Quantitative trait loci for root morphology traits under aluminum stress in common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Aluminum (Al) toxicity is a major limiting factor of crop production in acid soils, which are found mostly in developing countries of the tropics and sub-tropics. Common bean (Phaseolus vulgaris L.) is particularly sensitive to Al toxicity; and development of genotypes with better root growth in Al-toxic soils is a priority. The objectives of the present study were to physiologically assess root architectural traits in a recombinant inbred line (RIL) population of common bean that contrasts for Al resistance (DOR364 × G19833) and to identify quantitative trait loci (QTL) controlling root growth under two nutrient solutions, one with 20 μM Al concentration and the other without Al, both at pH 4.5. A total of 24 QTL were found through composite interval mapping analysis, 9 for traits under Al treatment, 8 for traits under control treatment, and 7 for relative traits. Root characteristics expressed under Al treatment were found to be under polygenic control, and some QTL were identified at the same location as QTL for tolerance to low phosphorous stress, thus, suggesting cross-links in genetic control of adaptation of common bean to different abiotic stresses.     

Genetic and QTL analysis of resistance to <Emphasis Type="Italic">Xiphinema index</Emphasis> in a grapevine cross

Resistance to the dagger nematode Xiphinema index has been an important objective in grape rootstock breeding programs. This nematode not only causes severe feeding damage to the root system, but it also vectors grapevine fanleaf virus (GFLV), the causal agent of fanleaf degeneration and one of the most severe viral diseases of grape. The established screening procedures for dagger nematode resistance are time consuming and can produce inconsistent results. A fast and reliable greenhouse-based system for screening resistance to X. index that is suitable for genetic studies and capable of evaluating breeding populations is needed. In this report, the dynamics of nematode numbers, gall formation, and root weight loss were investigated using a variety of soil mixes and pot sizes over a 52-week period. Results indicated that the number of galls formed was correlated with the size of the nematode population and with the degree of root weight loss. After inoculation with 100 nematodes, gall formation could be reliably evaluated in 4–8 weeks in most plant growth conditions and results were obtained 6 months more rapidly than past evaluation methods. This modified X. index resistance screening method was successfully applied to 185 of the 188 F₁ progeny from a cross of D8909-15 × F8909-17 (the 9621 population), which segregates for a form of X. index resistance originally derived from Vitis arizonica. Quantitative trait loci (QTL) analysis was carried out on both parental genetic maps of 255 markers using MapQTL 4.0. Results revealed that X. index resistance is controlled by a major QTL, designated Xiphinema index Resistance 1 (XiR1), near marker VMC5a10 on chromosome 19. The XiR1 QTL was supported by a LOD score of 36.9 and explained 59.9% of the resistance variance in the mapping population. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Quantitative trait loci controlling aluminium tolerance in two accessions of Arabidopsis thaliana (Landsberg erecta and Cape Verde Islands)

Quantitative trait loci (QTL) analysis of aluminium (Al) tolerance was performed using Ler/Cvi recombinant inbred (RI) lines of Arabidopsis thaliana. Relative root length (RRL) (root length with 4 µm Al/root length with no Al at pH 5.0) on day 5 was used as the Al tolerance index for QTL analysis. Al tolerance judged by RRL was well correlated to tolerance judged by other indexes, including accumulation of callose, reactive oxygen species in the root apex and growth performance on acid soil containing a large amount of exchangeable Al. Using data sets with an h_b² of 0.91, two QTLs were detected at the top of chromosome 1 and bottom of chromosome 3. These QTLs explained 40 and 16% of the phenotypic variation of Al tolerance, respectively, and the positive effect of the Cvi allele. The QTL on chromosome 1 overlapped with a major QTL in another recombinant inbred population, and is possibly related to malate excretion. A complete pair-wise search revealed 11 sets of epistatic interacting loci pairs, which accounted for the transgressive segregation among the RI population. Several epistatic interactions shared the same chromosomal region, indicating the possible involvement of regulatory proteins in Al tolerance in Arabidopsis.     

