Association Mapping Provides Insights into the Origin and the Fine Structure of the Sorghum Aluminum Tolerance Locus,AltSB

Root damage caused by aluminum (Al) toxicity is a major cause of grain yield reduction on acid soils, which are prevalent in tropical and subtropical regions of the world where food security is most tenuous. In sorghum, Al tolerance is conferred by SbMATE, an Al-activated root citrate efflux transporter that underlies the major Al tolerance locus, Alt_SB, on sorghum chromosome 3. We used association mapping to gain insights into the origin and evolution of Al tolerance in sorghum and to detect functional variants amenable to allele mining applications. Linkage disequilibrium across the Alt_SB locus decreased much faster than in previous reports in sorghum, and reached basal levels at approximately 1000 bp. Accordingly, intra-locus recombination events were found to be extensive. SNPs and indels highly associated with Al tolerance showed a narrow frequency range, between 0.06 and 0.1, suggesting a rather recent origin of Al tolerance mutations within Alt_SB. A haplotype network analysis suggested a single geographic and racial origin of causative mutations in primordial guinea domesticates in West Africa. Al tolerance assessment in accessions harboring recombinant haplotypes suggests that causative polymorphisms are localized to a ∼6 kb region including intronic polymorphisms and a transposon (MITE) insertion, whose size variation has been shown to be positively correlated with Al tolerance. The SNP with the strongest association signal, located in the second SbMATE intron, recovers 9 of the 14 highly Al tolerant accessions and 80% of all the Al tolerant and intermediately tolerant accessions in the association panel. Our results also demonstrate the pivotal importance of knowledge on the origin and evolution of Al tolerance mutations in molecular breeding applications. Allele mining strategies based on associated loci are expected to lead to the efficient identification, in diverse sorghum germplasm, of Al tolerant accessions able maintain grain yields under Al toxicity.     

Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum

Impaired root development caused by aluminum (Al) toxicity is a major cause of grain yield reduction in crops cultivated on acid soils, which are widespread worldwide. In sorghum, the major Al‐tolerance locus, Alt_SB, is due to the function of SbMATE, which is an Al‐activated root citrate transporter. Here we performed a molecular and physiological characterization of various Alt_SB donors and near‐isogenic lines harboring various Alt_SB alleles. We observed a partial transfer of Al tolerance from the parents to the near‐isogenic lines that was consistent across donor alleles, emphasizing the occurrence of strong genetic background effects related to Alt_SB. This reduction in tolerance was variable, with a 20% reduction being observed when highly Al‐tolerant lines were the Alt_SB donors, and a reduction as great as 70% when other Alt_SB alleles were introgressed. This reduction in Al tolerance was closely correlated with a reduction in SbMATE expression in near‐isogenic lines, suggesting incomplete transfer of loci acting in trans on SbMATE. Nevertheless, Alt_SB alleles from the highly Al‐tolerant sources SC283 and SC566 were found to retain high SbMATE expression, presumably via elements present within or near the Alt_SB locus, resulting in significant transfer of the Al‐tolerance phenotype to the derived near‐isogenic lines. Allelic effects could not be explained by coding region polymorphisms, although occasional mutations may affect Al tolerance. Finally, we report on the extensive occurrence of alternative splicing for SbMATE, which may be an important component regulating SbMATE expression in sorghum by means of the nonsense‐mediated RNA decay pathway.     

Genetic diversity for aluminum tolerance in sorghum

Genetic variation for aluminum (Al) tolerance in plants has allowed the development of cultivars that are high yielding on acidic, Al toxic soils. However, knowledge of intraspecific variation for Al tolerance control is needed in order to assess the potential for further Al tolerance improvement. Here we focused on the major sorghum Al tolerance gene, Alt _SB , from the highly Al tolerant standard SC283 to investigate the range of genetic diversity for Al tolerance control in sorghum accessions from diverse origins. Two tightly linked STS markers flanking Alt _SB were used to study the role of this locus in the segregation for Al tolerance in mapping populations derived from different sources of Al tolerance crossed with a common Al sensitive tester, BR012, as well as to isolate the allelic effects of Alt _SB in near-isogenic lines. The results indicated the existence not only of multiple alleles at the Alt _SB locus, which conditioned a wide range of tolerance levels, but also of novel sorghum Al tolerance genes. Transgressive segregation was observed in a highly Al tolerant breeding line, indicating that potential exists to exploit the additive or codominant effects of distinct Al tolerance loci. A global, SSR-based, genetic diversity analysis using a broader sorghum set revealed the presence of both multiple Alt _SB alleles and different Al tolerance genes within highly related accessions. This suggests that efforts toward broadening the genetic basis for Al tolerance in sorghum may benefit from a detailed analysis of Al tolerance gene diversity within subgroups across a target population. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Association and Linkage Analysis of Aluminum Tolerance Genes in Maize

Background

Aluminum (Al) toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa where these soils are very common. Al exclusion and intracellular tolerance have been suggested as two important mechanisms for Al tolerance in maize, but little is known about the underlying genetics.

