhanced performance in response to climate change.

Innovations in plant genetics adapting agriculture to climate change

Developing new genotypes of plants is one of the key options for adaptation of agriculture to climate change. Plants may be required to provide resilience in changed climates or support the migration of agriculture to new regions. Very different genotypes may be required to perform in the modified environments of protected agriculture. Consumers will continue to demand taste, convenience, healthy and safe food and sustainably and ethically produced food, despite the greater challenges of climate in the future. Improving the nutritional value of foods in response to climate change is a significant challenge. Genomic sequences of relevant germplasm and an understanding of the functional role of alleles controlling key traits will be an enabling platform for this innovation.

Slower development of lower canopy beans produces better coffee

The production of high-quality coffee is being challenged by changing climates in coffee-growing regions. The coffee beans from the upper and lower canopy at different development stages of the same plants were analyzed to investigate the impact of the microenvironment on gene expression and coffee quality. Compared with coffee beans from the upper canopy, lower canopy beans displayed more intense aroma with higher caffeine, trigonelline, and sucrose contents, associated with greater gene expression in the representative metabolic pathways. Global gene expression indicated a longer ripening in the lower canopy, resulting from higher expression of genes relating to growth inhibition and suppression of chlorophyll degradation during early bean ripening. Selection of genotypes or environments that enhance expression of the genes slowing bean development may produce higher quality coffee beans, allowing coffee production in a broader range of available future environments.

Genetic architecture underpinning yield component traits in wheat

Genetic atlas, reliable QTL and candidate genes of yield component traits in wheat were figured out, laying concrete foundations for map-based gene cloning and dissection of regulatory mechanisms underlying yield. Mining genetic loci for yield is challenging due to the polygenic nature, large influence of environment and complex relationship among yield component traits (YCT). Many genetic loci related to wheat yield have been identified, but its genetic architecture and key genetic loci for selection are largely unknown. Wheat yield potential can be determined by three YCT, thousand kernel weight, kernel number per spike and spike number. Here, we summarized the genetic loci underpinning YCT from QTL mapping, association analysis and homology-based gene cloning. The major loci determining yield-associated agronomic traits, such as flowering time and plant height, were also included in comparative analyses with those for YCT. We integrated yield-related genetic loci onto chromosomes based on their physical locations. To identify the major stable loci for YCT, 58 QTL-rich clusters (QRC) were defined based on their distribution on chromosomes. Candidate genes in each QRC were predicted according to gene annotation of the wheat reference genome and previous information on validation of those genes in other species. Finally, a technological route was proposed to take full advantage of the resultant resources for gene cloning, molecular marker-assisted breeding and dissection of molecular regulatory mechanisms underlying wheat yield.

Genetic diversity of gliadin-coding alleles in bread wheat (Triticum aestivum L.) from Northern Kazakhstan

Background

Spring bread wheat (Triticum aestivum L.) represents the main cereal crop in Northern Kazakhstan. The quality of wheat grain and flour strongly depends on the structure of gluten, comprised of gliadin and glutenin proteins. Electrophoresis spectra of gliadins are not altered by environmental conditions or plant growth, are easily reproducible and very useful for wheat germplasm identification in addition to DNA markers. Genetic polymorphism of two Gli loci encoding gliadins can be used for selection of preferable genotypes of wheat with high grain quality.

Methods

Polyacrylamide gel electrophoresis was used to analyse genetic diversity of gliadins in a germplasm collection of spring bread wheat from Northern Kazakhstan.

Results

The highest frequencies of gliadin alleles were found as follows, in Gli1: -A1f (39.3%), -B1e (71.9%), and -D1a (41.0%); and in Gli-2: -A2q (17.8%), -B2t (13.5%), and -D2q (20.4%). The combination of these alleles in a single genotype may be associated with higher quality of grain as well as better adaptation to the dry environment of Northern Kazakhstan; preferable for wheat breeding in locations with similar conditions.

Genetic Modification for Wheat Improvement: From Transgenesis to Genome Editing

To feed the growing human population, global wheat yields should increase to approximately 5 tonnes per ha from the current 3.3 tonnes by 2050. To reach this goal, existing breeding practices must be complemented with new techniques built upon recent gains from wheat genome sequencing, and the accumulated knowledge of genetic determinants underlying the agricultural traits responsible for crop yield and quality. In this review we primarily focus on the tools and techniques available for accessing gene functions which lead to clear phenotypes in wheat. We provide a view of the development of wheat transformation techniques from a historical perspective, and summarize how techniques have been adapted to obtain gain-of-function phenotypes by gene overexpression, loss-of-function phenotypes by expressing antisense RNAs (RNA interference or RNAi), and most recently the manipulation of gene structure and expression using site-specific nucleases, such as CRISPR/Cas9, for genome editing. The review summarizes recent successes in the application of wheat genetic manipulation to increase yield, improve nutritional and health-promoting qualities in wheat, and enhance the crop's resistance to various biotic and abiotic stresses.