Identification of new sources of aluminum resistance in wheat

Aluminum (Al) toxicity is a major constraint for wheat production in acidic soils. An Al resistance gene on chromosome 4DL that traces to Brazilian wheat has been extensively studied, and can provide partial protection from Al damage. To identify potentially new sources of Al resistance, 590 wheat accessions, including elite wheat breeding lines from the United States and other American and European countries, landraces and commercial cultivars from East Asia, and synthetic wheat lines from CIMMYT, Mexico, were screened for Al resistance by measuring relative root elongation in culture with a nutrient solution containing Al, and by staining Al-stressed root tips with hematoxylin. Eighty-eight wheat accessions demonstrated at least moderate resistance to Al toxicity. Those selected lines were subjected to analysis of microsatellite markers linked to an Al resistance gene on 4DL and a gene marker for the Al-activated malate transporter (ALMT1) locus. Many of the selected Al-resistant accessions from East Asia did not have the Al-resistant marker alleles of ALMT1, although they showed Al resistance similar to the US Al-resistant cultivar, Atlas 66. Most of the cultivars derived from Jagger and Atlas 66 have the Al-resistant marker alleles of ALMT1. Cluster analysis separated the selected Al-resistant germplasm into two major clusters, labeled as Asian and American–European clusters. Potentially new germplasm of Al resistance different from those derived from Brazil were identified. Further investigation of Al resistance in those new germplasms may reveal alternative Al-resistance mechanisms in wheat. Electronic supplementary material The online version of this article (doi:contains supplementary material, which is available to authorized users. Responsible Editor: Thomas B. Kinraide.     

A Comparison of Aluminum Resistance among Polygonum Species Originating on Strongly Acidic and Neutral Soils

Two kinds of Polygonum species (Polygonum aviculare L. and Polygonum lapathifolium L.) grown in tea garden soils at pH around 3.5 and one Polygonum bungeanum Turcz grown in neutral soils were collected to investigate the mechanisms involved in their high Al resistance. Hydroponic experiments showed that the root elongation was only inhibited by 15% in P. aviculare and 35% in P. lapathifolium after exposure to 50 μM Al for 24 h. Their Al resistance was respectively higher than and similar to that in an Al resistant buckwheat (Fagopyrum esculentum Moench) cultivar. In contrast, P. bungeanum was much more Al sensitive since the root elongation was inhibited by 80% under the same condition. The difference in Al resistance among Polygonum species was confirmed in a 10-d intermittent Al treatment experiment, the root biomass of the first two species were unaltered and decreased by 50% in the latter species. However, high Al accumulation was not found in the leaves, indicating these species were not Al accumulators. Oxalate efflux was detected in root exudates of both Al resistant species, efflux initiated within 30 min treatment of 50 μM Al. No organic acid anions were detected in the root exudates of the Al sensitive species. The anion channel inhibitor phenylglyoxal (PG) inhibited the oxalate efflux greatly. Inhibition of root elongation was greater in the presence of PG, confirming that oxalate efflux was associated with the Al resistance. However, since the efflux rate was much lower than their related species buckwheat, other mechanisms must be involved in Al resistance and these need to be studied further.     

Effect of pH and nitrogen source on aluminium tolerance of rye (Secale cereale L.) and yellow lupin (Lupinus luteus L.)

Soluble aluminium (Al) is a major factor limiting plant growth in acid mineral soils. Aluminium concentrations in soil solutions are mainly determined by soil pH. However, pH also affects the ratio between activities of protons and cationic Al species and the equilibrium between mono-and polynuclear hydroxy-Al species. The phytotoxicity of these species is not yet clear. The objective of the present study was to clarify the role of minor changes of pH in the rhizosphere on Al phytotoxicity in two Al-tolerant plant species by direct control of the pH in the nutrient solution (4.1, 4.3, 4.5) and in addition by varying the pH in the root apoplast using either nitrate or ammonium as N source. The plants were grown in solution culture at constant external pH. Whereas the Al-sensitive plant species barley and horse bean were damaged at very low Al supplies (1.85 μM and 9.3 μM respectively), 222 μM had to be applied to rye and yellw lupin for a comparable inhibition of root elongation. Yellow lupin was initially severely inhibited in root growth by Al, but then gradually recovered from this ‘Al shock’ within 3 days. In contrast to lupin, rye was hardly affected by Al initially, and it took about 16 h until maximum inhibition of root elongation. In the presence of nitrate, raising the pH from 4.1 to 4.5 aggravated root-growth depression by Al in rye and lupin. Whereas rye roots were severely damaged by ammonium especially at low pH, lupin was rather indifferent to the N source. Aluminium toxicity was less severe in presence of ammonium compared to nitrate N. This effect was less clear with rye at lower pH, because of it's higher proton sensitivity compared to lupin. Less Al injury at lower pH and in presence of ammonium was related to lower Al concentrations in the 1 cm root tips. The results are compatible with data showing high phytotoxicity of mononuclear and polynuclear hydroxy-Al species. However, they could also be interpreted in the light of proton amelioration of Al toxicity owing to competition for Al-sensitive binding sites in the root apoplast.     

