Barley stripe mosaic virus (BSMV) is the type member of the genus Hordeivirus. Brachypodium distachyon line Bd3-1 shows resistance to the BSMV ND18 strain, but is susceptible to an ND18 double mutant (β NDTGB1R390K, T392K) in which lysine is substituted for an arginine at position 390 and for threonine at position 392 of the triple gene block 1 (TGB1) protein. In order to understand differences in gene expression following infection with ND18 and double mutant ND18, Bd3-1 seedlings were subjected to RNA-seq analyses at 1, 6, and 14 days post inoculation (dpi). The results revealed that basal immunity genes involved in cellulose synthesis and pathogenesis-related protein biosynthesis were enhanced in incompatible interactions between Bd3-1 and ND18. Most of the differentially expressed transcripts are related to trehalose biosynthesis, ethylene, jasmonic acid metabolism, protein phosphorylation, protein ubiquitination, transcriptional regulation, and transport process, as well as pathogenesis-related protein biosynthesis. In compatible interactions between Bd3-1 and ND18 mutant, Bd3-1 developed weak basal resistance responses to the virus. Many genes involved in cellulose biosynthesis, protein amino acid phosphorylation, protein biosynthesis, protein glycosylation, glycolysis and cellular macromolecular complex assembly that may be related to virus replication, assembly and movement were up-regulated. Some genes involved in oxidative stress responses were also up-regulated at 14 dpi. BSMV ND18 mutant infection suppressed expression of genes functioning in regulation of transcription, protein kinase, cellular nitrogen compound biosynthetic process and photosynthesis. Differential expression patterns between compatible and incompatible interactions in Bd3-1 to the two BSMV strains provide important clues for understanding mechanism of resistance to BMSV in the model plant Brachypodium.
Among various functional genomics tools used to characterize genes in plants, transposon-based mutagenesis approaches offer great potential, especially in barley and wheat, which possess large genomes and in which genetic transformation is not routine. Two Ds transposon flanking sequences (TNPs), TNP-29 (27.4 cM (centiMorgan)) and TNP-79 (70.3 cM), were mapped in the vicinity of a malting quality QTL located on chromosome 4H of barley. Reactivation of the Ds transposon sequence from these TNP lines led to the identification of genes in the malting QTL regions. Several Ds (dissociation) lines were generated by crossing TNP-29 and TNP-79 with an AcTPase (activator) expressing line (25-B), and F2 progenies were subsequently screened for Ds insertions at new locations. To further characterize these Ds mutants, we mapped the new Ds flanking sequences on a barley genetic map and found that 29% of Ds were located in regions associated with the malting QTL located on chromosome 4H and in close proximity to other important malting-associated QTL across the barley chromosome. Using a sequence based approach, a linkage map was generated that confirmed the position of Ds loci in the barley genome map. Locating these Ds loci on the barley map opens avenues to dissect important malting QTL for facilitating identification of candidate malting genes.
Nuclear factor Y (NF-Y) is a ubiquitous transcription factor that regulates important physiological and developmental processes. In this study, we identified 34 OsNF-Y genes in rice, including 6 newly identified genes. Expression profile analysis covering the whole life cycle revealed that transcripts of OsNF-Y differentially accumulated in a tissue-specific, preferential or constitutive manner. In addition, gene duplication studies and expression analyses were performed to determine the evolutionary origins of the OsNF-Y gene family. Nine OsNF-Y genes were differentially expressed after treatment of seedlings with one or more abiotic stresses such as drought, salt and cold. Analysis of expression correlation and Gene Ontology annotation suggested that OsNF-Y genes were co-expressed with genes that participated in stress, accumulation of seed storage reserves, and plant development. Co-expression analysis also revealed that OsNF-Y genes might interact with each other, suggesting that NF-Y subunits formed complexes that take part in transcriptional regulation. These results provide useful information for further elucidating the function of the NF-Y family and their regulatory pathways.
