Intron-length polymorphism identifies a Y2K4 dehydrin variant linked to superior freezing tolerance in alfalfa

Breeding alfalfa (Medicago sativa L.) with superior freezing tolerance could be accelerated by the identification of molecular markers associated to that trait. Dehydrins are a group of highly hydrophilic proteins that have been related to low temperature tolerance. We previously identified a dehydrin restriction fragment length polymorphism (RFLP) among populations recurrently selected for superior tolerance to freezing (TF). Analysis of crosses between genotypes with (D+) or without (D−) that RFLP revealed a significant impact on freezing tolerance. In this study, we sought to develop a PCR marker for freezing tolerance based on prior evidence of a relationship between size variation in Y₂K₄ dehydrins and the RFLP. Results confirm the enrichment of Y₂K₄ sequences of intermediate size (G2 group) in response to recurrent selection and in the D+ progeny. Analysis of genomic sequences revealed significant intron-length polymorphism (ILP) within the G2 group. G2 sequences with a characteristic short intron were more frequently found in D+ genotypes. Amplification using sequence-characterized amplified region (SCAR) primers bordering the intron confirmed an increase in the number of fragments with small introns in the D+ progeny and in the ATF5 population obtained after five cycles of recurrent selection for superior TF within the cultivar Apica (ATF0). Conversely, there was a reduction in the number of fragments with long introns in the D+ progeny and in ATF5 as compared to ATF0. Recurrent selection for superior tolerance to freezing in combination with ILP identified a sequence variant of Y₂K₄ dehydrins associated to the phenotypic response to selection.     

Variation of total soluble seminal root proteins of tetraploid wild and cultivated wheat induced at cold acclimation and freezing

The relationship between total soluble seminal root proteins induced at cold acclimation and freezing tolerance in tetraploid wild wheat Aegilops L. (Ae. biuncialis, Ae. cylindrica) and cultivated wheat Triticum turgitum L. (Firat-93, Harran-95) was investigated. Cold acclimation was performed at 0 °C for 7 days. Freezing tolerance was determined with survived roots after freezing treatments at −5 and/or −7 °C for 3, 6, 12 and 24 h. At −5°C, all tetraploid genotypes showed over 60% tolerance for 3 h. This effect was also present in wild wheat for 6 h, but was decreased in cultivated wheat to 30–35% tolerance for 6 h. Only Ae. biuncialis was able to show 52% tolerance just for 3 h freezing period at −7 °C. However, all the genotypes were not survived at −7 °C, for 6, 12 and 24 h. Cold acclimation induced greater amounts of new soluble seminal root proteins in tolerant Ae. biuncialis (29–104 kDa, pI 5.4–7.4) than in sensitive Harran-95 (29–66 kDa, pI 6.1–8.3). Synthesis and accumulation of these proteins may be related to degree of freezing tolerance of these genotypes.     

Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.)

Nucleotide variation at several cold candidate genes including seven members of the dehydrin gene family was surveyed in haplotypes of Scots pine (Pinus sylvestris) sampled in populations showing divergence for cold tolerance in Europe. Patterns of nucleotide diversity, linkage disequilibrium, and frequency spectrum of alleles were compared between north and south populations to search for signs of directional selection potentially underlying adaptation to cold. Significant differentiation between populations in allelic frequency or haplotype structure was detected at dhn1, dhn3, and abaH loci. Allelic dimorphism with no evidence of haplotype clustering by geographical distribution was found at dhn9. An excess of fixed non-synonymous mutations as compared to the outgroup P. pinaster pine species was found at dhn1. Differences in nucleotide polymorphisms were found between the members of the Kn class of dehydrin upregulated during cold acclimation (average π_sil = 0.004) as compared to the SKn class (average π_sil = 0.024). The multilocus nucleotide diversity at silent sites (θ _W = 0.009) was moderate compared to other conifer species, but higher than previous estimates for Scots pine. There was an excess of rare and high frequency derived variants as revealed by significantly negative multilocus value of Tajima’s D (D = −0.72, P < 0.01) and negative mean value of Fay and Wu H statistics (H = −0.50). The level of linkage disequilibrium decayed rapidly with an average expected r ² of 0.2 at about 200 bp. Overall, there was a positive correlation between polymorphism and divergence at ten loci when outgroup sequence was available. The discovered polymorphism will be used for further evaluation of the adaptive role of genes through association mapping studies. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A 25-kDa dehydrin associated with genotype- and age-dependent leaf freezing-tolerance in Rhododendron: a genetic marker for cold hardiness?