Association mapping of quantitative resistance for <Emphasis Type="Italic">Leptosphaeria maculans</Emphasis> in oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Stem canker caused by the fungus Leptosphaeria maculans is a major disease of Brassica napus. Quantitative resistance factors appear to be important components for effective and durable control of this pathogen. Quantitative trait loci (QTL) for stem canker resistance have previously been identified in the Darmor variety. However, before these QTL can be used in marker-assisted selection (MAS) to breed resistant varieties, they must be validated in a wide range of genetic backgrounds. We used an association mapping approach to confirm the markers located within the QTL previously identified in Darmor and establish their usefulness in MAS. For this, we characterized the molecular diversity of an oilseed rape collection of 128 lines showing a large spectrum of responses to infection by L. maculans, using 72 pairs of primers for simple sequence repeat and other markers. We used different association mapping models which either do or do not take into account the population structure and/or family relatedness. In all, 61 marker alleles were found to be associated with resistance to stem canker. Some of these markers were associated with previously identified QTL, which confirms their usefulness in MAS. Markers located in regions not harbouring previously identified QTL were also associated with resistance, suggesting that new QTL or allelic variants are present in the collection. All of these markers associated with stem canker resistance will help identify accessions carrying desirable alleles and facilitate QTL introgression.     

Sensitivity to H- and Al ions limiting growth and distribution of the woodland grass Bromus benekenii

One pH experiment and two aluminium experiments were conducted in order to investigate the effects of H- and Al ions on growth of Bromus benekenii. Continuously flowing solution cultures were used with ion concentrations simulating natural soil solutions. In all experiments, treatment effects were more pronounced on root than on shoot growth. In the pH experiment, root growth decreased with decreasing pH within the pH range 4.5 to 3.5. The critical pH for root growth of Bromus benekenii was between 3.8 and 4.0. In the Al experiments, root growth started to decrease at 20 M of quickly reacting Al and almost ceased at 70 M Al. This characterizes Bromus benekenii as an Al sensitive species. In the pH experiment, shoot concentrations of Ca, Mg, K and P decreased with decreasing pH, but root concentrations were not affected. In the Al experiments, the Al concentrations of both shoots and roots increased with Al in the nutrient solution. At treatments of 70 M Al or higher, Ca, Mg, K and P concentrations in the shoots were reduced. The critical concentrations of H- and Al ions in the experiments were similar to the highest concentrations found at field sites of Bromus benekenii, analysed in soil solutions obtained by centrifugation technique. Both Al and H toxicity were considered to be of importance as limiting factors for the distribution of Bromus benekenii in south Sweden. Probably, Al toxicity starts to limit growth when also pH itself influences growth negatively. The importance of simulating natural soil solutions in experiments is emphazised, in order to obtain information on the importance of chemical soil factors to the distribution of plants.     

