Responses of Arabica coffee (<Emphasis Type="Italic">Coffea arabica</Emphasis> L. var. Catuaí) cell suspensions to chemically induced mutagenesis and salinity stress under <Emphasis Type="Italic">in vitro</Emphasis> culture conditions

Crop improvement of Coffea arabica L. (coffee) via mutagenesis could accelerate breeding programs; thus, the present study aimed to develop an in vitro protocol using the chemical mutagens sodium azide (NaN₃) and ethyl methanesulfonate (EMS) on embryogenic cell suspensions of Arabica coffee variety Catuaí and, subsequently, to evaluate the responses of the resulting mutagenized tissues to salinity stress. Embryogenic suspension cultures were incubated with 0.0, 2.5, 5.0, or 10.0 mM NaN₃ or 0.0, 185.2, 370.5, or 741.0 mM EMS. As the concentration of NaN₃ or EMS increased, the survival of embryogenic suspension cultures decreased compared to controls. The median lethal dose (LD₅₀) for NaN₃ was 5 mM for 15 min and for EMS it was 185.2 mM for 120 min. Embryogenic suspension cultures treated with NaN₃ or EMS were cultured on selective medium supplemented with 0, 50, 100, 150, 250, or 300 mM NaCl showed that 50 mM NaCl could be used as selection pressure. Plantlet growth and total amino acid content were affected by NaCl stress; some mutants had longer shoots and higher amino acid content than controls. Random amplified polymorphic DNA (RAPD) analysis was performed to determine whether the NaN₃ or EMS treatments could induce genetic variability and resulted in identifiable polymorphic markers. A total of 18 10-mer primers were used to amplify genomic DNA of putative mutant and non-mutant arabica coffee embryogenic cultures and produced 50 scorable bands, of which 22% were polymorphic.     

In vitro generation of somaclonal variant plants of sugarcane for tolerance to Fusarium sacchari

Key message

A combination of in vitro culture and mutagenesis using ethyl methanesulfonate (EMS) followed by culture filtrate-mediated selection produced variant sugarcane plants tolerant and resistant to Fusarium sacchari.

Abstract

Eldana saccharina is a destructive pest of the sugarcane crop in South Africa. Fusarium sacchari PNG40 (a fungal strain harmful to E. saccharina) has the potential to be an endophytic biological control agent of the stalk borer. However, the fungus causes Fusarium stalk rot in sugarcane. In the current study, sugarcane plants tolerant and resistant to F. sacchari PNG40 were produced by exposing embryogenic calli to the chemical mutagen ethyl methanesulfonate (EMS), followed by in vitro selection during somatic embryogenesis and plantlet regeneration on media containing F. sacchari culture filtrates (CF). The incorporation of 100 ppm CF in the culture media at the embryo maturation stage, at germination, or at both, resulted in callus necrosis and consequent reduced plantlet yield. Subsequent trimming of the roots of regenerated plants and their exposure to 1,500 ppm CF served as a further selection treatment. Plants produced from EMS-treated calli displayed improved root re-growth in the presence of CF pressure compared with those from non-treated calli. The tolerance of CF-selected plants was confirmed in greenhouse tests by inoculation with F. sacchari PNG40, re-isolation of Fusarium spp. from undamaged tissue of asymptomatic plants and establishment of the identity of fungal isolates as PNG40 using molecular analysis. The restriction of PNG40 presence to the inoculation lesion in some plants suggested their resistance to the fungus. Genotypes exhibiting symptomless endophytic colonization by PNG40 were identified and will be utilised for testing biological control strategies against E. saccharina.     

Somatic embryogenesis and cryostorage of eastern hemlock and Carolina hemlock for conservation and restoration

Key message

Embryogenic cultures of eastern and Carolina hemlocks could be initiated, and somatic embryos and plantlets produced using standard conifer protocols and media. Embryogenic hemlock cultures were cryostored and recovered.