Dehydrins are plant proteins that may play a critical role in stabilizing cell functions during freezing and other dehydrative stresses. This study examines whether dehydrin expression in leaves is associated with varying levels of freezing-tolerance among F₂ segregants, species, and cultivars of evergreen Rhododendron. Experiments were also conducted to determine whether physiological and chronological aging affects freezing-tolerance and dehydrin accumulation in Rhododendron leaf tissues. Our results indicate that in cold-acclimated F₂ populations, levels of a 25-kDa dehydrin were closely associated with differences in leaf freezing-tolerance (LFT) among segregants. Studies of wild and cultivated plants indicated that LFT increased with both chronological age and developmental phase-change (juvenile to mature plants) and that this trend was accompanied by increased accumulation of the 25-kDa dehydrin. It is suggested that presence or absence of the 25-kDa dehydrin could serve as a genetic marker to distinguish between super cold-hardy and less cold-hardy rhododendron genotypes. Similarly, the relative level of this protein within a genotype can serve as a physiological indicator of freezing-tolerance status under a range of phenological (acclimation) or developmental (age) conditions. Received: 5 March 1999 / Accepted: 12 May 1999     

The oatmeal nematode <Emphasis Type="Italic">Panagrellus redivivus</Emphasis> survives moderately low temperatures by freezing tolerance and cryoprotective dehydration

The cold tolerance abilities of only a few nematode species have been determined. This study shows that the oatmeal nematode, Panagrellus redivivus, has modest cold tolerance with a 50% survival temperature (S ₅₀) of −2.5°C after cooling at 0.5°C min⁻¹ and freezing for 1 h. It can survive low temperatures by freezing tolerance and cryoprotective dehydration; although freezing tolerance appears to be the dominant strategy. Freezing survival is enhanced by low temperature acclimation (7 days at 5°C), with the S ₅₀ being lowered by a small but significant amount (0.42°C). There is no cold shock or rapid cold hardening response under the conditions tested. Cryoprotective dehydration enhances the ability to survive freezing (the S ₅₀ is lowered by 0.55°C, compared to the control, after 4 h freezing at −1°C) and this effect is in addition to that produced by acclimation. Breeding from survivors of a freezing stress did not enhance the ability to survive freezing. The cold tolerance abilities of this nematode are modest, but sufficient to enable it to survive in the cold temperate environments it inhabits.     

Freezing tolerance of <Emphasis Type="Italic">Porphyra yezoensis</Emphasis> (Bangiales,Rhodophyta) gametophyte assessed by chlorophyll fluorescence

In January and February 2010, heavy sea ice formed along the coast of the Bohai Sea and the northern Yellow Sea, China. Intertidal organisms were subjected to serious freezing stress. In this study, we investigated the freezing tolerance of the upper intertidal economic seaweed Porphyra yezoensis. The maximum photochemical efficiency of PS II (F _v/F _m) in undehydrated thalli remained high after 24 h at −2°C and that in dehydrated thalli decreased in a proportion to thallial water loss. F _v/F _m dropped sharply after 24 h at −20°C, regardless of absolute cellular water content (AWC). The F _v/F _m in frozen thalli recovered rapidly at 0–20°C. A wide range of water loss in the thalli enhanced their tolerance to freezing. F _v/F _m values in undehydrated thalli dropped sharply after 3 d at −2°C or 10 d at −20°C while those in dehydrated thalli (20–53% AWCs) remained at high levels after 9 d at −2°C or 30 d at −20°C. These results indicate that P. yezoensis has high freezing tolerance by means of dehydration during the ebb tide and rapid recovery of F _v/F _m from freezing. A strategy of P. yezoensis industry to avoid heavy loss during freezing season is discussed based on these findings.     

Tissue culture evaluation of NaCl tolerance in Medicago species: Cellular versus whole plant response

Tissue culture responses to three levels of NaCl (0, 85mM and 170 mM) were evaluated in several Medicago species including: M. dzhawakhetica, M. marina, M. rhodopea, M. rupestris, M. sativa (alfalfa) and M. suffruticosa. The whole plant responses of the same genotypes were evaluated in half-strength Hoagland's solution containing 0, 51.5, and 103 mM NaCl. One or more genotypes of M. dzhawakhetica, M. rhodopea, M. rupestris, and M. sativa exhibited in vitro NaCl tolerance at 85 mM. In addition, one genotype each of M. dzhawakhetica, M. rhodopea, and M. sativa was tolerant of 170 mM NaCl. However, all of the genotypes that demonstrated NaCl tolerance in vitro were NaCl sensitive at the whole plant level. Conversely, M. marina the only species exhibiting whole plant NaCl tolerance, had the most NaCl sensitive genotypes at the in vitro level. Although an in vitro NaCl tolerance mechanism which confers whole plant NaCl tolerance was not observed, a potential NaCl tolerance germplasm source, M. marina, was identified.     