Aluminum Tolerance in Moso Bamboo (<Emphasis Type="Italic">Phyllostachys pubescens</Emphasis>)

Moso bamboo (Phyllostachys pubescens) is widely distributed in the acid soil region of Southern China, where great potential of aluminum (Al) toxicity exists. To evaluate the Al tolerance of Moso bamboo, seed germination and root elongation were compared with two rice cultivars, and physical and physiological damages were examined under various levels of Al stress. Results showed that Moso bamboo seed germination was inhibited when Al concentration increased to 500 μM, and the median lethal concentration was 2,000 μM. Comparatively, the rice seed germination was not inhibited even at a concentration of 2,000 μM Al. Aluminum accumulated mainly in the cell wall of root apices, and entered into protoplasts as treating time prolonged and/or Al concentration increased, which resulted in apoptosis. The bamboo root epidermis degraded significantly in the presence of 2,000 μM Al. In conclusion, Moso bamboo is moderately weak in Al tolerance.     

Evaluation of genes from <Emphasis Type="Italic">eIF4E</Emphasis> and <Emphasis Type="Italic">eIF4G</Emphasis> multigenic families as potential candidates for partial resistance QTLs to <Emphasis Type="Italic">Rice yellow mottle virus</Emphasis> in rice

QTLs for partial resistance to Rice yellow mottle virus (RYMV) in rice were mapped in two populations of doubled-haploid lines (DHLs) and recombinant inbred lines (RILs) derived from the same cross but evaluated for different resistance criteria (virus content and symptom severity). An integrative map was used to compare the two genetic maps and a global analysis of both populations was performed. Most of the QTLs previously identified in DHL population were confirmed with increased significance and precision. As many recent studies evidenced the role of eukaryotic translation initiation factors (eIF) of 4E and 4G families in plant susceptibility to RNA viruses, we checked if these genes co-locate with QTLs of resistance to RYMV. Their systematic in silico identification was carried out on the rice genome and their physical locations were compared to QTL positions on the integrative map. In order to confirm or not the co-locations observed, the analysis was completed by evaluation of near-isogenic lines, QTL fine mapping and sequencing of candidate genes. Three members from eIF4G family could be retained as reliable candidates whereas eIF4E genes, commonly found to govern resistances in other plant/virus interactions, were discarded. Together with the recent identification of an eIF(iso)4G as a major resistance gene, data suggests an important role of genes from eIF4G family in rice resistance to RYMV but does not exclude the contribution of factors different from the translation initiation complex. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Soil acidity factors and nodulation ofTrifolium repens

Summary Effects of factors associated with soil acidity (low pH, low calcium, high aluminium and high manganese) on theTrifolium repens-Rhizobium trifolii symbiosis were investigted under laboratory conditions using an axenic solution-culture technique. 200 μM manganese increased root elongation in the range pH 4.3–5.5, but had no effect on root hair formation, the number of Rhizobium in the rhizosphere, or nodule formation. Root elongation and root hair formation were unaffected at pH 4.3 when 500 or 1000μM calcium was supplied, whereas multiplication of Rhizobium in the rhizosphere and nodulation were inhibited at pH 4.3 and 4.7.50–1000μM calcium had no effect either on the multiplication of Rhizobium in the range pH 4.3–5.5, or on nodule formation in the absence of aluminium. 50 μM aluminium inhibited, root elongation and root hair formation at pH 4.3 and 4.7; the effect on root elongation was reduced by increasing the calcium concentration from 50 to 1000μM. 50μM aluminium also inhibited Rhizobium multiplication in the rhizosphere and reduced nodule formation at pH 5.5 (at which aluminium precipitated out of solution), but root elongation and root hair formation were unaffected. These, effects of aluminium at pH 5.5 may explain the poor response to inoculation by white clover in acid mineral soils after liming.     

Clubroot resistance QTL are modulated by nitrogen input in <Emphasis Type="Italic">Brassica napus</Emphasis>

Key message

Nitrogen levels can modulate the effectiveness of clubroot resistance in an isolate- and host-specific manner. While the same QTL were detected under high and low nitrogen, their effects were altered.