Methodology

An association panel of 282 diverse maize inbred lines and three F₂ linkage populations with approximately 200 individuals each were used to study genetic variation in this complex trait. Al tolerance was measured as net root growth in nutrient solution under Al stress, which exhibited a wide range of variation between lines. Comparative and physiological genomics-based approaches were used to select 21 candidate genes for evaluation by association analysis.

Conclusions

Six candidate genes had significant results from association analysis, but only four were confirmed by linkage analysis as putatively contributing to Al tolerance: Zea mays Alt_SB like (ZmASL), Zea mays aluminum-activated malate transporter2 (ALMT2), S-adenosyl-L-homocysteinase (SAHH), and Malic Enzyme (ME). These four candidate genes are high priority subjects for follow-up biochemical and physiological studies on the mechanisms of Al tolerance in maize. Immediately, elite haplotype-specific molecular markers can be developed for these four genes and used for efficient marker-assisted selection of superior alleles in Al tolerance maize breeding programs.     

How a microbial drug transporter became essential for crop cultivation on acid soils: aluminium tolerance conferred by the multidrug and toxic compound extrusion (MATE) family

Background

Aluminium (Al) toxicity is a major agricultural constraint for crop cultivation on acid soils, which comprise a large portion of the world''s arable land. One of the most widely accepted mechanisms of Al tolerance in plants is based on Al-activated organic acid release into the rhizosphere, with organic acids forming stable, non-toxic complexes with Al. This mechanism has recently been validated by the isolation of bona-fide Al-tolerance genes in crop species, which encode membrane transporters that mediate Al-activated organic acid release leading to Al exclusion from root apices. In crop species such as sorghum and barley, members in the multidrug and toxic compound extrusion (MATE) family underlie Al tolerance by a mechanism based on Al-activated citrate release.

Scope and Conclusions

The study of Al tolerance in plants as conferred by MATE family members is in its infancy. Therefore, much is yet to be discovered about the functional diversity and evolutionary dynamics that led MATE proteins to acquire transport properties conducive to Al tolerance in plants. In this paper we review the major characteristics of transporters in the MATE family and will relate this knowledge to Al tolerance in plants. The MATE family is clearly extremely flexible with respect to substrate specificity, which raises the possibility that Al tolerance as encoded by MATE proteins may not be restricted to Al-activated citrate release in plant species. There are also indications that regulatory loci may be of pivotal importance to fully explore the potential for Al-tolerance improvement based on MATE genes.     

Physiological and molecular analysis of aluminum tolerance in selected Kenyan maize lines

Aims

Aluminum (Al) toxicity is an important limitation to maize production in many tropical and sub-tropical acid soil areas. The aim of this study was to survey the variation in Al tolerance in a panel of maize lines adapted for Kenya and look for novel sources of Al tolerance.

Methods

112 Kenyan maize accessions were phenotyped for Al tolerance in solution culture. Several Al tolerance-related parameters including relative net root growth (RNRG), root apex Al accumulation, Al-activated root organic acid exudation, and expression of the maize Al tolerance gene, ZmMATE1, were used to classify Kenyan maize accessions.

Results

Based on RNRG, 42 %, 28 %, and 30 % of the lines were classified as highly tolerant, moderately tolerant and sensitive, respectively. Tolerant accessions accumulated less Al in their root apices compared to sensitive lines. The Kenyan maize line, CON 5, and the Brazilian standard for tolerance, Cateto, exhibited the greatest Al tolerance based on RNRG, but CON 5 had only about 50 % of ZmMATE1 gene expression relative to Cateto. CON 5 also had low root apex Al content and high citrate exudation, suggesting that it may employ a citrate transporter other than ZmMATE1.

Conclusions

We identified a very Al tolerant Kenyan maize line whose Al tolerance may be based in part on a novel tolerance gene. The maize lines identified in this study are useful germplasm for the development of varieties suitable for agriculture on acid soils in Kenya.