CCL2 −2518 A/G single nucleotide polymorphism as a risk factor for breast cancer

The contribution of the CCL2 −2518 A>G (rs 1024611) polymorphism in the occurrence and progression of various cancers has been found to be discordant. We studied the prevalence of the CCL2 −2518 A>G polymorphism in patients with breast cancer (n = 160) and controls (n = 323) in a sample of the Polish population. There were no significant differences in CCL2 −2518 A>G genotypes between patients with breast tumors and controls. Odds ratio (OR) for patients bearing the GG genotype was 1.481 (95% CI = 0.7711–2.845, P = 0.2358), and OR of the GG and AG genotypes was 0.7269 (95% CI = 0.4967–1.064, P = 0.1002). There was also no significant distinction in the prevalence of alleles between patients and healthy individuals. OR for the CCL2 −2518 G allele frequency was 0.8903 (95% CI = 0.6611–1.199, P = 0.4441). Analysis of the association between tumor size, lymph node metastases, histological grade, and distribution of genotypes and alleles for the CCL2 −2518 A>G polymorphism also did not show significant differences. Our results did not show association of the CCL2 −2518 A>G polymorphism with breast cancer occurrence and clinical characteristics in a sample of the Polish cohort.     

Freezing tolerance, cold acclimation and oxidative stress in potato. Paraquat tolerance is related to acclimation but is a poor indicator of freezing tolerance

Potato is a species commonly cultivated in temperate areas where the growing season may be interrupted by frosts, resulting in loss of yield. Cultivated potato, Solanum tuberosum, is freezing sensitive, but it has several freezing-tolerant wild potato relatives, one of which is S. commersonii. Our study was aimed to resolve the relationship between enhanced freezing tolerance, acclimation capacity and capacity to tolerate active oxygen species. To be able to characterize freezing tolerant ideotypes, a potato population (S1), which segregates in freezing tolerance, acclimation capacity and capacity to tolerate superoxide radicals, was produced by selfing a somatic hybrid between a freezing-tolerant Solanum commersonii (LT₅₀=-4.6°C) and -sensitive S. tuberosum (LT₅₀=-3.0°C). The distribution of non-acclimated freezing tolerance (NA-freezing tolerance) of the S1 population varied between the parental lines and we were able to identify genotypes, having significantly high or low NA-freezing tolerance. When a population of 25 genotypes was tested both for NA-freezing and paraquat (PQ) tolerance, no correlation was found between these two traits (R = 0.02). However, the most NA-freezing tolerant genotypes were also among the most PQ tolerant plants. Simultaneously, one of the NA-freezing sensitive genotypes (2022) (LT₅₀=-3.0°C) was observed to be PQ tolerant. These conflicting results may reflect a significant, but not obligatory, role of superoxide scavenging mechanisms in the NA-freezing tolerance of S. commersonii. The freezing tolerance after cold acclimation (CA-freezing tolerance) and the acclimation capacity (AC) was measured after acclimation for 7 days at 4/2°C. Lack of correlation between NA-freezing tolerance and AC (R =-0.05) in the S1 population points to independent genetic control of NA-freezing tolerance and AC in Solanum sp. Increased freezing tolerance after cold acclimation was clearly related to PQ tolerance of all S1 genotypes, especially those having good acclimation capacity. The rapid loss of improved PQ tolerance under deacclimation conditions confirmed the close relationship between the process of cold acclimation and enhanced PQ tolerance. Here, we report an increased PQ tolerance in cold-acclimated plants compared to non-acclimated controls. However, we concluded that high PQ tolerance is not a good indicator of actual freezing tolerance and should not be used as a selectable marker for the identification of a freezing-tolerant genotype.     

The effect of drought stress on chlorophyll fluorescence in Lolium-Festuca hybrids

