The Relationship between the Expression of Ethylene-Related Genes and Papaya Fruit Ripening Disorder Caused by Chilling Injury

Papaya (Carica papaya L.) is sensitive to low temperature and easy to be subjected to chilling injury, which causes fruit ripening disorder. This study aimed to investigate the relationship between the expression of genes related to ethylene and fruit ripening disorder caused by chilling injury. Papaya fruits were firstly stored at 7°C and 12°C for 25 and 30 days, respectively, then treated with exogenous ethylene and followed by ripening at 25°C for 5 days. Chilling injury symptoms such as pulp water soaking were observed in fruit stored at 7°C on 20 days, whereas the coloration and softening were completely blocked after 25 days, Large differences in the changes in the expression levels of twenty two genes involved in ethylene were seen during 7°C-storage with chilling injury. Those genes with altered expression could be divided into three groups: the group of genes that were up-regulated, including ACS1/2/3, EIN2, EIN3s/EIL1, CTR1/2/3, and ERF1/3/4; the group of genes that were down-regulated, including ACO3, ETR1, CTR4, EBF2, and ERF2; and the group of genes that were un-regulated, including ACO1/2, ERS, and EBF1. The results also showed that pulp firmness had a significantly positive correlation with the expression of ACS2, ACO1, CTR1/4, EIN3a/b, and EBF1/2 in fruit without chilling injury. This positive correlation was changed to negative one in fruit after storage at 7°C for 25 days with chilling injury. The coloring index displayed significantly negative correlations with the expression levels of ACS2, ACO1/2, CTR4, EIN3a/b, ERF3 in fruit without chilling injury, but these correlations were changed into the positive ones in fruit after storage at 7°C for 25 days with chilling injury. All together, these results indicate that these genes may play important roles in the abnormal softening and coloration with chilling injury in papaya.     

Growth and development temperature influences level of tolerance to high light stress

The influence of growth and development temperature on the relative tolerance of photosynthetic tissue to high light stress at chilling temperatures was investigated. Two tuber-bearing potato species, Solanum tuberosum L. cv Red Pontiac and Solanum commersonii were grown for 4 weeks, at either 12 or 24°C with 12 hours of about 375 micromoles per second per square meter of photosynthetically active radiation. Paired leaf discs were cut from directly across the midvein of leaflets of comparable developmental stage and light environment from each species at each growth temperature treatment. One disc of each pair was exposed to 1°C and about 1000 micromoles per second per square meter photosynthetically active radiation for 4 hours, and the other disc was held at 1°C in total darkness for the same duration. Photosynthetic tissue of S. tuberosum, developed at 12°C, was much more tolerant to high light and low temperature stress than tissue developed under 24°C conditions. Following the high light treatment, 24°C-grown S. tuberosum tissue demonstrated light-limited and light-saturated rates that were approximately 50% of their paired dark controls. In contrast, the 12°C-grown tissue from S. tuberosum that was subjected to the light stress showed only a 18 and 6% reduction in light-limited and light-saturated rates of photosynthetic oxygen evolution, respectively. Tissue from 24°C-grown S. commersonii was much less sensitive to the light stress than was tissue from S. tuberosum grown under the same conditions. The results presented here demonstrate that: (a) acclimation of S. tuberosum to lower temperature growth conditions with a constant light environment, results in the increased capacity of photosynthetic tissue to tolerate high light stress at chilling temperature and (b) following growth and development at relatively high temperatures S. commersonii, a frost- and heat-tolerant wild species, has a much greater tolerance to the high light stress at chilling temperature than does S. tuberosum cv Red Pontiac, a frost-sensitive cultivated species.     