Abstract

Clubroot, caused by Plasmodiophora brassicae, is one of the most damaging diseases of oilseed rape and is known to be affected by nitrogen fertilization. However, the genetic factors involved in clubroot resistance have not been characterized under nitrogen-limiting conditions. This study aimed to assess the variability of clubroot resistance under different nitrogen levels and to characterize the impact of nitrogen supply on genetic resistance factors. Linkage analyses and a genome-wide association study were conducted to detect QTL for clubroot resistance and evaluate their sensitivity to nitrogen. The clubroot response of a set of 92 diverse oilseed rape accessions and 108 lines derived from a cross between ‘Darmor-bzh’ (resistant) and ‘Yudal’ (susceptible) was studied in the greenhouse under high- and low-nitrogen conditions, following inoculation with the P. brassicae isolates eH and K92-16. Resistance to each isolate was controlled by a major QTL and a few small-effects QTL. While the same QTL were detected under both high and low nitrogen, their effects were altered. Clubroot resistance to isolate eH, but not K92-16, was greater under a low-N supply versus a high-N supply. New sources of resistance were found among the oilseed rape accessions under both low and high-N conditions. The results are discussed relative to the literature and from a crop improvement perspective.

     

Peroxidase activity against guaiacol,NADH, chlorogenic acid,ferulic acid and coniferyl alcohol in root tips of <Emphasis Type="Italic">Lotus japonicus</Emphasis> and <Emphasis Type="Italic">L. corniculatus</Emphasis> grown under low pH and aluminium stress

The purpose of this study was to examine the impact of low pH and Al stress on the apoplastic production of H₂O₂ and POD activity against guaiacol, ferulic acid, coniferyl alcohol, NADH and chlorogenic acid in the root tip (RT) of two cultivars of Lotus corniculatus and the model Lotus japonicus Gifu, with the goal to determine the possible role of POD activity in proton and Al tolerance. Our results suggest that Lotus corniculatus cv. UFRGS is more tolerant to low pH and Al than cv. Draco due to the high POD activities involved in CW strengthening. The enzymatic response of Lotus japonicus Gifu is similar rather to the sensitive cultivar. On the other hand, in cvs Draco and Gifu low pH induced the activation of CW-modifying PODs, which is probably a component of the defence response of roots to the presence of toxic protons. Aluminium did not activate further these activities suggesting that defence response and acclimation to low pH confers also effective defence against Al toxicity in Lotus species. The activity of NADH-POD and CGA-POD were not affected significantly by exposure to low pH or Al. Al and pH induced drop in H₂O₂ production, which was more relevant in cv. Gifu and Draco than in cv. UFRGS is probably associated with enhanced activity of peroxidases involved in secondary CW metabolism utilizing H₂O₂ as an electron acceptor.     

Three QTLs for <Emphasis Type="Italic">Botrytis cinerea</Emphasis> resistance in tomato

Tomato (Solanum lycopersicum) is susceptible to grey mold (Botrytis cinerea). Partial resistance to this fungus was identified in accessions of wild relatives of tomato such as S. habrochaites LYC4. In order to identify loci involved in quantitative resistance (QTLs) to B. cinerea, a population of 174 F₂ plants was made originating from a cross between S. lycopersicum cv. Moneymaker and S. habrochaites LYC4. The population was genotyped and tested for susceptibility to grey mold using a stem bioassay. Rbcq1, a QTL reducing lesion growth (LG) and Rbcq2, a QTL reducing disease incidence (DI) were identified. Rbcq1 is located on Chromosome 1 and explained 12% of the total phenotypic variation while Rbcq2 is located on Chromosome 2 and explained 15% of the total phenotypic variation. Both QTL effects were confirmed by assessing disease resistance in two BC₂S₁ progenies segregating for either of the two QTLs. One additional QTL, Rbcq4 on Chromosome 4 reducing DI, was identified in one of the BC₂S₁ progenies. F₂ individuals, homozygous for the Rbcq2 and Rbcq4 alleles of S. habrochaites showed a reduction of DI by 48%. QTLs from S. habrochaites LYC4 offer good perspectives for breeding B. cinerea resistant tomato cultivars. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Identification of quantitative trait loci for resistance to shoot fly in sorghum [<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench]

