Targeted mapping approaches to identify DNA markers linked to the Rfp1 restorer gene for the ‘Polima’ CMS of canola (Brassica napus L.)

 We have used two targeting approaches [pairs of nearly isogenic lines (NILs) and bulked segregant analysis] to identify DNA markers linked to the Rfp1 restorer gene for the pol CMS of canola (Brassica napus L.). We were able to target the Rfp1 locus as efficiently by comparing NILs as by bulked segregant analysis, and it was demonstrated in this instance that double-screening strategies could significantly improve the overall targeting efficiency. The chance occurrence of shared homozygosity at specific unlinked chromosomal regions in the bulks was found to limit the efficiency of bulked segregant analysis, while the efficiency of NIL comparison was limited by residual DNA from the donor cultivar at scattered sites throughout the genome of the NILs. Received: 6 June 1997 / Accepted: 12 February 1998     

Mutational analysis of <Emphasis Type="Italic">Arabidopsis PP2CA2</Emphasis> involved in abscisic acid signal transduction

The homozygous T-DNA mutant of the PP2CA2 gene in Arabidopsis thaliana was identified at DNA and RNA levels. The semi-quantitative RT-PCR analysis showed expression of PP2CA2 was induced by NaCl and ABA. When grown in presence of increasing concentration of exogenous ABA the pp2ca2 mutant showed a significant loss of ABA sensitivity in terms of seed germination, efficiency of post-germination growth and root growth. In presence of all ABA and NaCl concentrations tested the germination percentage of wild-type seeds was lower than that of mutant ppca2 seeds. Furthermore, in the presence of exogenous ABA, the pp2ca2 seeds showed higher germination percentages than wild-type at different stages of development and the pp2ca2 seedlings showed a reduced inhibition of root growth compared with wild-type plants. The above results indicated that the pp2ca2 was an ABA-hyposensitive mutant.     

Mapping a high oleic acid mutation in winter oilseed rape (Brassica napus L.)

Two winter oilseed rape mutant lines, 7488 and 19661, with a high oleic (HO) acid content in the seed oil were characterized phenotypically. In both mutant lines the HO trait was monogenically inherited. Segregation analysis in an F₂ population derived from a cross between 7488 and 19661 showed the two mutations to be allelic. From a comparison of seed, leaf and root fatty acid composition it was concluded that fad2, the endoplasmic oleic acid desaturase, is affected by the mutation. In a bulked segregant analysis three AFLP markers linked to this mutation were detected and localized on the genetic map of Brassica napus. The markers mapped near the locus of one copy of the fad2 gene in the rapeseed genome. Received: 16 February 2000 / Accepted: 28 March 2000     

Identification and Expression Analysis of Abscisic Acid Signal Transduction Genes in Hemp Seeds

Abscisic acid (ABA) is involved in regulating diverse biological processes, but its signal transduction genes and roles in hemp seed germination are not well known. Here, the ABA signaling pathway members, PYL, PP2C and SnRK2 gene families, were identified from the hemp reference genome, including 7 CsPYL (pyrab-actin resistance1-like, ABA receptor), 8 CsPP2CA (group A protein phosphatase 2c), and 7 CsSnRK2 (sucrose nonfermenting1-related protein kinase 2). The content of ABA in hemp seeds in germination stage is lower than that in non-germination stage. Exogenous ABA (1 or 10 μM) treatment had a significant regulatory effect on the selected PYL, PP2C, SnRK2 gene families. CsAHG3 and CsHAI1 were most significantly affected by exogenous ABA treatment. Yeast two-hybrid experiments were performed to reveal that CsPYL5, CsSnRK2.2, and CsSnRK2.3 could interact with CsPP2CA7 and demonstrate that this interaction was ABA-independent. Our results indicated that CsPYL5, CsSnRK2.2, CsSnRK2.3 and CsPP2CA7 might involve in the ABA signaling transduction pathway of hemp seeds during the hemp seed germination stages. This study suggested that novel genetic views can be brought into investigation of ABA signaling pathway in hemp seeds and lay the foundation for further exploration of the mechanism of hemp seed germination.     