Chilling- and Freezing- Induced Alterations in Cytosine Methylation and Its Association with the Cold Tolerance of an Alpine Subnival Plant,Chorispora bungeana

Chilling (0–18°C) and freezing (<0°C) are two distinct types of cold stresses. Epigenetic regulation can play an important role in plant adaptation to abiotic stresses. However, it is not yet clear whether and how epigenetic modification (i.e., DNA methylation) mediates the adaptation to cold stresses in nature (e.g., in alpine regions). Especially, whether the adaptation to chilling and freezing is involved in differential epigenetic regulations in plants is largely unknown. Chorispora bungeana is an alpine subnival plant that is distributed in the freeze-thaw tundra in Asia, where chilling and freezing frequently fluctuate daily (24 h). To disentangle how C. bungeana copes with these intricate cold stresses through epigenetic modifications, plants of C. bungeana were treated at 4°C (chilling) and -4°C (freezing) over five periods of time (0–24 h). Methylation-sensitive amplified fragment-length polymorphism markers were used to investigate the variation in DNA methylation of C. bungeana in response to chilling and freezing. It was found that the alterations in DNA methylation of C. bungeana largely occurred over the period of chilling and freezing. Moreover, chilling and freezing appeared to gradually induce distinct DNA methylation variations, as the treatment went on (e.g., after 12 h). Forty-three cold-induced polymorphic fragments were randomly selected and further analyzed, and three of the cloned fragments were homologous to genes encoding alcohol dehydrogenase, UDP-glucosyltransferase and polygalacturonase-inhibiting protein. These candidate genes verified the existence of different expressive patterns between chilling and freezing. Our results showed that C. bungeana responded to cold stresses rapidly through the alterations of DNA methylation, and that chilling and freezing induced different DNA methylation changes. Therefore, we conclude that epigenetic modifications can potentially serve as a rapid and flexible mechanism for C. bungeana to adapt to the intricate cold stresses in the alpine areas.     

Iron Superoxide Dismutase Protects against Chilling Damage in the Cyanobacterium Synechococcus species PCC7942

A strain of Synechococcus sp. PCC7942 lacking functional Fe superoxide dismutase (SOD), designated sodB⁻, was characterized by its growth rate, photosynthetic pigments, inhibition of photosynthetic electron transport activity, and total SOD activity at 0°C, 10°C, 17°C, and 27°C in moderate light. At 27°C, the sodB⁻ and wild-type strains had similar growth rates, chlorophyll and carotenoid contents, and cyclic photosynthetic electron transport activity. The sodB⁻ strain was more sensitive to chilling stress at 17°C than the wild type, indicating a role for FeSOD in protection against photooxidative damage during moderate chilling in light. However, both the wild-type and sodB⁻ strains exhibited similar chilling damage at 0°C and 10°C, indicating that the FeSOD does not provide protection against severe chilling stress in light. Total SOD activity was lower in the sodB⁻ strain than in the wild type at 17°C and 27°C. Total SOD activity decreased with decreasing temperature in both strains but more so in the wild type. Total SOD activity was equal in the two strains when assayed at 0°C.     

Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms

IntroductionLow temperature is one of the major environmental factors that adversely affect plant growth and yield. Many cereal crops from tropical regions, such as rice, are chilling sensitive and, therefore, are affected already at <10°C. Interestingly, it has been demonstrated that chilling susceptibility varies greatly among rice varieties, which indicates differences in the underlying molecular responses. Understanding these differences is vital for continued development of rational breeding and transgenic strategies for more tolerant varieties. Thus, in this study, we conducted a comparative global gene expression profiling analysis of the chilling tolerant varieties Sijung and Jumli Marshi (spp. Japonica) during early chilling stress (<24 h, 10°C).ConclusionsBased on the results inferred from this study, we conclude that different, but overlapping, strategies are undertaken by the two varieties to cope with the chilling stress; in Sijung the initial molecular responses seem to be mainly targeted at strengthening the cell wall and plasma membrane, whereas in Jumli Marshi the protection of chloroplast translation and detoxification is prioritized.     

