Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways.

Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa), we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs, as well as salinity-related candidate genes. In doing so, we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs, as well as the similarities between genomic locations that the traits were mapped to. Finally, we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes, including OsKS7 (ENT-KAURENE SYNTHASE 7), OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs, but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways.

Accumulation of Health-Promoting Compounds in Upland Black Rice by Interacting Mycorrhizal and Endophytic Fungi.

There is an increasing interest in finding eco-friendly and safe approaches to increase agricultural productivity and deliver healthy foods. Arbuscular mycorrhizal fungi (AMF) and endophytic fungi (EPF) are important components of sustainable agriculture in view of their ability to increase productivity and various plant secondary metabolites with health-promoting effects. In a pot experiment, our main research question was to evaluate the additive and synergistic effects of an AMF and four root-endophytic fungi on plant performance and on the accumulation of health-promoting secondary compounds. Plant growth varied between the treatments with both single inoculants and co-inoculation of an AMF and four EPF strains. We found that inoculation with a single EPF positively affected the growth and biomass production of most of the plant-endophyte consortia examined. The introduction of AMF into this experiment (dual inoculation) had a beneficial effect on plant growth and yield. AMF, Rhizophagus variabilis KS-02 co-inoculated with EPF, Trichoderma zelobreve PBMP16 increased the highest biomass, exceeding the growth rate of non-inoculated plants. Co-inoculated R. variabilis KS-02 and T. zelobreve PBMP16 had significantly greater beneficial effects on almost all aspects of plant growth, photosynthesis-related parameters, and yield. It also promoted root growth quality and plant nutrient uptake. The phenolic compounds, anthocyanin, and antioxidant capacity in rice seeds harvested from plants co-inoculated with AMF and EPF were dramatically increased compared with those from non-inoculated plants. In conclusion, our results indicated that EPF and AMF contributed to symbiosis in Maled Phai cultivar and were coordinately involved in promoting plant growth performance under a pot trial.

The Potential of Endophytic Fungi for Enhancing the Growth and Accumulation of Phenolic Compounds and Anthocyanin in Maled Phai Rice (Oryza sativa L.).

Rice (Oryza sativa L.) is one of the most popular cereal crops, being consumed by almost half of the world's population. Among several cultivars widely distributed in Thailand, Maled Phai is a Thai pigmented-upland rice with exceptionally high nutritional value and high demand in the local Thai market. This study aimed to investigate the feasibility of producing plant growth-promoting properties (PGP) and enhancing the accumulation of phytochemicals in Maled Phai rice seeds of endophytic fungi isolated from upland black rice. Among a total of 56 isolates, the 4 most effective PGP isolates were identified as Trichoderma zelobreve PBMP16, Talaromyces pinophilus PBMP28, Aspergillus flavus KKMP34, and Trichoderma sp. PBMP4 based on their morphological characteristics and multigene (ITS, rpb2, tef-1, CaM, and BenA) phylogenetic analyses. These four endophytic fungi could promote plant growth parameters under greenhouse conditions. Outstandingly, upland rice inoculated with Tr. zelobreve PBMP16 had a significant increase in total seed weight, root length, phenolic compounds, anthocyanin, antioxidants, and N uptake, which were higher than those of the noninoculated control, and even better than the chemical fertilizer. Overall, this report shows that endophytic fungi efficiently promoted growth and increased the phenolic compounds, anthocyanin, and antioxidants of Maled Phai rice.

Photosynthesis Performance at Different Growth Stages, Growth, and Yield of Rice in Saline Fields.

Photosynthetic performance and biomass at different growth stages of the salt-sensitive KDML105 rice cultivar, three improved lines (RD73, CSSL8-94, and TSKC1-144), and the salt-tolerant standard genotype (Pokkali) were investigated under non-saline, semi-saline, and the heavy-saline field conditions in the northeast of Thailand. In the non-saline field, net photosynthesis rates (Pn) of all genotypes remained high from the early vegetative stage to the milky stage and then dramatically reduced at maturity. In contrast, in both saline fields, Pn was the highest at the early vegetative stage and continuously declining until maturity. Leaf chlorophyll content remained high from the early vegetative to milky stage then reduced at maturity for all three field conditions. During the reproductive phase, Pn of KDML105 and the improved lines were reduced by 4-17% in the heavy-saline field, while that of Pokkali was increased (11-19% increase over that of the non-saline). Pokkali also showed a prominent increase in water use efficiency (WUE) under salinity. Nevertheless, rice leaves under saline conditions maintained the PSII integrity, as indicated by the pre-dawn values of maximum quantum yield of PSII photochemistry (Fv/Fm) of higher than 0.8. Pokkali under the semi-saline and the heavy-saline conditions exhibited 51% and 27% increases in final biomass, and 64% and 42% increases in filled grain weight plant-1, respectively. In the semi-saline condition, RD73, TSKC1-144, CSSL8-94, and KDML105 showed moderate salt tolerance by displaying 24%, 18.6%, 15%, and 11.3% increases in final biomass, and 24%, 4%, 13%, and 6% increases in filled grain weight plant-1, respectively. In contrast, in the heavy-saline field, final biomass of RD73, KDML105, CSSL8-94, and TSKC1-144 showed 48%, 45%, 38%, and 36% reductions from that in the non-saline field, while the filled grain weight plant-1 were reduced by 45%, 58%, 35%, and 32%, respectively. This indicated that the improved lines carrying drought- and/or salt-tolerance genes achieved an increased salt tolerance level than the parental elite cultivar, KDML105.