The shoot fly is one of the most destructive insect pests of sorghum at the seedling stage. Deployment of cultivars with improved shoot fly resistance would be facilitated by the use of molecular markers linked to QTL. The objective of this study was to dissect the genetic basis of resistance into QTL, using replicated phenotypic data sets obtained from four test environments, and a 162 microsatellite marker-based linkage map constructed using 168 RILs of the cross 296B (susceptible) × IS18551 (resistant). Considering five component traits and four environments, a total of 29 QTL were detected by multiple QTL mapping (MQM) viz., four each for leaf glossiness and seedling vigor, seven for oviposition, six for deadhearts, two for adaxial trichome density and six for abaxial trichome density. The LOD and R ² (%) values of QTL ranged from 2.6 to 15.0 and 5.0 to 33%, respectively. For most of the QTL, IS18551 contributed resistance alleles; however, at six QTL, alleles from 296B also contributed to resistance. QTL of the related component traits were co-localized, suggesting pleiotropy or tight linkage of genes. The new morphological marker Trit for trichome type was associated with the major QTL for component traits of resistance. Interestingly, QTL identified in this study correspond to QTL/genes for insect resistance at the syntenic maize genomic regions, suggesting the conservation of insect resistance loci between these crops. For majority of the QTL, possible candidate genes lie within or very near the ascribed confidence intervals in sorghum. Finally, the QTL identified in the study should provide a foundation for marker-assisted selection (MAS) programs for improving shoot fly resistance in sorghum.     

Identification of quantitative trait loci influencing aerial morphogenesis in the model legume <Emphasis Type="Italic">Medicago truncatula</Emphasis>

In many legume crops, especially in forage legumes, aerial morphogenesis defined as growth and development of plant organs, is an essential trait as it determines plant and seed biomass as well as forage quality (protein concentration, dry matter digestibility). Medicago truncatula is a model species for legume crops. A set of 29 accessions of M. truncatula was evaluated for aerial morphogenetic traits. A recombinant inbred lines (RILs) mapping population was used for analysing quantitative variation in aerial morphogenetic traits and QTL detection. Genes described to be involved in aerial morphogenetic traits in other species were mapped to analyse co-location between QTLs and genes. A large variation was found for flowering date, morphology and dynamics of branch elongation among the 29 accessions and within the RILs population. Flowering date was negatively correlated to main stem and branch length. QTLs were detected for all traits, and each QTL explained from 5.2 to 59.2% of the phenotypic variation. A QTL explaining a large part of genetic variation for flowering date and branch growth was found on chromosome 7. The other chromosomes were also involved in the variation detected in several traits. Mapping of candidate genes indicates a co-location between a homologue of Constans gene or a flowering locus T (FT) gene and the QTL of flowering date on chromosome 7. Other candidate genes for several QTLs are described. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic analysis for drought resistance of rice at reproductive stage in field with different types of soil

Drought resistance of rice is a complex trait and is mainly determined by mechanisms of drought avoidance and drought tolerance. The present study was conducted to characterize the genetic basis of drought resistance at reproductive stage in field by analyzing the QTLs for drought response index (DRI, normalized by potential yield and flowering time), relative yield, relative spikelet fertility, and four traits of plant water status and their relationships with root traits using a recombinant inbred population derived from a cross between an indica rice and upland rice. A total of 39 QTLs for these traits were detected with individual QTL explained 5.1–32.1% of phenotypic variation. Only two QTLs for plant water status were commonly detected in two environments, suggesting different mechanisms might exist in two types of soil conditions. DRI has no correlation with potential yield and flowering time under control, suggesting that it can be used as a good drought resistance index in field conditions. The co-location of QTLs for canopy temperature and delaying in flowering time suggested a usefulness of these two traits as indexes in drought resistance screening. Correlation and QTL congruence between root traits and putative drought tolerance traits revealed that drought avoidance (via thick and deep root traits) was the main genetic basis of drought resistance in sandy soil condition, while drought tolerance may play more role in the genetic basis of drought resistance in paddy soil condition. Therefore, both drought mechanisms and soil textures must be considered in the improvement of drought resistance at reproductive stage in rice.     