Abstract

Eastern hemlock (Tsuga canadenesis) and Carolina hemlock (Tsuga caroliniana) are threatened with extirpation from their native ranges in eastern North America by the introduction of the hemlock woolly adelgid (HWA; Adelges tsugae), an exotic insect pest that has already killed millions of hemlock trees. Efforts to conserve and restore these members of the Pinaceae could be greatly enhanced by the availability of an in vitro propagation system. We conducted experiments to initiate embryogenic cultures from eastern and Carolina hemlock zygotic embryos at different stages of development using three media supplemented with 2,4-dichlorophenoxyacetic acid (2,4-D) and 6-Benzylaminopurine (BA). Cone collection date, medium and source tree had significant effects on induction of embryogenic tissue from zygotic embryo explants of both species, which ranged as high as 52 % for eastern hemlock and 17 % for Carolina hemlock. Embryogenic hemlock cultures could be cryostored using a protocol employing sorbitol and DMSO, and recovered following several months of frozen storage. Transfer of embryogenic tissue from proliferation media containing 2, 4-D and BA to a Litvay medium with abscisic acid promoted the development of somatic embryos, which were stimulated to mature by slow drying under semi-permeable plastic film. Embryos moved to an imbibition-germination medium without plant growth regulators and incubated in the light elongated and subsequently germinated. A small number of germinated embryos survived transfer to ex vitro conditions and grew into somatic seedlings. The embryogenesis and cryostorage systems developed in the study are already being integrated with hemlock breeding efforts to develop clones with resistance or tolerance to HWA.     

Cloning mature holm oak trees by somatic embryogenesis

Key message

Integuments from holm oak developing ovules were suitable initial explants to obtain embryogenic lines from which plants could be regenerated.

Abstract

The implementation of multivarietal forestry as part of breeding strategies is expected to provide more productive forest plantations. To achieve this, a reliable and effective method for mass production of clonal plants is needed. Somatic embryogenesis is considered the enabling technology for implementing multivarietal forestry. The holm oak (Quercus ilex L.) is a Mediterranean evergreen tree of economic interests because of the acorn production for animal feed and edible fungi mycorrhization. The aim of this work was to obtain clonal plants by inducing somatic embryogenesis in tissues of female flowers from mature trees. The influence of the developmental stage of the explant, the genotype and medium composition, and the effect of arabinogalactan proteins on the induction frequency, were assessed. Somatic embryogenesis induction (frequency ranging from 1.2 to 3.2 %) was restricted to ovules excised at an advanced stage of development, when they were at least 3–4 mm wide and the rest of the ovules within the ovary had aborted. Somatic embryos arose from the integuments of those fertilized ovules. Embryogenic response was obtained on media with and without plant growth regulators. All the genotypes that were cultured on medium containing “as reported by Schenk and Hildebrandt (Can J Bot 50:199–204, 1972)” SH macronutrients could be captured. Treatments including Larix arabinogalactan proteins did not improve induction, while those from Acacia inhibited the embryogenic response. Several embryogenic lines were multiplied by repetitive embryogenesis on medium lacking plant growth regulators. Mature somatic embryos of three genotypes were germinated at frequencies ranging from 41 to 58 %, and converted into plants at frequencies from 11 to 30 %, depending on the genotype.     

Somatic embryogenesis and plant regeneration from suspension cultures of Acanthopanax koreanum Nakai

High-frequency somatic embryogenesis was achieved from an embryogenic cell suspension culture of Acanthopanax koreanum Nakai. Stem segments were cultured on Murashige and Skoog (MS) medium containing auxins and cytokinins. Opaque and friable embryogenic callus formed on MS medium with 4.5 μm 2,4-dichlorophenoxyacetic acid (2,4-D) and 2.0 μm kinetin or zeatin, but was highest on medium containing 4.5 μm 2,4-D alone. Embryogenic calli were transferred to MS liquid medium containing 4.5 μm 2,4-D and maintained by subculture at 2-week intervals. Initiation of somatic embryogenesis and development up to the globular stage from embryogenic cell clumps occurred in medium containing 0.45 μm 2,4-D, whereas maturation and germination of somatic embryos occurred in MS medium lacking 2,4-D. Cytokinin treatment suppressed the normal growth of embryos, but stimulated secondary somatic embryogenesis from the surfaces of primary embryos. Plants from somatic embryos were acclimatized in a greenhouse. Received: 14 January 1997 / Revision received: 17 June 1997 / Accepted: 5 July 1997     

Haploid plants carrying a sodium azide-induced mutation (fdr1) produce fertile pollen grains due to first division restitution (FDR) in maize (Zea mays L.)