The effect of salinity on soil chemical characteristics, enzyme activity and bacterial community composition in rice rhizospheres in Northeastern Thailand.

Saline soil is one of the major problems limiting rice productivity in the Northeastern area of Thailand. Thus, the aims of this study were to determine soil physicochemical analysis and soil enzyme activities, and bacterial communities in the rhizosphere of 'RD 6' rice grown in salt-affected rice fields. The Ban Thum sample showed the highest electrical conductivity (EC; greater than 6 dS m-1) and total Na, while the EC in other fields were at non- or slightly saline levels. The principal component analysis revealed that soil chemical characteristics and soil enzymes activities explained 73.4% of total variation. Soil enzyme activities including dehydrogenase and fluorescein diacetate (FDA) hydrolysis, and soil characteristics including organic matter (OM) and organic carbon (OC) were significantly negatively correlated to EC. This indicated that these soil properties were adversely impacted by salts. Interestingly, activities of all hydrolytic enzymes were not affected by soil salinity. Bacteria that were able to colonize the rhizosphere soils were Achromobacter cholinophagum, Rhizobium tarimense, and unculturable bacteria. In this regard, study on the relationship of soil chemical characteristics and soil enzyme activities together with bacterial communities provided promising data for assessing rice field soil quality in the future.

Effect of Heat Stress on Some Physiological and Anatomical Characteristics of Rice (Oryza sativa L.) cv. KDML105 Callus and Seedling.

Global warming is a serious problem, with significant negative impacts on agricultural productivity. To better understand plant anatomical adaptation mechanisms as responses to heat stress, improved basic knowledge is required. This research studied the physiological and anatomical responses of Khao Dawk Mali 105 (KDML105) to artificial heat stress. Dehusked seeds were sterilized and cultured on Murashige and Skoog (MS) medium, supplemented with 3 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D) for callus induction. The cultures were maintained at 25 °C and 35 °C for 4 weeks, while the other culture was treated with heat shock at 42 °C for 1 week before further incubation at 25 °C for 3 weeks. Results revealed that elevated temperatures (35 °C and 42 °C) adversely impacted seedling growth. Plant height, root length, leaf number per plant, fresh and dry weight, chlorophyll a, chlorophyll b and total chlorophyll content decreased after heat stress treatment, while malondialdehyde (MDA) and electrolyte leakage percentage significantly increased, compared to the control. Heat stress induced ROS accumulation, leading to lipid peroxidation and membrane instability. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) results also confirmed negative correlations between MDA, electrolyte leakage and other parameters. MDA content and electrolyte leakage are effective indicators of heat stress in rice. Surface anatomical responses of rice seedlings to heat stress were studied but significant alterations were not observed, and heat stress had no significant negative effects on KDML105 calli. Size and mass of calli increased because heat stress stimulated gene expression that induced thermotolerance. Our results provide useful information for rice breeding and heat stress tolerance programs to benefit long-term global food security.

Physiological and Proteomic Responses of Cassava to Short-Term Extreme Cool and Hot Temperature.

Temperature is one of the most critical factors affecting cassava metabolism and growth. This research was conducted to investigate the effects of short-term exposure to extreme cool (15 °C) and hot (45 °C) temperature on photosynthesis, biochemical and proteomics changes in potted plants of two cassava cultivars, namely Rayong 9 and Kasetsart 50. One-month-old plants were exposed to 15, 30, and 45 °C for 60 min in a temperature chamber under light intensity of 700 µmol m-2 s-1. Compared to the optimum temperature (30 °C), exposure to 15 °C resulted in 28% reduction in stomatal conductance (gs) and 62% reduction in net photosynthesis rate (Pn). In contrast, gs under 45 °C increased 2.61 folds, while Pn was reduced by 50%. The lower Pn but higher electron transport rate (ETR) of the cold-stressed plants indicated that a greater proportion of electrons was transported via alternative pathways to protect chloroplast from being damaged by reactive oxygen species (ROS). Moreover, malondialdehyde (MDA) contents, a marker related to the amount of ROS, were significantly higher at low temperature. Proteomics analysis revealed some interesting differentially expressed proteins (DEPs) including annexin, a multi-functional protein functioning in early events of heat stress signaling. In response to low-temperature stress, AP2/ERF domain-containing protein (a cold-related transcription factor) and glutaredoxin domain-containing protein (a component of redox signaling network under cold stress) were detected. Taken together, both cultivars were more sensitive to low than high temperature. Moreover, Rayong 9 displayed higher Pn under both temperature stresses, and was more efficient in controlling ROS under cold stress than Kasetsart 50.

High Temperature Alters Leaf Lipid Membrane Composition Associated with Photochemistry of PSII and Membrane Thermostability in Rice Seedlings.