     

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.     

Tolerance of Hordeum marinum accessions to O2 deficiency, salinity and these stresses combined

Background and Aims

When root-zone O₂ deficiency occurs together with salinity, regulation of shoot ion concentrations is compromised even more than under salinity alone. Tolerance was evaluated amongst 34 accessions of Hordeum marinum, a wild species in the Triticeae, to combined salinity and root-zone O₂ deficiency. Interest in H. marinum arises from the potential to use it as a donor for abiotic stress tolerance into wheat.

Methods

Two batches of 17 H. marinum accessions, from (1) the Nordic Gene Bank and (2) the wheat belt of Western Australia, were exposed to 0·2 or 200 mol m⁻³ NaCl in aerated or stagnant nutrient solution for 28–29 d. Wheat (Triticum aestivum) was included as a sensitive check species. Growth, root porosity, root radial O₂ loss (ROL) and leaf ion (Na⁺, K⁺, Cl⁻) concentrations were determined.

Key Results

Owing to space constraints, this report is focused mainly on the accessions from the Nordic Gene Bank. The 17 accessions varied in tolerance; relative growth rate was reduced by 2–38 % in stagnant solution, by 8–42 % in saline solution (aerated) and by 39–71 % in stagnant plus saline treatment. When in stagnant solution, porosity of adventitious roots was 24–33 %; salinity decreased the root porosity in some accessions, but had no effect in others. Roots grown in stagnant solution formed a barrier to ROL, but variation existed amongst accessions in apparent barrier ‘strength’. Leaf Na⁺ concentration was 142–692 µmol g⁻¹ d. wt for plants in saline solution (aerated), and only increased to 247–748 µmol g⁻¹ d. wt in the stagnant plus saline treatment. Leaf Cl⁻ also showed only small effects of stagnant plus saline treatment, compared with saline alone. In comparison with H. marinum, wheat was more adversely affected by each stress alone, and particularly when combined; growth reductions were greater, adventitious root porosity was 21 %, it lacked a barrier to ROL, leaf K⁺ declined to lower levels, and leaf Na⁺ and Cl⁻ concentrations were 3·1–9-fold and 2·8–6-fold higher, respectively, in wheat.

Conclusions

Stagnant treatment plus salinity reduced growth more than salinity alone, or stagnant alone, but some accessions of H. marinum were still relatively tolerant of these combined stresses, maintaining Na⁺ and Cl⁻ ‘exclusion’ even in an O₂-deficient, saline rooting medium.Key words: Aerenchyma, combined salinity and waterlogging, leaf Cl⁻, leaf K⁺, leaf Na⁺, radial O₂ loss, salt tolerance, salinity–waterlogging interaction, sea barleygrass, waterlogging tolerance, wheat, wild Triticeae     

The lateral root initiation index: an integrative measure of primordium formation

Background and Aims

Lateral root initiation is an essential and continuous process in the formation of root systems; therefore, its quantitative analysis is indispensable. In this study a new measure of lateral root initiation is proposed and analysed, namely the lateral root initiation index (I_LRI), which defines how many lateral roots and/or primordia are formed along a parent-root portion corresponding to 100 cortical cells in a file.

Methods

For data collection, a commonly used root clearing procedure was employed, and a new simple root clearing procedure is also proposed. The I_LRI was determined as 100dl, where d is the density of lateral root initiation events (number mm⁻¹) and l is the average fully elongated cortical cell length (mm).

Key Results

Analyses of different Arabidopsis thaliana genotypes and of a crop plant, tomato (Solanum lycopersicum), showed that I_LRI is a more precise parameter than others commonly used as it normalizes root growth for variations in cell length. Lateral root primordium density varied in the A. thaliana accessions Col, Ler, Ws, and C24; however, in all accessions except Ws, I_LRI was similar under the same growth conditions. The nitrogen/carbon ratio in the growth medium did not change the lateral root primordium density but did affect I_LRI. The I_LRI was also modified in a number of auxin-related mutants, revealing new root branching phenotypes in some of these mutants. The rate of lateral root initiation increased with Arabidopsis seedling age; however, I_LRI was not changed in plants between 8 and 14 d post-germination.