Key message

We induced a fdr1 mutation in maize which makes haploid plants male fertile due to first division restitution; the optimum sodium azide treatment on maize kernels has been identified.

Abstract

Sodium azide mutagenesis experiments were performed on haploid and diploid maize plants. Kernels with haploid embryos of maize inbred line B55 were induced by pollinating with RWS pollen. These kernels were treated with 0.2, 0.5, or 1.0 mM sodium azide solution for 2 h. The 0.5 mM solution was optimal for inducing numerous albino sectors on the treated plants without significant damage. Kernels of a maize hybrid, Oh43 × B55, were treated with sodium azide solutions at concentrations of 1.5, 2.0, 2.5, and 3.0 mM. Haploids were generated by pollinating RWS pollen. The highest rate of chlorophyll mutations in seedlings (15.3 % [13/85]) was recorded with the 2.5 mM concentration. A mutated haploid plant (PP1-50) with higher pollen fertility was isolated during the experiments. This haploid plant produced four kernels on the ear after selfing. These kernels were germinated and produced ears with full seed set after selfing. The haploid plants induced from PP1-50 diploids also exhibited high pollen fertility. In situ hybridization studies showed that meiocytes in PP1-50 haploid anthers underwent first division restitution at a rate of 48 % and produced equally divided dyads. We designated the genetic factor responsible for this high pollen fertility as fdr1. PP1-50 haploid ears exhibited high levels of sterility, as seen for regular haploids. Diploid PP1-50 meiocytes in the anther underwent normal meiosis, and all selfed progenies were normal diploids. We concluded that the fdr1 phenotype is only expressed in the anthers of haploid plants and not in the anthers of diploid plants.     

Purple-leaved Ficus lyrata plants produced by overexpressing a grapevine VvMybA1 gene

Key message

This study established an efficient method of regenerating plants of Ficus lyrata and producing purple-leaved F. lyrata plants through genetic transformation using a VvMybA1 gene of grapevine.

Abstract

Ficus lyrata, a species with unique violin- or guitar-shaped leaves, was regenerated from leaf-derived calli cultured on Murashige and Skoog (MS) basal medium supplemented with 4.5 μM N-phenyl-N’-1, 2, 3-thiadiazol-5-yl urea (TDZ) and 0.5 μM α-naphthalene acetic acid (NAA). Leaf discs were inoculated with Agrobacterium tumefaciens strain EHA 105 harboring a binary vector DEAT that contains the VvMybA1 gene and neomycin phosphotransferase (npt II) gene and subsequently cultured on the established regeneration medium supplemented with 100 mg l^?1 kanamycin. Results showed that 87.5 % of the leaf discs produced kanamycin-resistant callus, and 68.8 % of them produced adventitious shoots. Transgenic plants with three leaf colors including green, green-purple, and purple were produced. Regular and quantitative real-time PCR analyses confirmed the integration of transgenes into the host genome. Semi-quantitative RT-PCR analysis indicated that the VvMybA1 gene was responsible for the purple-colored phenotype. Purple-leaved plants with strong color stability grew vigorously in a greenhouse. This study illustrated the feasibility of using a genetically engineered VvMybA1 gene for drastic modification of leaf color of an important woody ornamental plant.     

Visualization of grapevine root colonization by the Saharan soil isolate Saccharothrix algeriensis NRRL B-24137 using DOPE-FISH microscopy

Background and aim

There is currently a gap of knowledge regarding whether some beneficial bacteria isolated from desert soils can colonize epi- and endophytically plants of temperate regions. In this study, the early steps of the colonization process of one of these bacteria, Saccharothrix algeriensis NRRL B-24137, was studied on grapevine roots to determine if this beneficial strain can colonize a non-natural host plant. An improved method of fluorescence in situ hybridization (FISH), the double labeling of oligonucleotide probes (DOPE)-FISH technique was used to visualize the colonization behavior of such bacteria as well as to determine if the method could be used to track microbes on and inside plants.