Species Origin of Genomic Factors in Nicotiana nudicaulis Watson Controlling Hybrid Lethality in Interspecific Hybrids between N. nudicaulis Watson and N. tabacum L

Hybrid lethality is expressed at 28°C in the cross Nicotiana nudicaulis×N. tabacum. The S subgenome of N. tabacum has been identified as controlling this hybrid lethality. To clarify the responsible genomic factor(s) of N. nudicaulis, we crossed N. trigonophylla (paternal progenitor of N. nudicaulis) with N. tabacum, because hybrids between N. sylvestris (maternal progenitor of N. nudicaulis) and N. tabacum are viable when grown in a greenhouse. In the cross N. trigonophylla×N. tabacum, approximately 50% of hybrids were vitrified, 20% were viable, and 20% were nonviable at 28°C. To reveal which subgenome of N. tabacum was responsible for these phenotypes, we crossed N. trigonophylla with two progenitors of N. tabacum, N. sylvestris (SS) and N. tomentosiformis (TT). In the cross N. sylvestris×N. trigonophylla, we confirmed that over half of hybrids of N. sylvestris×N. trigonophylla were vitrified, and none of the hybrids of N. trigonophylla×N. tomentosiformis were. The results imply that the S subgenome, encoding a gene or genes inducing hybrid lethality in the cross between N. nudicaulis and N. tabacum, has one or more genomic factors that induce vitrification. Furthermore, in vitrified hybrids of N. trigonophylla×N. tabacum and N. sylvestris×N. trigonophylla, we found that nuclear fragmentation, which progresses during expression of hybrid lethality, was accompanied by vitrification. This observation suggests that vitrification has a relationship to hybrid lethality. Based on these results, we speculate that when N. nudicaulis was formed approximately 5 million years ago, several causative genomic factors determining phenotypes of hybrid seedlings were inherited from N. trigonophylla. Subsequently, genome downsizing and various recombination-based processes took place. Some of the causative genomic factors were lost and some became genomic factor(s) controlling hybrid lethality in extant N. nudicaulis.     

New taxa of tribe Gastrodieae (Epidendroideae,Orchidaceae) from Yunnan,China and its conservation implication

Gastrodia longistyla, a new species of Orchidaceae from Yunnan Province, China, is described and illustrated. It is morphologically similar to Gastrodia peichatieniana, but can be easily distinguished from the latter by having a rhombic epichile, long column (6.0–7.5 mm long), and a needle-shaped appendage (1.8–3.2 mm in length) at the base of the stigma. Identification key and colour photographs are provided. A preliminary risk-of-extinction assessment, according to the IUCN Red List Categories and Criteria, is given for the new species. The plastome of G. longistyla is 30464 bp in length with GC content approximately 24.8%, and the plastome does not contain some housekeeping genes, such as matK, rpl16, or all photosynthesis genes. In addition, the G. longistyla plastome lacks an IR region. This indicates that the plastome is in the last stage of degradation.     

Involvement of Abscisic Acid in Regulating Water Status in Phaseolus vulgaris L. during Chilling

During the first hours of chilling, bean (Phaseolus vulgaris L., cv Mondragone) seedlings suffer severe water stress and wilt without any significant increase in leaf abscisic acid (ABA) content (P. Vernieri, A. Pardossi, F. Tognoni [1991] Aust J Plant Physiol 18: 25-35). Plants regain turgor after 30 to 40 h. We hypothesized that inability to rapidly synthesize ABA at low temperatures contributes to chilling-induced water stress and that turgor recovery after 30 to 40 h is mediated by changes in endogenous ABA content. Entire bean seedlings were subjected to long-term (up to 6 d) chilling (3°C, 0.2-0.4 kPa vapor pressure deficit, 100 μmol·m⁻²·s⁻¹ photosynthetic photon flux density, continuous fluorescent light). During the first 24 h, stomata remained open, and plants rapidly wilted as leaf transpiration exceeded root water absorption. During this phase, ABA did not accumulate in leaves or in roots. After 24 h, ABA content increased in both tissues, leaf diffusion resistance increased, and plants rehydrated and regained turgor. No osmotic adjustment was associated with turgor recovery. Following turgor recovery, stomata remained closed, and ABA levels in both roots and leaves were elevated compared with controls. The application of ABA (0.1 mm) to the root system of the plants throughout exposure to 3°C prevented the chilling-induced water stress. Excised leaves fed 0.1 mm ABA via the transpiration stream had greater leaf diffusion resistance at 20 and 3°C compared with non-ABA fed controls, but the amount of ABA needed to elicit a given degree of stomatal closure was higher at 3°C compared with 20°C. These findings suggest that endogenous ABA may play a role in ameliorating plant water status during chilling.     