Conclusions

The I_LRI allows for a more precise comparison of lateral root initiation under different growth conditions, treatments, genotypes and plant species than other comparable methods.Key words: Arabidopsis thaliana, auxin, lateral root density, lateral root initiation index, mutant phenotype, pericycle, root architecture, root branching, root primordium, Solanum lycopersicum     

Natural variation reveals relationships between pre-stress carbohydrate nutritional status and subsequent responses to xenobiotic and oxidative stress in Arabidopsis thaliana

Background

Soluble sugars are involved in responses to stress, and act as signalling molecules that activate specific or hormone cross-talk transduction pathways. Thus, exogenous sucrose treatment efficiently induces tolerance to the herbicide atrazine in Arabidopsis thaliana plantlets, at least partially through large-scale modifications of expression of stress-related genes.

Methods

Availability of sugars in planta for stress responses is likely to depend on complex dynamics of soluble sugar accumulation, sucrose–starch partition and organ allocation. The question of potential relationships between endogenous sugar levels and stress responses to atrazine treatment was investigated through analysis of natural genetic accessions of A. thaliana. Parallel quantitative and statistical analysis of biochemical parameters and of stress-sensitive physiological traits was carried out on a set of 11 accessions.

Key Results

Important natural variation was found between accessions of A. thaliana in pre-stress shoot endogenous sugar levels and responses of plantlets to subsequent atrazine stress. Moreover, consistent trends and statistically significant correlations were detected between specific endogenous sugar parameters, such as the pre-stress end of day sucrose level in shoots, and physiological markers of atrazine tolerance.

Conclusions

These significant relationships between endogenous carbohydrate metabolism and stress response therefore point to an important integration of carbon nutritional status and induction of stress tolerance in plants. The specific correlation between pre-stress sucrose level and greater atrazine tolerance may reflect adaptive mechanisms that link sucrose accumulation, photosynthesis-related stress and sucrose induction of stress defences.Key words: Arabidopsis thaliana, natural variation, atrazine sensitivity, carbon nutrition, endogenous soluble sugars, oxidative stress, sucrose, xenobiotic stress     

Targeted expression of SbMATE in the root distal transition zone is responsible for sorghum aluminum resistance

Aluminum (Al) toxicity is one of the major limiting factors for crop production on acid soils that comprise significant portions of the world's lands. Aluminum resistance in the cereal crop Sorghum bicolor is mainly achieved by Al‐activated root apical citrate exudation, which is mediated by the plasma membrane localized citrate efflux transporter encoded by SbMATE. Here we precisely localize tissue‐ and cell‐specific Al toxicity responses as well as SbMATE gene and protein expression in root tips of an Al‐resistant near‐isogenic line (NIL). We found that Al induced the greatest cell damage and generation of reactive oxygen species specifically in the root distal transition zone (DTZ), a region 1–3 mm behind the root tip where transition from cell division to cell elongation occurs. These findings indicate that the root DTZ is the primary region of root Al stress. Furthermore, Al‐induced SbMATE gene and protein expression were specifically localized to the epidermal and outer cortical cell layers of the DTZ in the Al‐resistant NIL, and the process was precisely coincident with the time course of Al induction of SbMATE expression and the onset of the recovery of roots from Al‐induced damage. These findings show that SbMATE gene and protein expression are induced when and where the root cells experience the greatest Al stress. Hence, Al‐resistant sorghum plants have evolved an effective strategy to precisely localize root citrate exudation to the specific site of greatest Al‐induced root damage, which minimizes plant carbon loss while maximizing protection of the root cells most susceptible to Al damage.     

Aluminium tolerance and high phosphorus efficiency helps Stylosanthes better adapt to low-P acid soils

Backgrond and Aims

Stylosanthes spp. (stylo) is one of the most important pasture legumes used in a wide range of agricultural systems on acid soils, where aluminium (Al) toxicity and phosphorus (P) deficiency are two major limiting factors for plant growth. However, physiological mechanisms of stylo adaptation to acid soils are not understood.

Methods

Twelve stylo genotypes were surveyed under field conditions, followed by sand and nutrient solution culture experiments to investigate possible physiological mechanisms of stylo adaptation to low-P acid soils.

Key Results

Stylo genotypes varied substantially in growth and P uptake in low P conditions in the field. Three genotypes contrasting in P efficiency were selected for experiments in nutrient solution and sand culture to examine their Al tolerance and ability to utilize different P sources, including Ca-P, K-P, Al-P, Fe-P and phytate-P. Among the three tested genotypes, the P-efficient genotype ‘TPRC2001-1’ had higher Al tolerance than the P-inefficient genotype ‘Fine-stem’ as indicated by relative tap root length and haematoxylin staining. The three genotypes differed in their ability to utilize different P sources. The P-efficient genotype, ‘TPRC2001-1’, had superior ability to utilize phytate-P.