Nitrate,abscisic acid and gibberellin interactions on the thermoinhibition of lettuce seed germination

Germination of lettuce seeds has obvious thermoinhibition, but the mechanism for thermoinhibition of seed germination is poorly understood. Here, we investigated the interactions of nitrate, abscisic acid (ABA) and gibberellin on seed germination at high temperatures to understand further the mechanism for thermoinhibition of seed germination. Our results showed that lettuce (Lactuca sativa L. ‘Jianye Xianfeng No. 1’) seeds exhibited notable thermoinhibiton of germination at ≥17°C in darkness, and at ≥23°C in light, but the thermoinhibited seeds did not exhibit secondary dormancy. Thermoinhibition of seed germination at 23 or 25°C in light was notably decreased by 5 and 10 mM nitrate, and the stimulatory effects were markedly prevented by nitric oxide (NO) scavenger 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide. The sensitivity of seed germination to exogenous ABA increased with increasing temperature. Thermoinhibition of seed germination was markedly decreased by fluridone (an inhibitor of ABA biosynthesis) and GA₃, and was increased by diniconazole (an inhibitor of the ABA-catabolizing enzyme ABA 8′-hydroxylase) and paclobutrazol (an inhibitor of GA biosynthetic pathway). The effect of fluridone in decreasing thermoinhibition of seed germination was obviously antagonized by paclobutrazol, and that of GA₃ was notably added to by fluridone, and that of nitrate was antagonized by paclobutrazol, diniconazole and ABA and was added to by GA₃ and fluridone. Our data show that thermoinhibition of lettuce seed germination is decreased by nitrate in a NO-dependent manner, which is antagonized by ABA, diniconazole and paclobutrazol and added by fluridone.     

Analysis of phytochrome- and ABA-deficient mutants suggests that ABA degradation is controlled by light in Nicotiana plumbaginifolia

The phytochrome chromophore-deficient mutant, pew1, of Nicotiana plumbaginifolia exhibited decreased germination and slower dehydration of detached leaves during water stress as compared with the wild-type. These physiological processes are controlled by abscisic acid (ABA) and we examined, therefore, whether phytochrome plays a specific role in the regulation of ABA metabolism using the pew1 mutant. The ABA contents of mature seeds and young leaves were analysed and in both cases mutant material was found to contain higher amounts of ABA as compared with the wild-type. This indicates that the phytochrome activation can lead to a decrease of the ABA level in the wild-type plant. The role of phytochromes was investigated in greater detail using the ABA-deficient mutant aba1 of N. plumbaginifolia exhibiting an early and synchronous germination. This mutant accumulates at very high levels a metabolite derived from a precursor (ABA-aldehyde) in the ABA biosynthetic pathway. The first biochemical characterization of this molecule, which corresponds to the glucose-conjugated ABA-alcohol (ABA-AG) is described. A pew1-aba1 double mutant exhibiting both an etiolated growth and early germination was also obtained. The comparable accumulation of ABA-AG in the pew1-aba1 double mutant as compared with the aba1 mutant allowed the proposition that, in a wild-type plant, the phytochrome-mediated light signal enhances ABA degradation rather than inhibits its biosynthesis.     

Seed dormancy in Acer: Endogenous germination inhibitors and dormancy in Acer pseudoplatanus L.

Summary Dormant seeds of Acer pseudoplatanus L. contain two zones of inhibition on paper chromatograms in 10:1:1 as detected by the lettuce and cress seed germination, and the wheat coleoptile bioassays. One zone at R_f 0.6–0.8 was partitioned into ethyl acetate at acid pH and was shown to contain ABA by its behaviour on GLC and isomerization under ultra-violet light. The other zone at R_f 0.9 was detected only in the germination bioassays and was partitioned into ethyl acetate over a range of pH indicating the presence of one or more neutral compounds.The inhibitors present in the embryo of dormant sycamore seeds inhibited the germination of non-dormant sycamore seeds at relatively low concentrations. A comparison with the effects of application of exogenous ABA indicated that endogenous ABA could not solely account for the inhibitory activity of seed extracts, which appeared to be due partly to the presence of ABA and partly to that of neutral compounds present in the embryo. Leaching treatments that removed dormancy led to a decrease in the level of inhibitors present mainly in the basic fraction. The exogenous application of kinetin to dormant sycamore seeds increased germination whereas gibberellic acid had no effect. Similar responses were obtained with lettuce seeds inhibited by the basic fraction of dormant sycamore seeds.It is suggested that an inhibitor-cytokinin interaction may be involved in the dormancy of sycamore seeds.     

CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula

Processing of double‐stranded RNA precursors into small RNAs is an essential regulator of gene expression in plant development and stress response. Small RNA processing requires the combined activity of a functionally diverse group of molecular components. However, in most of the plant species, there are insufficient mutant resources to functionally characterize each encoding gene. Here, mutations in loci encoding protein machinery involved in small RNA processing in soya bean and Medicago truncatula were generated using the CRISPR/Cas9 and TAL‐effector nuclease (TALEN) mutagenesis platforms. An efficient CRISPR/Cas9 reagent was used to create a bi‐allelic double mutant for the two soya bean paralogous Double‐stranded RNA‐binding2 (GmDrb2a and GmDrb2b) genes. These mutations, along with a CRISPR/Cas9‐generated mutation of the M. truncatula Hua enhancer1 (MtHen1) gene, were determined to be germ‐line transmissible. Furthermore, TALENs were used to generate a mutation within the soya bean Dicer‐like2 gene. CRISPR/Cas9 mutagenesis of the soya bean Dicer‐like3 gene and the GmHen1a gene was observed in the T₀ generation, but these mutations failed to transmit to the T₁ generation. The irregular transmission of induced mutations and the corresponding transgenes was investigated by whole‐genome sequencing to reveal a spectrum of non‐germ‐line‐targeted mutations and multiple transgene insertion events. Finally, a suite of combinatorial mutant plants were generated by combining the previously reported Gmdcl1a, Gmdcl1b and Gmdcl4b mutants with the Gmdrb2ab double mutant. Altogether, this study demonstrates the synergistic use of different genome engineering platforms to generate a collection of useful mutant plant lines for future study of small RNA processing in legume crops.     

MutMap+: Genetic Mapping and Mutant Identification without Crossing in Rice

Advances in genome sequencing technologies have enabled researchers and breeders to rapidly associate phenotypic variation to genome sequence differences. We recently took advantage of next-generation sequencing technology to develop MutMap, a method that allows rapid identification of causal nucleotide changes of rice mutants by whole genome resequencing of pooled DNA of mutant F2 progeny derived from crosses made between candidate mutants and the parental line. Here we describe MutMap+, a versatile extension of MutMap, that identifies causal mutations by comparing SNP frequencies of bulked DNA of mutant and wild-type progeny of M3 generation derived from selfing of an M2 heterozygous individual. Notably, MutMap+ does not necessitate artificial crossing between mutants and the wild-type parental line. This method is therefore suitable for identifying mutations that cause early development lethality, sterility, or generally hamper crossing. Furthermore, MutMap+ is potentially useful for gene isolation in crops that are recalcitrant to artificial crosses.     

Fast Isogenic Mapping-by-Sequencing of Ethyl Methanesulfonate-Induced Mutant Bulks