Methods

A probe specific to Saccharothrix spp. was firstly designed. Visualization of the colonization behavior of S. algeriensis NRRL B-24137 on and inside roots of grapevine plants was then carried out with DOPE-FISH microscopy.

Results

The results showed that 10 days after inoculation, the strain could colonize the root hair zone, root elongation zone, as well as root emergence sites by establishing different forms of bacterial structures as revealed by the DOPE-FISH technique. Further observations showed that the strain could be also endophytic inside the endorhiza of grapevine plants.

Conclusions

Taking into account the natural niches of this beneficial strain, this study exemplifies that, in spite of its isolation from desert soil, the strain can establish populations as well as subpopulations on and inside grapevine plants and that the DOPE-FISH tool can allow to detect it.     

Directed evolution and site-specific mutagenesis of <Emphasis Type="SmallCaps">l</Emphasis>-isoleucine dioxygenase derived from <Emphasis Type="Italic">Bacillus weihenstephanensis</Emphasis>

Objectives

l-isoleucine dioxygenase (IDO) specifically transforms l-isoleucine (Ile) to 4-hydroxyisoleucine (4-HIL), and 4-HIL is a promising drug for diabetes. To enhance the activity and catalytic efficiency of IDO, we used directed evolution and site-specific mutagenesis.

Results

The IDO gene (ido) derived from Bacillus weihenstephanensis was cloned and expressed in Escherichia coli. Directed evolution using error prone (EP)-PCR and site-specific mutagenesis were conducted. Two improved mutants were obtained after one round of EP-PCR, with Ido^N126H exhibiting a 2.8-fold increase in activity. Two improved mutants were obtained through site-specific mutagenesis, with Ido^T130K showing a 170% increase in activity. Although the activity of the combined mutant Ido^N126H/T130K (0.95?±?0.08 U/mg) was slightly higher than that of the wild-type Ido, its catalytic efficiency was 2.4-fold and 3.0-fold higher than Ido with Ile and α-ketoglutaric acid as substrates. After biotransformation of Ile by E. coli BL21(DE3) expressing Ido^N126H/T130K and Ido, 66.50?±?0.99 mM and 26.09?±?1.85 mM 4-HIL was synthesized, respectively, in 24 h.

Conclusion

Ido^N126H/T130K had a higher enzyme activity and catalytic efficiency and can therefore be used as a more suitable candidate for 4-HIL production.

     

Storage of ethyl methanesulphonate-treated barley seeds with 15 per cent moisture. Influence of treatment and washing conditions

Barley seeds were treated with ethyl methanesulphonate (EMS), washed for 24 h, redried to 15 per cent moisture and stored at 25°C. The criteria used for expressing the effect of storage were chromosomal aberrations in root tips, M₁ germination, M₁ seedling height, M₁ survival and the frequency of M₂ chlorophyll mutants. The increase of the M₁ biological injury due to storage was not influenced:

1. by applying EMS solutions at pH 2, pH 7 and pH 10,
2. by lowering the EMS concentration and increasing the treatment time,
3. by different variations of washing with water and by washings with 0.005 N NaOH, 200 mM cysteine or 200 mM thiourea. The rate of the increase of the M₁ injury due to storage depends on the EMS dose. With a decrease in the EMS dose the storage effect is more delayed.

     

Overexpression of citrate operon in Herbaspirillum seropedicae Z67 enhances organic acid secretion,mineral phosphate solubilization and growth promotion of Oryza sativa

Background and aims

Herbaspirillum seropedicae Z67, nitrogen fixing endophyte, significantly promotes the growth of cereals. Organic acid secreting nitrogen fixing rhizobacteria have better plant growth promotion abilities due to mineral phosphate solubilization.

Method

Plasmids pAB7, pJNK3 and pJNK4 containing Escherichia coli cs (gltA), NADH insensitive cs (gltA1), and citrate operon consisting of gltA1 gene along with Salmonella typhimurium Na⁺ dependent citrate transporter (citC) gene under constitutive lac promoter were constructed in broad host range plasmid pUCPM18-Km^r. The plasmid transformants of H. seropedicae Z67 were obtained by electroporation.