Conclusions

The findings suggest that possible physiological mechanisms of stylo adaptation to low-P acid soils might involve superior ability of plant roots to tolerate Al toxicity and to utilize organic P and Al-P.Key words: Stylosanthes, phosphorus, P efficiency, organic P, Al toxicity, acid soil     

Uptake of aluminium into Arabidopsis root cells measured by fluorescent lifetime imaging

Background and Aims

Measuring the Al³⁺ uptake rate across the plasma membrane of intact root cells is crucial for understanding the mechanisms and time-course of Al toxicity in plants. However, a reliable method with the sufficient spatial and temporal resolution to estimate Al³⁺ uptake in intact root cells does not exist.

Methods

In the current study, fluorescent lifetime imaging (FLIM) analysis was used to quantify Al³⁺ uptake in the root-cell cytoplasm in vivo. This was performed via the estimation of the fluorescence lifetime of Al–lumogallion {5-chloro-3[(2,4-dihydroxyphenyl)azo]-2-hydroxybenzenesulfonic acid} complexes and measurements of intracellular pH while exposing arabidopsis seedlings to acidic and Al³⁺ stresses.

Key Results

The lifetime of Al–lumogallion complexes fluorescence is pH-dependent. The primary sites for Al³⁺ entry are the meristem and distal elongation zones, while Al³⁺ uptake via the cortex and epidermis of the mature root zone is limited. The maximum rates of Al uptake into the cytoplasm (2–3 µmol m⁻³ min⁻¹ for the meristematic root zone and 3–7 µmol m⁻³ min⁻¹ for the mature zone) were observed after a 30-min exposure to 100 µm AlCl₃ (pH 4·2). Intracellular Al concentration increased to 0·4 µm Al within the first 3 h of exposure to 100 µm AlCl₃.

Conclusions

FLIM analysis of the fluorescence of Al–lumogallion complexes can be used to reliably quantify Al uptake in the cytoplasm of intact root cells at the initial stages of Al³⁺ stress.Key words: Acid stress, Al³⁺, aluminium toxicity, Arabidopsis thaliana, low pH, fluorescent lifetime imaging (FLIM), lumogallion     

Genotypic differences in Al resistance and the role of cell-wall pectin in Al exclusion from the root apex in Fagopyrum tataricum

Background and Aims

Aluminium (Al) toxicity is one of the factors limiting crop production on acid soils. However, genotypic differences exist among plant species or cultivars in response to Al toxicity. This study aims to investigate genotypic differences among eight cultivars of tatary buckwheat (Fagopyrum tataricum) for Al resistance and explore the possible mechanisms of Al resistance.

Methods

Al resistance was evaluated based on relative root elongation (root elongation with Al/root elongation without Al). Root apex Al content, pectin content and exudation of root organic acids were determined and compared.

Key Results

Genotypic differences among the eight cultivars were correlated with exclusion of Al from the root apex. However, there was a lack of correlation between Al exclusion and Al-induced oxalate secretion. Interestingly, cell-wall pectin content of the root apex was generally lower in Al-resistant cultivars than in Al-sensitive cultivars. Although we were unable to establish a significant correlation between Al exclusion and pectin content among the eight cultivars, a strong correlation could be established among six cultivars, in which the pectin content in the most Al-resistant cultivar ‘Chuan’ was significantly lower than that in the most Al-sensitive cultivar ‘Liuku2’. Furthermore, root apex cell-wall pectin methylesterase activity (PME) was similar in ‘Chuan’ and ‘Liuku2’ in the absence of Al, but Al treatment resulted in increased PME activity in ‘Liuku2’ compared with ‘Chuan’. Immunolocalization of pectins also showed that the two cultivars had similar amounts of either low-methyl-ester pectins or high-methyl-ester pectins in the absence of Al, but Al treatment resulted in a more significant increase of low-methyl-ester pectins and decrease of high-methyl-ester pectins in ‘Liuku2’.

Conclusions

Cell-wall pectin content may contribute, at least in part, to differential Al resistance among tatary buckwheat cultivars.     

Root cortical burden influences drought tolerance in maize

Background and Aims

Root cortical aerenchyma (RCA) increases water and nutrient acquisition by reducing the metabolic costs of soil exploration. In this study the hypothesis was tested that living cortical area (LCA; transversal root cortical area minus aerenchyma area and intercellular air space) is a better predictor of root respiration, soil exploration and, therefore, drought tolerance than RCA formation or root diameter.