Mapping-by-sequencing (or SHOREmapping) has revitalized the powerful concept of forward genetic screens in plants. However, as in conventional genetic mapping approaches, mapping-by-sequencing requires phenotyping of mapping populations established from crosses between two diverged accessions. In addition to the segregation of the focal phenotype, this introduces natural phenotypic variation, which can interfere with the recognition of quantitative phenotypes. Here, we demonstrate how mapping-by-sequencing and candidate gene identification can be performed within the same genetic background using only mutagen-induced changes as segregating markers. Using a previously unknown suppressor of mutants of like heterochromatin protein1 (lhp1), which in its functional form is involved in chromatin-mediated gene repression, we identified three closely linked ethyl methanesulfonate-induced changes as putative candidates. In order to assess allele frequency differences between such closely linked mutations, we introduced deep candidate resequencing using the new Ion Torrent Personal Genome Machine sequencing platform to our mutant identification pipeline and thereby reduced the number of causal candidate mutations to only one. Genetic analysis of two independent additional alleles confirmed that this mutation was causal for the suppression of lhp1.In Arabidopsis (Arabidopsis thaliana) research, ethyl methanesulfonate (EMS) mutagenesis is a powerful tool that has been widely explored to uncover the functionality of many genes in a broad spectrum of pathways (Page and Grossniklaus, 2002). Recent advances in sequencing technology have greatly reduced the time required to pinpoint induced mutations. In a proof-of-principle experiment, mapping-by-sequencing (SHOREmapping) was first demonstrated on a mutant in the background of the Arabidopsis reference accession Columbia (Col-0) crossed to the diverged accession Landsberg erecta. A pool of DNA isolated from bulked segregants was sequenced and used for the simultaneous mapping and mutant identification (Schneeberger et al., 2009b). This first application was followed by other studies successfully applying similar methods (Cuperus et al., 2010; Austin et al., 2011).Although all described approaches are straightforward and extremely fast, their application is hindered by the requirement for interaccession crosses that impedes the success rate of screens based on quantitative traits, such as screens for genetic modifiers. The major obstacle is that the considerable phenotypic variation in F2 populations from crosses between diverged accessions impairs the recognition of mutants with subtle phenotypic alterations. In addition, if genetic screens involve modifiers of a preexisting mutant, the mapping depends on the availability of the primary mutant in another suitable accession, the introgression of the mutation in such a background, or the laborious additional genotyping for the presence of the first-site mutation.Avoiding these disadvantages, Ashelford et al. (2011) have demonstrated that the isolation of a causative EMS-induced change is possible by direct resequencing of a complete mutant genome. However, their approach initially resulted in 103 putative causal mutations that had the potential to change the amino acid sequences of 48 putative proteins. In addition, the mutations were clustered in two separate regions of the genome, even though the mutant had been backcrossed four times to the parental line.Recently, Abe et al. (2012) reduced the large number of candidate mutations by backcrossing mutant genomes to their nonmutagenized progenitor, followed by sequencing bulk segregants from these crosses. This drastically reduced the number of causal candidates, although it was not possible to pinpoint the causal change from the sequencing data alone. The main problem remains the short-read coverage at each of the candidate mutations, which is typically lower than the number of individuals combined within the bulked DNA. This hinders accurate allele frequency estimations based on the whole-genome sequencing data alone and thus makes it impossible to distinguish between causal and closely linked mutations.In this study, we combined isogenic bulk segregant analysis with deep candidate resequencing (dCARE) to facilitate the mutation identification of genetic modifiers based on bulked DNA and sequencing data alone. Our approach relies on the assumption that in pools of bulked segregants, the causative change occurs with the highest frequency among all EMS-induced changes (Fig. 1). Using resequencing data alone, it is not possible to distinguish between the subtle allele frequencies of EMS changes that are closely linked. However, dCARE of all candidate mutations using the new Ion Torrent sequencing technology enables quick and cost-effective detection of subtle allele frequency differences between closely linked mutations and thus allows the identification of causal candidates.Open in a separate windowFigure 1.Schematic illustration of the fast isogenic mapping approach. Chemical mutagens typically introduce hundreds of novel mutations. Within the M2 generation, mutants are screened for phenotypes. Selected plants are backcrossed to the nonmutagenized progenitor. The F2 offspring of such a cross forms an isogenic mapping population, as only novel mutations are segregating. Backcrossed individuals that display the mutant phenotype are selected, bulked, and their DNA is prepared as a pool and whole-genome sequenced. If the parental line is genetically different from the reference line Col-0, it needs to be resequenced in order to control for naturally occurring differences that need to be differentiated from novel mutations. Thus, all novel EMS-induced mutations can be selected for SHOREmap analysis by filtering for mutations that do not reside in the parental line. Candidate mutations (gray box) that show high mutant allele frequencies and linkage are selected for dCARE to pinpoint the causal mutation.The mutant identified by this fast isogenic mapping approach was isolated as a suppressor of developmental aberrations caused by defects in LIKE HETEROCHROMATIN PROTEIN1 (LHP1), which participates in the Polycomb Group (PcG) gene regulatory pathway in Arabidopsis. Enhancer/suppressor screens have been successfully used to identify genes that play a role in chromatin-mediated gene repression and activation in Drosophila melanogaster. For example, many components of the repressive PcG pathway were isolated as genetic enhancers or suppressors of homeotic mutations, whereas components of the Trithorax Group protein pathway were originally identified as suppressors of PcG-related mutations (Landecker et al., 1994; Gildea et al., 2000; Alonso et al., 2007).     