Results

Hs (pAB7) and Hs (pJNK3) had increased CS activity but citric acid secretion was not significant. Hs (pJNK3) secreted 45 mM acetic acid while Hs (pJNK4) secreted 2.7 mM citric and 51 mM acetic acids. Hs (pJNK3) and Hs (pJNK4) released 80 μM and 110 μM amount of P from rock phosphate, respectively, in buffered medium under both aerobic and micro aerobic conditions. These transformants showed better plant growth promoting factors. Upon inoculation to rice plants (Gujarat – 17), increase of Fresh weight, Dry weight N, P and K content was observed.

Conclusion

Thus the study demonstrates that artificial citrate operon in H. seropedicae Z67 enhances phosphate solubilization and plant growth promotion abilities.     

Variations in genomic DNA methylation during the long-term in vitro proliferation of oil palm embryogenic suspension cultures

Key message

The long-term proliferation of embryogenic cell suspensions of oil palm is associated with changes in both genomic methylation rates and embryogenic capacities.

Abstract

In the aim of exploring the relationship between epigenetic stability and the long-term in vitro proliferation of plant tissues, we have studied changes in genomic DNA methylation levels in embryogenic suspensions of oil palm (Elaeis guineensis Jacq.). Five embryogenic callus lines were obtained from selected hybrid seeds and then proliferated as suspension cultures. Each clonal line obtained from a single genotype was subdivided into three independent subclonal lines. Once established, cultures proliferated for 12 months and genomic DNA was sampled at 4 months intervals for the estimation of global DNA methylation rates through high performance liquid chromatography (HPLC) quantitation of deoxynucleosides. Our results show that in vitro proliferation induces DNA hypermethylation in a time-dependent fashion. Moreover, this trend is statistically significant in several clonal lines and shared between subclonal lines originating from the same genotype. Interestingly, the only clonal line undergoing loss of genomic methylation in the course of proliferation has been found unable to generate somatic embryos. We discuss the possible implications of genome-wide DNA methylation changes in proliferating cells with a view to the maintenance of genomic and epigenomic stability.     

Characterization of a recombinant l-fucose isomerase from Caldicellulosiruptor saccharolyticus that isomerizes l-fucose, d-arabinose, d-altrose, and l-galactose

A recombinant l-fucose isomerase from Caldicellulosiruptor saccharolyticus was purified as a single 68 kDa band with an activity of 76 U mg^?1. The molecular mass of the native enzyme was 204 kDa as a trimer. The maximum activity for l-fucose isomerization was at pH 7 and 75°C in the presence of 1 mM Mn²⁺. Its half-life at 70°C was 6.1 h. For aldose substrates, the enzyme displayed activity in decreasing order for l-fucose, with a k _cat of 11,910 min^?1 and a K _m of 140 mM, d-arabinose, d-altrose, and l-galactose. These aldoses were converted to the ketoses l-fuculose, d-ribulose, d-psicose, and l-tagatose, respectively, with 24, 24, 85, 55% conversion yields after 3 h.     

Heritability and identification of QTLs and underlying candidate genes associated with the architecture of the grapevine cluster (Vitis vinifera L.)

Key message

We have identified 19 QTLs for rachis architecture, a key and complex trait for grapevine production. Fifty out of 1,173 genes underlying these QTLs are candidates to be further explored.

Abstract

In the table grape industry, the rachis architecture has economic and management implications. Therefore, understanding the genetics of this trait is key for its breeding. The aim of this work was to identify genetic determinants of traits associated with the cluster architecture. Characterisations of eight traits was performed on a ‘Ruby Seedless’ × ‘Sultanina’ crossing (F₁: n = 137) during three seasons, with and without gibberellic acid (GA₃) applications. The genotypic effects and the genotype × GA₃ interactions were significant for several traits. Rachis length (rl), lateral shoulder length and node number along the central axis were the most prominent traits. On average, the heritability of these traits was ~71 %, with heritability of rl being 76 % as estimated under different seasons. Quantitative trait loci (QTLs) analyses showed that linkage group 5 (LG₅) and LG₁₈ harboured the largest number of QTLs for these traits. According to the variance explained, the main QTL (corresponding to rl) was found on LG₉. These QTLs were supported mainly by a paternal additive effect and revealed possible pleiotropic effects. Based on the grapevine reference genome, we identified 1,173 genes located under these QTL confidence intervals. Fifty of the 891 annotated genes of this list were selected for their further characterisation because of their possible participation in the rachis architecture. In conclusion, the QTLs detected indicate that these traits and their GA₃ responsiveness have a clear genetic basis. Due to the percentage of the total variance explained, they are good candidates to participate in the genetic determination of the cluster architecture.     