Methods

RCA, LCA, root respiration, root length and biomass loss in response to drought were evaluated in maize (Zea mays) recombinant inbred lines grown with adequate and suboptimal irrigation in soil mesocosms.

Key Results

Root respiration was highly correlated with LCA. LCA was a better predictor of root respiration than either RCA or root diameter. RCA reduced respiration of large-diameter roots. Since RCA and LCA varied in different parts of the root system, the effects of RCA and LCA on root length were complex. Greater crown-root LCA was associated with reduced crown-root length relative to total root length. Reduced LCA was associated with improved drought tolerance.

Conclusions

The results are consistent with the hypothesis that LCA is a driver of root metabolic costs and may therefore have adaptive significance for water acquisition in drying soil.     

Development of a Novel Aluminum Tolerance Phenotyping Platform Used for Comparisons of Cereal Aluminum Tolerance and Investigations into Rice Aluminum Tolerance Mechanisms

The genetic and physiological mechanisms of aluminum (Al) tolerance have been well studied in certain cereal crops, and Al tolerance genes have been identified in sorghum (Sorghum bicolor) and wheat (Triticum aestivum). Rice (Oryza sativa) has been reported to be highly Al tolerant; however, a direct comparison of rice and other cereals has not been reported, and the mechanisms of rice Al tolerance are poorly understood. To facilitate Al tolerance phenotyping in rice, a high-throughput imaging system and root quantification computer program was developed, permitting quantification of the entire root system, rather than just the longest root. Additionally, a novel hydroponic solution was developed and optimized for Al tolerance screening in rice and compared with the Yoshida''s rice solution commonly used for rice Al tolerance studies. To gain a better understanding of Al tolerance in cereals, comparisons of Al tolerance across cereal species were conducted at four Al concentrations using seven to nine genetically diverse genotypes of wheat, maize (Zea mays), sorghum, and rice. Rice was significantly more tolerant than maize, wheat, and sorghum at all Al concentrations, with the mean Al tolerance level for rice found to be 2- to 6-fold greater than that in maize, wheat, and sorghum. Physiological experiments were conducted on a genetically diverse panel of more than 20 rice genotypes spanning the range of rice Al tolerance and compared with two maize genotypes to determine if rice utilizes the well-described Al tolerance mechanism of root tip Al exclusion mediated by organic acid exudation. These results clearly demonstrate that the extremely high levels of rice Al tolerance are mediated by a novel mechanism, which is independent of root tip Al exclusion.Aluminum (Al) is the most abundant metal in the earth''s crust, constituting approximately 7% of the soil (Wolt, 1994). Al is predominately found as a key component of soil clays; however, under highly acidic soil conditions (pH < 5.0), Al³⁺ is solubilized into the soil solution and is highly phytotoxic. Al³⁺ causes a rapid inhibition of root growth that leads to a reduced and stunted root system, thus having a direct effect on the ability of a plant to acquire both water and nutrients. Approximately 30% of the world''s total land area and over 50% of potentially arable lands are acidic, with the majority (60%) found in the tropics and subtropics (von Uexkull and Mutert, 1995). Thus, acidic soils are a major limitation to crop production, particularly in the developing world.As a whole, cereal crops (Poaceae) provide an excellent model for studying Al tolerance because of their abundant genetic resources, large, active research communities, and importance to agriculture. In addition, work in one cereal species can rapidly translate into impact throughout the family. Previous research has focused on understanding the genetic and physiological mechanisms of Al tolerance in maize (Zea mays), sorghum (Sorghum bicolor), and wheat (Triticum aestivum). The most recognized physiological mechanism conferring Al tolerance in plants involves exclusion of Al from the root tip (Miyasaka et al., 1991; Delhaize and Ryan, 1995; Kochian, 1995; Kochian et al., 2004a, 2004b). The exclusion mechanism is primarily mediated by Al-activated exudation of organic acids such as malate, citrate, or oxalate from the root apex, the site of Al toxicity (Ryan et al., 1993, 2001; Ma et al., 2001). These organic acids chelate Al in the rhizosphere, reducing the concentration and toxicity of Al at the growing root tip (Ma et al., 2001). Phosphate has also been identified as a class of root exudates involved in cation chelation and therefore can be considered a potential exudate involved in Al exclusion from the root tip (Pellet et al., 1996).Al-activated malate and citrate anion efflux transporters have been cloned from wheat (ALMT1; Sasaki et al., 2004) and sorghum (SbMATE; Magalhaes et al., 2007), and root citrate efflux transporters have been implicated in Al tolerance in maize (Piñeros and Kochian, 2001; Zhang et al., 2001). Recently, a maize homolog of sorghum SbMATE was shown to be the root citrate efflux transporter