The effects of drought on photochemical efficiency of PSII in leaves of 22 hybrids of Festuca pratensis × Lolium multiflorum and Festuca pratensis × Lolium perenne and of Festuca pratensis cv. Skra were investigated. A significant decrease of electron transport efficiency (about 25%) in PSII (Φ_PSII) was not found before 9 days of seedling growth in hydroponics with water potential (Ψ_w) equal to −0.8 MPa (simulated “soil drought”). The decrease of Φ_PSII was similarly related to that of excitation energy capture by open PSII reaction centre (Fv’/Fm’) and also to the decrease of the proportion of oxidized to reduced Q_A (photochemical fluorescence quenching, q_p). According to the drought prolongation, variation of all parameters of fluorescence between genotypes significantly increased. The seedlings of some genotypes were able to recover electron transport efficiency in PSII after increasing water potential in nutrient solution (removing the “soil drought”). When plants grew in containers with soil and 4 genotypes with the highest sensitivity of electron transport to drought (S) as well as 4 genotypes with the highest tolerance (T) were compared 17 days after watering ceased, Ψ_w in leaves considerably decreased, but the differences between S and T genotypes were often not significant in this respect. The differences between S and T genotypes, as values of Fv/Fm were concerned, also appeared small (about 5%), similarly as that of Fv’/Fm’ (5%), q_p (12%) and Φ_PSII (about 15%). Drought stress increased non-photochemical quenching of chlorophyll fluorescence (NPQ) 15 to 47% and this could protect the PSII reaction centres from damages because of energy excess. The increase of NPQ was not closely connected with drought resistance of plants because it was similar in some genotypes tolerant to dehydration as well as in sensitive ones. The results of the experiments suggest that resources of genetic variability in Festulolium may be sufficient for revealing differences between genotypes on the basis of measurement of chlorophyll a fluorescence, as far as their tolerance to soil drought is concerned. As the tolerance of PSII against drought is high, the determinations of fluorescence should be performed rather under severe stress. Such methods seem to be useful for selection of genotypes with high drought tolerance as well as with the ability to at least partial repairing of PSII after drought.     

Association of the −33C/G <Emphasis Type="Italic">OSF</Emphasis>-<Emphasis Type="Italic">2</Emphasis> and the 140A/G <Emphasis Type="Italic">LF</Emphasis> gene polymorphisms with the risk of chronic rhinosinusitis with nasal polyps in a Polish population

Nasal polyps are strongly associated with a risk of chronic rhinosinusitis development as well as other obstruction including asthma and allergy. The following study tested the association of the 140A/G polymorphism of lactoferine (LF) encoding gene and the −33C/G polymorphism of osteoblast-specific factor-2 (OSF-2) encoding gene with a risk of chronic rhinosinusitis with nasal polyps in a Polish population. One hundred ninety five patients of chronic rhinosinusitis with nasal polyps as well as 200 sex, age and ethnicity matched control subjects without chronic sinusitis and nasal polyps were enrolled in this study. Among the group of patients 63 subjects were diagnosed with allergy and 65 subjects with asthma, respectively. DNA was isolated from peripheral blood lymphocytes of patients as well as controls and gene polymorphisms were analyzed by restriction fragments length polymorphism polymerase chain reaction (RFLP-PCR). We reported that the 140A/G LF (OR 4.78; 95% CI 3.07–7.24), the −33C/G OSF-2 OR 3.48; 95% CI 2.19–5.52) and the −33G/G OSF-2 (OR 16.45; 95% CI 6.71–40.30) genotypes were associated with an increased risk of chronic rhinosinusitis with nasal polyps among analyzed group of patients. Moreover, the group of patients without allergy or asthma indicated the association of the −33C/G (OR 3.72; 95% CI 2.24–6.19 and OR 15.11; 95% CI 5.91–38.6) and −33G/G (OR 3.73; 95% CI 2.24–6.19 and OR 14.07; 95% CI 5.47–36.16) genotypes of the OSF-2 as wells as 140A/G (OR 3.89; 95% CI 2.40–6.31 and OR 3.62; 95% CI 2.45–5.34) genotype of OSF-2 with an increased risk of chronic rhinosinusitis with nasal polyps. Finally, it was also found that the selected group of patients with allergy or asthma indicated a very strong association of the −33C/G (OR 2.40; 95% CI 1.23–4.69 and OR 2.40; 95% CI 1.23–4.69, respectively) and −33G/G (OR 16.01; 95% CI 5.77–44.41 and OR 17.90; 95% CI 6.53–49.05, respectively) genotypes of the OSF-2 as wells as 140A/G (OR 3.22; 95% CI 1.74–6.11 and OR 3.25; 95% CI 1.75–6.04, respectively) genotypes with an increased risk of chronic rhinosinusitis with nasal polyps. Thus, our results suggest that LF and OSF-2 gene polymorphisms may have deep impact on the risk of rhinosinusitis nasal polyps’ formation which may also depend on asthma or allergy. Our results showed that the 140A/G polymorphism of LF gene and the −33C/G polymorphism of the OSF-2 gene may be associated with the risk of chronic rhinosinusitis with nasal polyps in a Polish population.     