Abscisic Acid Inhibition of Kinetin Nucleotide Formation in Germinating Lettuce Seeds

Imbibing ‘Grand Rapids’ lettuce (Lactuca saliva L.) seeds take up ¹⁴C-kinetin, and metabolize this cytokinin to the 5′-nucleotide. The identity of the labeled nucleotide in seed extracts was verified by Sephadex LH-20 column chromatography, paper and thin layer chromatography, and high voltage paper electrophoresis. Incubations with kinetin in the presence of abscisic acid lead to an apparent specific inhibition of kinetin nucleotide formation. ABA has no effect on kinetin uptake, and does not inhibit kinetin nucleotide synthesis in vitro by a cell-free preparation from lettuce seeds. Additionally, ABA does not inhibit adenylate synthesis from exogenously supplied adenine. These results represent a specific cytokinin-ABA interaction, which might play a significant role in the hormonal regulation of lettuce seed germination.     

Effects of Exogenously Applied Gibberellin and Red Light on the Endogenous Levels of Abscisic Acid in Photoblastic Lettuce Seeds

Endogenous levels of ABA in photoblastic lettuce seeds weredecreased both by red-light irradiation and exogenously appliedgibberellin. Since red light increases endogenous levels ofGA₁ and exogenously applied ABA inhibits both red-light- andgibberellin-induced germination, a decrease in ABA may be importantfor germination. (Received August 27, 1993; Accepted November 5, 1993)     

Functional relationships of <Emphasis Type="Italic">phytoene synthase 1</Emphasis> alleles on chromosome 7A controlling flour colour variation in selected Australian wheat genotypes

Thermoinhibition, or failure of seeds to germinate when imbibed at warm temperatures, can be a significant problem in lettuce (Lactuca sativa L.) production. The reliability of stand establishment would be improved by increasing the ability of lettuce seeds to germinate at high temperatures. Genes encoding germination- or dormancy-related proteins were mapped in a recombinant inbred line population derived from a cross between L. sativa cv. Salinas and L. serriola accession UC96US23. This revealed several candidate genes that are located in the genomic regions containing quantitative trait loci (QTLs) associated with temperature and light requirements for germination. In particular, LsNCED4, a temperature-regulated gene in the biosynthetic pathway for abscisic acid (ABA), a germination inhibitor, mapped to the center of a previously detected QTL for high temperature germination (Htg6.1) from UC96US23. Three sets of sister BC₃S₂ near-isogenic lines (NILs) that were homozygous for the UC96US23 allele of LsNCED4 at Htg6.1 were developed by backcrossing to cv. Salinas and marker-assisted selection followed by selfing. The maximum temperature for germination of NIL seed lots with the UC96US23 allele at LsNCED4 was increased by 2–3°C when compared with sister NIL seed lots lacking the introgression. In addition, the expression of LsNCED4 was two- to threefold lower in the former NIL lines as compared to expression in the latter. Together, these data strongly implicate LsNCED4 as the candidate gene responsible for the Htg6.1 phenotype and indicate that decreased ABA biosynthesis at high imbibition temperatures is a major factor responsible for the increased germination thermotolerance of UC96US23 seeds.     