Cloning and characterisation of a phenylalanine ammonia-lyase gene from Rhus chinensis

Key message

The gene and cDNA sequence encoding PAL from Chinese medicinal plant Rhus chinensis were cloned and analyzed, furthermore the biochemical properties, kinetic parameters, differential expression and key sites were studied.

Abstract

Rhus chinensis is a well-known Chinese medicinal plant. Phenylalanine ammonia-lyase (PAL) is the first enzyme of phenylpropanoid pathway. Several recent studies suggested that PAL also play an important role in plant–aphid interaction. In this study, both the cDNA and the genomic sequence encoding PAL from Rhus chinensis (designated as RcPAL) were cloned and analyzed. The 3,833 bp gene contained a 1,342 bp intron and two extrons. The ORF was 2,124 bp and predicted to encode a 707-amino acid polypeptide. The results of real-time PCR showed that RcPAL expressed in all tested tissues and followed the order: stems > young leaves > petioles > roots > seeds > mature leaves. RcPAL was successfully expressed in E. coli with the pET-28a-RcPAL recombinant vector. The recombinant protein exhibited a high level of PAL activity. Biochemical properties and kinetic parameters of recombinant RcPAL were further studied. The results showed that the optimal temperature and pH for RcPAL activity were 45 °C and 9.0, and the K _m and K _cat values were 7.90 mM and 52.31 s^?1, respectively. The active sites and substrate selectivity site were also investigated with site-directed mutagenesis methods, suggesting that Phe¹²⁶ is responsible for the substrate selectivity. To our knowledge, this was the first full-length PAL gene cloned and characterized from the family Anacardiaceae so far.     

Transportable and Non-transportable Inhibitors of L-glutamate Uptake Produce Astrocytic Stellation and Increase EAAT2 Cell Surface Expression

Astrocytic excitatory amino acid transporters (EAATs) regulate excitatory transmission and limit excitotoxicity. Evidence for a functional interface between EAATs and glial fibrillary acidic protein (GFAP) relevant to astrocytic morphology led to investigations of actions of transportable (d-Aspartate (d-Asp) and (2S,3S,4R)-2-(carboxycyclopropyl)glycine (l-CCG-III)) and non-transportable (dl-threo-β-benzyloxyaspartate (dl-TBOA)) inhibitors of Glu uptake in murine astrocytes. d-Asp (1 mM), l-CCG-III (0.5 mM) and dl-TBOA (0.5 mM) produced time-dependent (24–72 h) reductions in ³[H]d-Asp uptake (approximately 30–70%) with little or no gliotoxicity. All drugs induced a profound change in phenotype from cobblestone to stellate morphology and image analysis revealed increases in the intensity of GFAP immunolabelling for l-CCG-III and dl-TBOA. Cytochemistry indicated localized changes in F-actin distribution. Cell surface expression of EAAT2, but not EAAT1, was elevated at 72 h. Blockade of Glu uptake by both types of EAAT inhibitor exerts longer-term effects on astrocytic morphology and a compensatory homeostatic rise in EAAT2 abundance.     

Directed evolution of GH43 β-xylosidase XylBH43 thermal stability and L186 saturation mutagenesis

Directed evolution of β-xylosidase XylBH43 using a single round of gene shuffling identified three mutations, R45K, M69P, and L186Y, that affect thermal stability parameter K _t ^0.5 by ?1.8 ± 0.1, 1.7 ± 0.3, and 3.2 ± 0.4 °C, respectively. In addition, a cluster of four mutations near hairpin loop-D83 improved K _t ^0.5 by ~3 °C; none of the individual amino acid changes measurably affect K _t ^0.5 . Saturation mutagenesis of L186 identified the variant L186K as having the most improved K _t ^0.5 value, by 8.1 ± 0.3 °C. The L186Y mutation was found to be additive, resulting in K _t ^0.5 increasing by up to 8.8 ± 0.3 °C when several beneficial mutations were combined. While k _cat of xylobiose and 4-nitrophenyl-β-d-xylopyranoside were found to be depressed from 8 to 83 % in the thermally improved mutants, K _m, K _ss (substrate inhibition), and K _i (product inhibition) values generally increased, resulting in lessened substrate and xylose inhibition.     