that plays a role in maize Al tolerance (Maron et al., 2010). Although organic acids have been shown to play a major role in Al tolerance in these species, another exclusion mechanism has been identified in an Arabidopsis (Arabidopsis thaliana) mutant, where a root-mediated increase in rhizosphere pH lowers the Al³⁺ activity and thus participates in Al exclusion from the root apex (Degenhardt et al., 1998). Furthermore, there is clear evidence that tolerance in maize cannot be fully explained by organic acid release (Piñeros et al., 2005). These types of findings strongly suggest that multiple Al tolerance mechanisms exist in plants.Rice (Oryza sativa) has been reported to be the most Al-tolerant cereal crop under field conditions, capable of withstanding significantly higher concentrations of Al than other major cereals (Foy, 1988). Despite this fact, very little is known about the physiological mechanisms of Al tolerance in rice. Two independent studies have identified increased Al accumulation in the root apex in susceptible compared with Al-tolerant rice varieties, but no differences were observed in organic acid exudation or rhizosphere pH (Ma et al., 2002; Yang et al., 2008). These studies suggest that rice may contain novel physiological and/or genetic mechanisms that confer significantly higher levels of Al tolerance than those found in other cereals. A more thorough analysis is required to clarify the mechanism of Al tolerance in rice.Cultivated rice is characterized by deep genetic divergence between the two major varietal groups: Indica and Japonica (Dally and Second, 1990; Garris et al., 2005; Hu et al., 2006; Londo et al., 2006). Extensive selection pressure over the last 10,000 years has resulted in the formation of five genetically distinct subpopulations: indica and aus within the Indica varietal group, and temperate japonica, tropical japonica, and aromatic/groupV within the Japonica varietal group (Garris et al., 2005; Caicedo et al., 2007; K. Zhao and S. McCouch, personal communication). (Note: When referring to varietal groups, the first letter will be capitalized, while lowercase letters will be used to refer to the subpopulation groups.) Subpopulation differences in trait performance are often significant, particularly with respect to biotic and abiotic stress (Champoux et al., 1995; Lilley et al., 1996; Garris et al. 2003; Xu et al., 2009). This can lead to confusion because trait or performance differences may be confounded with subpopulation structure, leading to false positives (type 1 error; Devlin and Roeder, 1999; Pritchard and Donnelly, 2001; Yu et al., 2006; Zhao et al., 2007). Therefore, it is important to consider the subpopulation origin of genotypes being compared when studying the genetics and physiology of Al tolerance in rice.Al tolerance screening is typically conducted by comparing root growth of seedlings grown in hydroponic solutions, with and without Al (Piñeros and Kochian, 2001; Magalhaes et al., 2004; Sasaki et al., 2004). Sorghum and maize are often screened for Al tolerance in Magnavaca''s nutrient solution (Piñeros and Kochian, 2001; Magalhaes et al., 2004; Piñeros et al., 2005), while rice seedlings are typically grown in Yoshida''s solution (Yoshida et al., 1976). Furthermore, Al concentrations used to screen for Al tolerance in maize (222 μm), sorghum (148 μm), and wheat (100 μm) are significantly lower than those used for screening Al tolerance in rice (1,112–1,482 μm; Wu et al., 2000; Nguyen et al., 2001, 2002, 2003). These differences in chemical composition of the nutrient solutions make it difficult to directly compare plant response to Al across these cereals. In rice, the high Al concentrations required to observe significant differences in root growth between susceptible and resistant varieties also complicate Al tolerance screening due to the precipitation of Al along with other elements. The result is that control (−Al) and treatment (+Al) solutions may differ with regard to essential mineral nutrients that react with Al, leading to differences in growth not directly attributable to Al. Additionally, because the active form of Al that is toxic to root growth is Al³⁺, any Al that precipitates out of solution has no effect on root growth (Kochian et al., 2004a). In a hydroponic solution, Al may be found in one of four forms: (1) as free Al³⁺, where it actively inhibits root growth; (2) precipitated with other elements and essentially unavailable to inhibit plant growth; (3) different hydroxyl monomers of Al, which are not believed to be toxic to roots (Parker et al., 1988); or (4) complexed with other elements in an equilibrium between its active and inactive states. The degree to which Al inhibits root growth is primarily dependent upon the activity of free Al³⁺ in solution (Kochian et al., 2004a).The objectives of this study were to (1) develop and optimize a suitable nutrient solution and high-throughput Al tolerance screening method for rice; (2) quantify and compare differences in Al tolerance between maize, sorghum, wheat, and rice; and (3) use the developed screening methods to determine if rice utilizes the organic acid-mediated Al exclusion mechanism that is observed in maize, sorghum, and wheat.     