The genus Chenopodium comprises about 150 species, of which Chenopodium quinoa and C. album are important for their nutritional value. Evaluation of variation in qualitative morphological traits of plants and SNPs in chloroplast rbcL and matK gene sequences in 19 accessions representing C. quinoa and C. album indicated that the accessions IC-411824 and IC-411825, which have white seeds, belong to C. quinoa rather than C. album. This observation was also supported by a time tree that indicated IC-411824 and IC-411825 to be a sister clade to accessions of C. quinoa with an estimated age of 1.2 Mya. Whereas multiple alignments of rbcL gene sequences from the 19 accessions revealed 1.26% parsimony-informative sites with 0.68% interspecific sequence diversity, alignment of nucleotide sequences of amplicons representing the matK gene revealed 4.97% parsimony-informative sites and 2.81% interspecific sequence diversity. Validation of SNPs in the cp rbcL and matK regions of 36 accessions belonging to C. quinoa and C. album was performed by allele-specific PCR with primers carrying a single base change at the 3′ end. We report the first C. quinoa-specific SNP-based primer, R1RQ-AFR, designed from rbcL sequences, that could differentiate quinoa from 64 genera including 13 species of the genus Chenopodium. With an estimated age of 10.5-4.1 million years (Myr), the Himalayan chenopods are evolutionarily younger than the Andean chenopods. The results establish the paraphyletic origin of the genus Chenopodium.
Variation in weather conditions during grain filling has substantial effects on maize kernel weight (KW). The objective of this work was to characterize variation in KW with sowing date-associated weather conditions and examine the relationship between KW, grain filling parameters, and weather factors. Maize was sown on eight sowing dates (SD) at 15-20-day intervals from mid-March to mid-July during 2012 and 2013 in the North China Plain. With sowing date delay, KW increased initially and later declined, and the greatest KW was obtained at SD6 in both years. The increased KW at SD6 was attributed mainly to kernel growth rate (Gmean), and effective grain-filling period (P). Variations in temperature and radiation were the primary factors that influenced KW and grain-filling parameters. When the effective cumulative temperature (AT) and radiation (Ra) during grain filling were 950°C and 1005.4 MJ m−2, respectively, P and KW were greatest. High temperatures (daily maximum temperature [Tmax]>30.2°C) during grain filling under early sowing conditions, or low temperatures (daily minimum temperature [Tmin]<20.7°C) under late sowing conditions combined with high diurnal temperature range (Tmax-min>7.1°C) decreased kernel growth rate and ultimately final KW. When sowing was performed from May 25 through June 27, higher KW and yield of maize were obtained. We conclude that variations in environmental conditions (temperature and radiation) during grain filling markedly affect growth rate and duration of grain filling and eventually affect kernel weight and yield of maize.
The size and distribution of leaf area determine light interception in a crop canopy and influence overall photosynthesis and yield. Optimized plant architecture renders modern maize hybrids (Zea mays L.) more productive, owing to their tolerance of high plant densities. To determine physiological and yield response to maize plant architecture, a field experiment was conducted in 2010 and 2011. With the modern maize hybrid ZD958, three plant architectures, namely triangle, diamond and original plants, were included at two plant densities, 60,000 and 90,000 plants ha− 1. Triangle and diamond plants were derived from the original plant by spraying the chemical regulator Jindele (active ingredients, ethephon, and cycocel) at different vegetative stages. To assess the effects of plant architecture, a light interception model was developed. Plant height, ear height, leaf size, and leaf orientation of the two regulated plant architectures were significantly reduced or altered compared with those of the original plants. On average across both plant densities and years, the original plants showed higher yield than the triangle and diamond plants, probably because of larger leaf area. The two-year mean grain yield of the original and diamond plants were almost the same at 90,000 plants ha− 1 (8714 vs. 8798 kg ha− 1). The yield increase (up to 5%) of the diamonds plant at high plant densities was a result of increased kernel number per ear, which was likely a consequence of improved plant architecture in the top and middle canopy layers. The optimized light distribution within the canopy can delay leaf senescence, especially for triangle plants. The fraction of incident radiation simulated by the interception model successfully reflected plant architecture traits. Integration of canopy openness is expected to increase the simulation accuracy of the present model. Maize plant architecture with increased tolerance of high densities is probably dependent on the smaller but flatter leaves around the ear.