Zeaxanthin Synthesis, Energy Dissipation, and Photoprotection of Photosystem II at Chilling Temperatures

When leaves of a mangrove, Rhizophora mangle, were exposed to an excess of light at chilling temperatures, synthesis of zeaxanthin through violaxanthin de-epoxidation as well as nonphotochemical fluorescence quenching were markedly reduced. The results suggest a protective role of energy dissipation against the adverse effects of high light and chilling temperatures: leaves of R. mangle that had been preilluminated in 2% O₂, 0% CO₂ at low photon flux density and showed a high level of zeaxanthin, and leaves that had been kept in the dark and contained no zeaxanthin, were both exposed to high light and chilling temperatures (5°C leaf temperature) in air and then held under control conditions in low light in air at 25°C. Measurements of chlorophyll a fluorescence at room temperature showed that the photochemical efficiency of PSII and the yield of maximum fluorescence of the preilluminated leaf recovered completely within 1 to 3 hours under the control conditions. In contrast, the fluorescence responses of the predarkened leaf in high light at 5°C did not recover at all. During a dark/light transient in 2% O₂, 0% CO₂ in low light at 5°C, nonphotochemical fluorescence quenching increased linearly with an increase in the zeaxanthin content in leaves of R. mangle. In soybean (Glycine max) leaves, which contained a background level of zeaxanthin in the dark, a similar treatment with excess light induced a level of nonphotochemical fluorescence quenching that was not paralleled by an increase in the zeaxanthin content.     

Colorectal cancer DNA methylation patterns from patients in Manaus,Brazil

Background

DNA methylation is commonly linked with the silencing of the gene expression for many tumor suppressor genes. As such, determining DNA methylation patterns should aid, in times to come, in the diagnosis and personal treatment for various types of cancers. Here, we analyzed the methylation pattern from five colorectal cancer patients from the Amazon state in Brazil for four tumor suppressor genes, viz.: DAPK, CDH1, CDKN2A, and TIMP2 by employing a polymerase chain reaction (PCR) specific to methylation. Efforts in the study of colorectal cancer are fundamental as it is the third most of highest incidence in the world.

Results

Tumor biopsies were methylated in 1/5 (20 %), 2/5 (40 %), 4/5 (80 %), and 4/5 (80 %) for CDH1, CDKN2A, DAPK, and TIMP2 genes, respectively. The margin biopsies were methylated in 3/7 (43 %), 2/7 (28 %), 7/7 (100 %), and 6/7 (86 %) for CDH1, CDKN2A, DAPK, and TIMP2, respectively.

Conclusions

Our findings showed DAPK and TIMP2 to be methylated in most samples from both tumor tissues and adjacent non-neoplastic margins; thus presenting distinct methylation patterns. This emphasizes the importance of better understanding of the relation of these patterns with cancer in the context of different populations.     

Abscisic Acid-induced chilling tolerance in maize suspension-cultured cells

The induction of chilling tolerance by abscisic acid (ABA) in maize (Zea mays L. cv Black Mexican Sweet) suspension cultured cells was examined. Cell viability during exposure to chilling was estimated by triphenyl tetrazolium chloride reduction immediately after chilling and a filter paper growth assay. Both methods yielded comparable results. Chilling tolerance was induced by transferring 5-day-old cultures (late log phase) to a fresh medium containing ABA (10 to 100 micromolar). The greatest chilling tolerance was achieved with ABA at 100 micromolar. Growth of cells was inhibited at this concentration. After a 7-day exposure to 4°C in the dark, the survival of ABA-treated cells (100 micromolar ABA, 28°C for 24 h in the dark) was sevenfold greater than untreated cells. Effective induction of chilling tolerance was first observed when cells were held at 28°C for 6 hours after adding ABA. No tolerance was induced if the culture was chilled at the inception of ABA treatment. Induction of chilling tolerance was inhibited by cycloheximide. These results indicate that ABA is capable of inducing chilling tolerance when ABA-treated cells are incubated at a warm temperature before exposure to chilling, and this induction requires de novo synthesis of proteins.     