Detection and validation of stay-green QTL in post-rainy sorghum involving widely adapted cultivar,M35-1 and a popular stay-green genotype B35

Background

Sorghum [Sorghum bicolor (L.) Moench] is an important dry-land cereal of the world providing food, fodder, feed and fuel. Stay-green (delayed-leaf senescence) is a key attribute in sorghum determining its adaptation to terminal drought stress. The objective of this study was to validate sorghum stay-green quantitative trait loci (QTL) identified in the past, and to identify new QTL in the genetic background of a post-rainy adapted genotype M35-1.

Results

A genetic linkage map based on 245 F₉ Recombinant Inbred Lines (RILs) derived from a cross between M35-1 (more senescent) and B35 (less senescent) with 237 markers consisting of 174 genomic, 60 genic and 3 morphological markers was used. The phenotypic data collected for three consecutive post-rainy crop seasons on the RIL population (M35-1 × B35) was used for QTL analysis. Sixty-one QTL were identified for various measures of stay-green trait and each trait was controlled by one to ten QTL. The phenotypic variation explained by each QTL ranged from 3.8 to 18.7%. Co-localization of QTL for more than five traits was observed on two linkage groups i.e. on SBI-09-3 flanked by S18 and Xgap206 markers and, on SBI-03 flanked by XnhsbSFCILP67 and Xtxp31. QTL identified in this study were stable across environments and corresponded to sorghum stay-green and grain yield QTL reported previously. Of the 60 genic SSRs mapped, 14 were closely linked with QTL for ten traits. A genic marker, XnhsbSFCILP67 (Sb03g028240) encoding Indole-3-acetic acid-amido synthetase GH3.5, was co-located with QTL for GLB, GLM, PGLM and GLAM on SBI-03. Genes underlying key enzymes of chlorophyll metabolism were also found in the stay-green QTL regions.

Conclusions

We validated important stay-green QTL reported in the past in sorghum and detected new QTL influencing the stay-green related traits consistently. Stg2, Stg3 and StgB were prominent in their expression. Collectively, the QTL/markers identified are likely candidates for subsequent verification for their involvement in stay-green phenotype using NILs and to develop drought tolerant sorghum varieties through marker-assisted breeding for terminal drought tolerance in sorghum.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-909) contains supplementary material, which is available to authorized users.     

The evolutionary history of sea barley (Hordeum marinum) revealed by comparative physical mapping of repetitive DNA

Background and Aims Hordeum marinum

is a species complex that includes the diploid subspecies marinum and both diploid and tetraploid forms of gussoneanum. Their relationships, the rank of the taxa and the origin of the polyploid forms remain points of debate. The present work reports a comparative karyotype analysis of six H. marinum accessions representing all taxa and cytotypes.

Methods

Karyotypes were determined by analysing the chromosomal distribution of several tandemly repeated sequences, including the Triticeae cloned probes pTa71, pTa794, pAs1 and pSc119·2 and the simple sequence repeats (SSRs) (AG)₁₀, (AAC)₅, (AAG)₅, (ACT)₅ and (ATC)₅.

Key Results

The identification of each chromosome pair in all subspecies and cytotypes is reported for the first time. Homologous relationships are also established. Wide karyotypic differences were detected within marinum accessions. Specific chromosomal markers characterized and differentiated the genomes of marinum and diploid gussoneanum. Two subgenomes were detected in the tetraploids. One of these had the same chromosome complement as diploid gussoneanum; the second subgenome, although similar to the chromosome complement of diploid H. marinum sensu lato, appeared to have no counterpart in the marinum accessions analysed here.

Conclusions

The tetraploid forms of gussoneanum appear to have come about through a cross between a diploid gussoneanum progenitor and a second, related—but unidentified—diploid ancestor. The results reveal the genome structure of the different H. marinum taxa and demonstrate the allopolyploid origin of the tetraploid forms of gussoneanum.