Population structure and association mapping of yield contributing agronomic traits in foxtail millet

Key message

Association analyses accounting for population structure and relative kinship identified eight SSR markers ( p < 0.01) showing significant association ( R ²  = 18 %) with nine agronomic traits in foxtail millet.

Abstract

Association mapping is an efficient tool for identifying genes regulating complex traits. Although association mapping using genomic simple sequence repeat (SSR) markers has been successfully demonstrated in many agronomically important crops, very few reports are available on marker-trait association analysis in foxtail millet. In the present study, 184 foxtail millet accessions from diverse geographical locations were genotyped using 50 SSR markers representing the nine chromosomes of foxtail millet. The genetic diversity within these accessions was examined using a genetic distance-based and a general model-based clustering method. The model-based analysis using 50 SSR markers identified an underlying population structure comprising five sub-populations which corresponded well with distance-based groupings. The phenotyping of plants was carried out in the field for three consecutive years for 20 yield contributing agronomic traits. The linkage disequilibrium analysis considering population structure and relative kinship identified eight SSR markers (p < 0.01) on different chromosomes showing significant association (R ² = 18 %) with nine agronomic traits. Four of these markers were associated with multiple traits. The integration of genetic and physical map information of eight SSR markers with their functional annotation revealed strong association of two markers encoding for phospholipid acyltransferase and ubiquitin carboxyl-terminal hydrolase located on the same chromosome (5) with flag leaf width and grain yield, respectively. Our findings on association mapping is the first report on Indian foxtail millet germplasm and this could be effectively applied in foxtail millet breeding to further uncover marker-trait associations with a large number of markers.     

Site-directed mutagenesis in <Emphasis Type="Italic">Petunia</Emphasis> × <Emphasis Type="Italic">hybrida</Emphasis> protoplast system using direct delivery of purified recombinant Cas9 ribonucleoproteins

Key message

Site-directed mutagenesis of nitrate reductase genes using direct delivery of purified Cas9 protein preassembled with guide RNA produces mutations efficiently in Petunia × hybrida protoplast system.

Abstract

The clustered, regularly interspaced, short palindromic repeat (CRISPR)-CRISPR associated endonuclease 9 (CRISPR/Cas9) system has been recently announced as a powerful molecular breeding tool for site-directed mutagenesis in higher plants. Here, we report a site-directed mutagenesis method targeting Petunia nitrate reductase (NR) gene locus. This method could create mutations efficiently using direct delivery of purified Cas9 protein and single guide RNA (sgRNA) into protoplast cells. After transient introduction of RNA-guided endonuclease (RGEN) ribonucleoproteins (RNPs) with different sgRNAs targeting NR genes, mutagenesis at the targeted loci was detected by T7E1 assay and confirmed by targeted deep sequencing. T7E1 assay showed that RGEN RNPs induced site-specific mutations at frequencies ranging from 2.4 to 21 % at four different sites (NR1, 2, 4 and 6) in the PhNR gene locus with average mutation efficiency of 14.9 ± 2.2 %. Targeted deep DNA sequencing revealed mutation rates of 5.3–17.8 % with average mutation rate of 11.5 ± 2 % at the same NR gene target sites in DNA fragments of analyzed protoplast transfectants. Further analysis from targeted deep sequencing showed that the average ratio of deletion to insertion produced collectively by the four NR-RGEN target sites (NR1, 2, 4, and 6) was about 63:37. Our results demonstrated that direct delivery of RGEN RNPs into protoplast cells of Petunia can be exploited as an efficient tool for site-directed mutagenesis of genes or genome editing in plant systems.