Carotenoids are antioxidants and vitamin A precursors that have important roles in human health. Hence, improving the carotenoid contents in maize kernels is a priority objective for breeders in order to obtain nutritional biofortification outcomes. In the current study, the genetic architecture of carotenoids in maize kernels was explored using a recombinant inbred line (RIL) population derived from a cross between inbred lines By804 and B73. A total of 81 QTLs were detected by using a high-density bin map and a simple sequence repeat (SSR)-based linkage map, with one to seven QTLs for each trait explaining 4.21%-47.53% of the phenotypic variation. A comparison of the QTL mapping efficiency between the two linkage maps revealed that the high-density bin map had higher resolution. In the current study 46 additional QTLs were identified, with 16 being common with previous studies and 14 newly identified. Among the results, 29.6% (24/81) of QTLs explained > 10% of the phenotypic variation in the RIL population, and 70.4% (57/81) explained ≤ 10%. These results suggest that a few large-effect QTLs, together with a variable number of minor-effect QTLs, contributed to most of the genetic components of carotenoids in maize kernels.
Wheat (Triticum aestivum L.) lines T1, T4, and T6 were genetically modified to increase glycine betaine (GB) synthesis by introduction of the BADH (betaine aldehyde dehydrogenase, BADH) gene from mountain spinach (Atriplex hortensis L.). These transgenic lines and WT of wheat (T. aestivum L.) were used to study the effect of increased GB synthesis on wheat tolerance to salt stress. Salt stress due to 200 mmol L− 1 NaCl impaired the photosynthesis of the four wheat lines, as indicated by declines in net photosynthetic rate (Pn), stomatal conductance (Gs), maximum photochemical efficiency of PSII (Fv/Fm), and actual photochemical efficiency of PSII (ФPSII) and an increase in intercellular CO2 concentration (Ci). In comparison with WT, the effect of salinity on the three transgenic lines was mild. Salt stress caused disadvantageous changes in lipids and their fatty acid compositions in the thylakoid membrane of the transgenic lines and WT. Under salt stress, the three transgenic lines showed slightly higher chlorophyll and carotenoid contents and higher Hill reaction activities and Ca2 +-ATPase activity than WT. All the results suggest that overaccumulation of GB resulting from introduction of the BADH gene can enhance the salt tolerance of transgenic plants, especially in the protection of the components and function of thylakoid membranes, thereby making photosynthesis better. Changes in lipids and fatty acid compositions in the thylakoid membrane may be involved in the increased salt stress tolerance of the transgenic lines.
Inversions are DNA rearrangements that are essential for plant gene evolution and adaptation to environmental changes. We demonstrate the creation of targeted inversions and previously reported targeted deletion mutations via delivery of a pair of RNA-guided endonucleases (RGENs) of CRISPR/Cas9. The efficiencies of the targeted inversions were 2.6% and 2.2% in the Arabidopsis FLOWERING TIME (AtFT) and TERMINAL FLOWER 1 (AtTFL1) loci, respectively. Thus, we successfully established an approach that can potentially be used to introduce targeted DNA inversions of interest for functional studies and crop improvement.
The availability of stable cytoplasmic male sterile (CMS or A) lines coupled with a robust restoration system (R lines) is an essential prerequisite for efficient hybrid breeding. CMS-enabled hybrid technology holds immense potential to enhance the long-stagnant productivity of pigeonpea. In the present investigation, cytoplasmic substitutions were made in the nuclear backgrounds of early-maturing pigeonpea varieties or lines. Three new CMS lines (ICPL 88039A, Pusa 992A, and DPP 3-2A) resulted from genetic crosses involving cytoplasmic donors from A2 (GT 288A) and A4 (ICPA 2089) categories. In addition to visual inspection of anthers, pollen-staining techniques and scanning electron microscopy (SEM) analysis were used to confirm pollen sterility. Further, given the relevance of the plant mitochondrial genome to CMS manifestation, 25 mitochondrion-specific DNA markers were assayed on these newly developed A lines and isogenic maintainer (B) lines. DNA polymorphism between Pusa 992A and Pusa 992B as revealed by the nad7a_del marker confirmed the successful combination of sterilizing cytoplasm (A4) and nonrestoring nuclear background (Pusa 992). Such cytoplasm-specific DNA markers are required for A2-CMS as well. Further, to assess restoration ability, potential restorers were crossed with these CMS lines, and as a consequence, promising A × R combinations exhibiting 100% pollen fertility could be identified. In parallel, we also analyzed the inheritance patterns underlying fertility restoration using ICPL 88039A-derived F2 and BC1F1 populations, and established a monogenic dominant model to explain the phenomenon of A2-CMS restoration. In summary, we report the successful development of new CMS lines and describe their effective deployment in hybrid breeding of pigeonpea.