Quantitative trait loci and candidate gene mapping of aluminum tolerance in diploid alfalfa

Aluminum (Al) toxicity in acid soils is a major limitation to the production of alfalfa (Medicago sativa subsp. sativa L.) in the USA. Developing Al-tolerant alfalfa cultivars is one approach to overcome this constraint. Accessions of wild diploid alfalfa (M. sativa subsp. coerulea) have been found to be a source of useful genes for Al tolerance. Previously, two genomic regions associated with Al tolerance were identified in this diploid species using restriction fragment length polymorphism (RFLP) markers and single marker analysis. This study was conducted to identify additional Al-tolerance quantitative trait loci (QTLs); to identify simple sequence repeat (SSR) markers that flank the previously identified QTLs; to map candidate genes associated with Al tolerance from other plant species; and to test for co-localization with mapped QTLs. A genetic linkage map was constructed using EST-SSR markers in a population of 130 BC₁F₁ plants derived from the cross between Al-sensitive and Al-tolerant genotypes. Three putative QTLs on linkage groups LG I, LG II and LG III, explaining 38, 16 and 27% of the phenotypic variation, respectively, were identified. Six candidate gene markers designed from Medicago truncatula ESTs that showed homology to known Al-tolerance genes identified in other plant species were placed on the QTL map. A marker designed from a candidate gene involved in malic acid release mapped near a marginally significant QTL (LOD 2.83) on LG I. The SSR markers flanking these QTLs will be useful for transferring them to cultivated alfalfa via marker-assisted selection and for pyramiding Al tolerance QTLs.     

Freezing tolerance of ectomycorrhizal fungi in pure culture

The ability to survive freezing and thawing is a key factor for the existence of life forms in large parts of the world. However, little is known about the freezing tolerance of mycorrhizal fungi and their role in the freezing tolerance of mycorrhizas. Threshold temperatures for the survival of these fungi have not been assessed experimentally. We grew isolates of Suillus luteus, Suillus variegatus, Laccaria laccata, and Hebeloma sp. in liquid culture at room temperature. Subsequently, we exposed samples to a series of temperatures between +5°C and −48°C. Relative electrolyte leakage (REL) and re-growth measurements were used to assess the damage. The REL test indicated that the lethal temperature for 50% of samples (LT₅₀) was between −8.3°C and −13.5°C. However, in the re-growth experiment, all isolates resumed growth after exposure to −8°C and higher temperatures. As many as 64% of L. laccata samples but only 11% in S. variegatus survived −48°C. There was no growth of Hebeloma and S. luteus after exposure to −48°C, but part of their samples survived −30°C. The fungi tolerated lower temperatures than was expected on the basis of earlier studies on fine roots of ectomycorrhizal trees. The most likely freezing tolerance mechanism here is tolerance to apoplastic freezing and the concomitant intracellular dehydration with consequent concentrating of cryoprotectant substances in cells. Studying the properties of fungi in isolation promotes the understanding of the role of the different partners of the mycorrhizal symbiosis in the freezing tolerance.     

The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins

The presence of shared conserved inserts and deletions (indels or signature sequences) in proteins provides a powerful means for understanding the evolutionary relationships among the Bacteria. Using such indels, all of the main groups within the Bacteria can be defined in clear molecular terms and it has become possible to deduce that they branched from a common ancestor in the following order: Low G+C Gram-positive → High G+C Gram-positive → Deinococcus–Thermus → Cyanobacteria → Spirochetes → Aquifex–Chlamydia–Cytophaga → Proteobacteria-1 (ε, δ) → Proteobacteria-2 (α)→ Proteobacteria-3 (β) → Proteobacteria -4 (γ). The usefulness of this approach for understanding bacterial phylogeny was examined here using sequence data from various completed bacterial genomes. By using 12 indels in highly conserved and widely represented proteins, the species from all 41 completed bacterial genomes were assigned to different groups; and the observed distribution of these indels in different species was then compared with that predicted by the signature sequence model. The presence or absence of these indels in various proteins in different bacteria followed the pattern exactly as predicted; and, in more than 450 observations, no exceptions or contradictions in the placement of indels were observed. These results provide strong evidence that lateral gene transfer events have not affected the genes containing these indels to any significant extent. The phylogenetic placement of bacteria into different groups based on signature sequences also showed an excellent correlation with the 16 S rRNA with 39 of the 41 species assigned to the same group by both methods. These results strongly vindicate the usefulness of the signature sequence approach to understanding phylogeny within the Bacteria and show that it provides a reliable and internally consistent means for the placement of bacterial species into different groups and for determining the relative branching order of the groups. Electronic Publication