Sensitivity of Altitudinal Ecotypes of the Wild Tomato Lycopersicon hirsutum to Chilling Injury

The transition temperature of the leaf polar lipids and the critical temperature for chill-induced inhibition of photosynthesis was determined for three altitudinal ecotypes of the wild tomato Lycopersicon hirsutum. Photosynthesis was measured as CO₂-dependent O₂ evolution at 25°C after leaf slices were exposed to chilling temperatures for 2 hours at a moderate photon flux density of 450 micromoles per square meter per second. The transition temperature of the leaf polar lipids was detected from the change in the temperature coefficient of the fluorescence intensity of trans-parinaric acid. Chill-induced photoinhibition was evident in the three tomato ecotypes when they were chilled below a critical temperature of 10°, 11°, and 13°C, respectively, for the high (LA1777), mid (LA1625), and low (LA1361) altitudinal ecotypes. The temperature differential, below the critical temperature, required to produce a 50% inhibition was also similar for the three ecotypes. A transition was detected in the leaf polar lipids of these plants at a temperature similar to that of the critical temperature for photoinhibition. The results show that the three tomato ecotypes are similar with respect to their critical temperature for chilling-induced photoinhibition and the rate of their response to the chilling stress. They are, thus, similarly sensitive to chilling.     

Raffinose Synthesis in Chlorella vulgaris Cultures after a Cold Shock

Chlorella vulgaris cultures have been submitted to a chilling shock, bringing down the growing temperature from to 24°C to 4°C. Growth was stopped immediately, and concomitantly there was an accumulation of sucrose and a decrease in the starch content. The enzymes involved in sucrose metabolism were differentially affected by the chilling shock. Sucrose phosphate synthase activity increased while sucrose synthase was not affected. Simultaneously with the chilling shock, raffinose began to accumulate. When algal cultures were returned at 24°C, raffinose disappeared. The presence of raffinose in algal cells has not been reported before.     

Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds

Background

The availability of high-density SNP assays including the BovineSNP50 (50 K) enables the identification of novel quantitative trait loci (QTL) and improvement of the resolution of the locations of previously mapped QTL. We performed a series of genome-wide association studies (GWAS) using 50 K genotypes scored in 18,274 animals from 10 US beef cattle breeds with observations for twelve body weights, calving ease and carcass traits.

Results

A total of 159 large-effects QTL (defined as 1-Mb genome windows explaining more than 1% of additive genetic variance) were identified. In general, more QTL were identified in analyses with bigger sample sizes. Four large-effect pleiotropic or closely linked QTLs located on BTA6 at 37–42 Mb (primarily at 38 Mb), on BTA7 at 93 Mb, on BTA14 at 23–26 Mb (primarily at 25 Mb) and on BTA20 at 4 Mb were identified in more than one breed. Several breed-specific large-effect pleiotropic or closely linked QTL were also identified. Some identified QTL regions harbor genes known to have large effects on a variety of traits in cattle such as PLAG1 and MSTN and others harbor promising candidate genes including NCAPG, ARRDC3, ERGIC1, SH3PXD2B, HMGA2, MSRB3, LEMD3, TIGAR, SEPT7, and KIRREL3. Gene ontology analysis revealed that genes involved in ossification and in adipose tissue development were over-represented in the identified pleiotropic QTL. Also, the MAPK signaling pathway was identified as a common pathway affected by the genes located near the pleiotropic QTL.

Conclusions

This largest GWAS ever performed in beef cattle, led us to discover several novel across-breed and breed-specific large-effect pleiotropic QTL that cumulatively account for a significant percentage of additive genetic variance (e.g. more than a third of additive genetic variance of birth and mature weights; and calving ease direct in Hereford). These results will improve our understanding of the biology of growth and body composition in cattle.

Electronic supplementary material

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