<Emphasis Type="Italic">Arabidopsis</Emphasis><Emphasis Type="Italic"> ALS1</Emphasis> encodes a root tip and stele localized half type ABC transporter required for root growth in an aluminum toxic environment

Aluminum toxicity in acid soils severely limits crop productivity through inhibition of root growth and, consequently, shoot development. Several Arabidopsis mutants were previously identified as having roots with Al hypersensitivity, suggesting that these represent deleterious mutations affecting genes required for either Al tolerance or resistance mechanisms. For this report, the als1-1 mutant was chosen for further characterization. The phenotype of als1-1 is most obviously presented in Al challenged roots, as evidenced by exaggerated root growth inhibition in conjunction with increased expression of Al-responsive genes compared to wt. Using a map-based cloning approach, the als1-1 mutation was isolated and found to represent a deleterious amino acid substitution in a previously uncharacterized half type ABC transporter, At5g39040, which is expressed in a non-Al dependent manner in all organs tested. GUS-dependent analyses revealed that ALS1 expression is primarily localized to the root tip and the vasculature throughout the plant. Concomitant with this, an ALS1: GFP fusion accumulates at the vacuolar membrane of root cells, indicating that ALS1 may be important for intracellular movement of some substrate, possibly chelated Al, as part of a mechanism of Al sequestration.     

Comparative mapping of <Emphasis Type="Italic">Phytophthora</Emphasis> resistance loci in pepper germplasm: evidence for conserved resistance loci across Solanaceae and for a large genetic diversity

Phytophthora capsici Leonian, known as the causal agent of the stem, collar and root rot, is one of the most serious problems limiting the pepper crop in many areas in the world. Genetic resistance to the parasite displays complex inheritance. Quantitative trait locus (QTL) analysis was performed in three intraspecific pepper populations, each involving an unrelated resistant accession. Resistance was evaluated by artificial inoculations of roots and stems, allowing the measurement of four components involved in different steps of the plant-pathogen interaction. The three genetic maps were aligned using common markers, which enabled the detection of QTLs involved in each resistance component and the comparison of resistance factors existing among the three resistant accessions. The major resistance factor was found to be common to the three populations. Another resistance factor was found conserved between two populations, the others being specific to a single cross. This comparison across intraspecific germplasm revealed a large variability for quantitative resistance loci to P. capsici. It also provided insights both into the allelic relationships between QTLs across pepper germplasm and for the comparative mapping of resistance factors across the Solanaceae.     

Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan

Background

Aluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition to naturally occurring acid soils, agricultural practices may decrease soil pH, leading to yield losses due to Al toxicity. Elucidating the genetic and molecular mechanisms underlying maize Al tolerance is expected to accelerate the development of Al-tolerant cultivars.

Results

Five genomic regions were significantly associated with Al tolerance, using 54,455 SNP markers in a recombinant inbred line population derived from Cateto Al237. Candidate genes co-localized with Al tolerance QTLs were further investigated. Near-isogenic lines (NILs) developed for ZmMATE2 were as Al-sensitive as the recurrent line, indicating that this candidate gene was not responsible for the Al tolerance QTL on chromosome 5, qALT5. However, ZmNrat1, a maize homolog to OsNrat1, which encodes an Al³⁺ specific transporter previously implicated in rice Al tolerance, was mapped at ~40 Mbp from qALT5. We demonstrate for the first time that ZmNrat1 is preferentially expressed in maize root tips and is up-regulated by Al, similarly to OsNrat1 in rice, suggesting a role of this gene in maize Al tolerance. The strongest-effect QTL was mapped on chromosome 6 (qALT6), within a 0.5 Mbp region where three copies of the Al tolerance gene, ZmMATE1, were found in tandem configuration. qALT6 was shown to increase Al tolerance in maize; the qALT6-NILs carrying three copies of ZmMATE1 exhibited a two-fold increase in Al tolerance, and higher expression of ZmMATE1 compared to the Al sensitive recurrent parent. Interestingly, a new source of Al tolerance via ZmMATE1 was identified in a Brazilian elite line that showed high expression of ZmMATE1 but carries a single copy of ZmMATE1.

Conclusions

High ZmMATE1 expression, controlled either by three copies of the target gene or by an unknown molecular mechanism, is responsible for Al tolerance mediated by qALT6. As Al tolerant alleles at qALT6 are rare in maize, marker-assisted introgression of this QTL is an important strategy to improve maize adaptation to acid soils worldwide.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-153) contains supplementary material, which is available to authorized users.