AtPER1 enhances primary seed dormancy and reduces seed germination by suppressing the ABA catabolism and GA biosynthesis in Arabidopsis seeds

Seed is vital to the conservation of germplasm and plant biodiversity. Seed dormancy is an adaptive trait in numerous seed‐plant species, enabling plants to survive under stressful conditions. Seed dormancy is mainly controlled by abscisic acid (ABA) and gibberellin (GA) and can be classified as primary and secondary seed dormancy. The primary seed dormancy is induced by maternal ABA. Here we found that AtPER1, a seed‐specific peroxiredoxin, is involved in enhancing primary seed dormancy. Two loss‐of‐function atper1 mutants, atper1‐1 and atper1‐2, displayed suppressed primary seed dormancy accompanied with reduced ABA and increased GA contents in seeds. Furthermore, atper1 mutant seeds were insensitive to abiotic stresses during seed germination. The expression of several ABA catabolism genes (CYP707A1, CYP707A2, and CYP707A3) and GA biosynthesis genes (GA20ox1, GA20ox3, and KAO3) in atper1 mutant seeds was increased compared to wild‐type seeds. The suppressed primary seed dormancy of atper1‐1 was completely reduced by deletion of CYP707A genes. Furthermore, loss‐of‐function of AtPER1 cannot enhance the seed germination ratio of aba2‐1 or ga1‐t, suggesting that AtPER1‐enhanced primary seed dormancy is dependent on ABA and GA. Additionally, the level of reactive oxygen species (ROS) in atper1 mutant seeds was significantly higher than that in wild‐type seeds. Taken together, our results demonstrate that AtPER1 eliminates ROS to suppress ABA catabolism and GA biosynthesis, and thus improves the primary seed dormancy and make the seeds less sensitive to adverse environmental conditions.     

Differential effects of camptothecin and interactions with plant hormones on seed germination and seedling growth

Effects of camptothecin, a naturally occurring alkaloid, on seed germination varied from promotive to inhibitory, depending on the species used. It markedly inhibited seedling root growth but its inhibition of hypocotyl growth varied among species. Camptothecin inhibited GA₃-induced dark germination of lettuce (Lactuca sativa L.) seeds and hypocotyl elongation of seedlings. In contrast to ABA, the camptothecin inhibition of GA₃-induced germination could not be overcome by cytokinin. When seeds were germinated at 29C with a 0.5 h light treatment, little or no germination occurred in the camptothecin treatment, but addition of cytokinin overcame this inhibition.     

Restoration of Seed Germination at Supraoptimal Temperatures by Fluridone, an Inhibitor of Abscisic Acid Biosynthesis

Fluridone, an inhibitor of ABA biosynthesis, restored the seedgermination of lettuce (Lactuca sativa L. cv. Grand Rapids)and many other plant species at supra-optimal temperatures.ABA content in lettuce seeds after imbibition quickly decreasedat 23°C, but not at 33°C (a supraoptimal temperature).Fluridone caused a decrease in ABA content at 33°C, whichsuggests that the maintenance of high ABA content could be responsiblefor high-temperature inhibition of germination of lettuce seeds.This probably results from an increase in the rate of ABA biosynthesisat the higher temperature. The present study indicates thatABA plays a decisive role in the regulation of seed germinationat supraoptimal temperatures. ¹ Corresponding author: fax 81-22-717-8834; e-mail yoshi@bios.tohoku.ac.jp     

Interactions between abscisic acid and ethylene signaling cascades

We screened for mutations that either enhanced or suppressed the abscisic acid (ABA)-resistant seed germination phenotype of the Arabidopsis abi1-1 mutant. Alleles of the constitutive ethylene response mutant ctr1 and ethylene-insensitive mutant ein2 were recovered as enhancer and suppressor mutations, respectively. Using these and other ethylene response mutants, we showed that the ethylene signaling cascade defined by the ETR1, CTR1, and EIN2 genes inhibits ABA signaling in seeds. Furthermore, epistasis analysis between ethylene- and ABA-insensitive mutations indicated that endogenous ethylene promotes seed germination by decreasing sensitivity to endogenous ABA. In marked contrast to the situation in seeds, ein2 and etr1-1 roots were resistant to both ABA and ethylene. Our data indicate that ABA inhibition of root growth requires a functional ethylene signaling cascade, although this inhibition is apparently not mediated by an increase in ethylene biosynthesis. These results are discussed in the context of the other hormonal regulations controlling seed germination and root growth.