Rice cultivated in the tropics is exposed to high temperature (HT) stress which threatens its growth and survival. This study aimed at characterizing the HT response in terms of PSII efficiency and membrane stability, and to identify leaf fatty acid changes that may be associated with HT tolerance or sensitivity of rice genotypes. Twenty-eight-day-old seedlings of two Thai rice cultivars (CN1 and KDML105), a standard heat tolerance (N22), and a heat sensitive (IR64) rice genotype were treated at 42 °C for 7 days. Under HT, N22 showed the highest heat tolerance displaying the lowest increase in electrolyte leakage (EL), no increments in malondialdehyde (MDA) and stable maximum quantum yield of PSII efficiency (Fv/Fm). Compared to KDML105 and IR64, CN1 was more tolerant of HT, showing a lower increase in EL and MDA, and less reduction in Fv/Fm. N22 and CN1 showed a higher percentage reduction of unsaturated fatty acids (C18:2 and C18:3), which are the major components of the thylakoid membrane, rendering the optimum thylakoid membrane fluidity and intactness of PSII complex. Moreover, they exhibited sharp increases in long-chain fatty acids, particularly C22:1, while the heat sensitive IR64 and KDML105 showed significant reductions. Dramatic increases in long-chain fatty acids may lead to cuticular wax synthesis which provides protective roles for heat tolerance. Thus, the reduction in unsaturated fatty acid composition of the thylakoid membrane and dramatic increases in long-chain fatty acids may lead to high photosynthetic performance and an enhanced synthesis of cuticular wax which further provided additional protective roles for heat tolerance ability in rice.

Physiological evaluation for salt tolerance in green and purple leaf color rice cultivars at seedling stage.

Anthocyanin, a water-soluble pigment found in plants, has been reported to be associated with abiotic stress tolerance including salt stress. For a better understanding of the role of anthocyanin in response to salt stress, two salt-tolerant rice genotypes having different leaf anthocyanin content, one having green ('Pokkali'; PK) and the other purple leaves ('Niew Dam 019'; ND 019), were used in this study. After being subjected to salt stress (150 mM NaCl) for 5 d, the 3-week-old rice genotypes PK and ND 019 exhibited significant physiological responses (water content, Na+/K+ ratio, osmolyte accumulation, osmotic adjustment, antioxidant capacity, membrane damage and chlorophyll) and expression of ion transporter genes, indicating overall salt tolerance ability. However, the green-leaved rice variety, PK, had better root-to-shoot Na+ exclusion mechanism than the purple-leaved variety, ND 019 as evidenced by lower Na+ accumulation in leaves compared to ND 019 despite the fact that they accumulated the similar level of Na+ in roots. On the other hand, ND 019 accumulated higher concentration of osmolytes leading to more enhanced osmotic adjustment. These results revealed that Na+ ion exclusion was the prominent salt tolerance mechanism in the green-leaved PK whereas in the purple-leaved ND 019 osmotic adjustment was the more significant strategy. Under salt stress, there was no remarkable change in anthocyanin in PK while a reduction was found in ND 019. Thus, it could be proposed that anthocyanin did not play a vital role in protecting the purple-leaved rice, ND 019 from salt stress during seedling stage. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01114-y.

High Performance of Photosynthesis and Osmotic Adjustment Are Associated With Salt Tolerance Ability in Rice Carrying Drought Tolerance QTL: Physiological and Co-expression Network Analysis.

Understanding specific biological processes involving in salt tolerance mechanisms is important for improving traits conferring tolerance to salinity, one of the most important abiotic stresses in plants. Under drought and salinity stresses, plants share overlapping responsive mechanisms such as physiological changes and activation of signaling molecules, which induce and transmit signals through regulator genes in a regulatory network. In this study, two near isogenic lines of rice carrying chromosome segments of drought tolerance QTL on chromosome 8 from IR68586-F2-CA-31 (DH103) in the genetic background of sensitive cultivar "Khao Dawk Mali 105; KDML105" (designated as CSSL8-94 and CSSL8-95) were used to investigate physiological responses to salt stress [namely growth, Na+/K+ ratio, water status, osmotic adjustment, photosynthetic parameters, electrolyte leakage (EL), malondialdehyde (MDA), proline and sugar accumulations], compared with the standard salt tolerant (Pokkali; PK) and their recurrent parent (KDML105) rice cultivars. Physiological examination indicated that both CSSLs showed superior salt-tolerant level to KDML105. Our results suggested that salt tolerance ability of these CSSL lines may be resulted from high performance photosynthesis, better osmotic adjustment, and less oxidative stress damage under salt conditions. Moreover, to explore new candidate genes that might take part in salt tolerance mechanisms, we performed co-expression network analysis for genes identified in the CSSL rice, and found that Os08g419090, the gene involved with tetrapyrrole and porphyrin biosynthetic process (chlorophyll biosynthetic process), Os08g43230 and Os08g43440 (encoded TraB family protein and cytochrome P450, respectively) might have unprecedented roles in salt stress tolerance.

Nanopriming technology for enhancing germination and starch metabolism of aged rice seeds using phytosynthesized silver nanoparticles.

Application of nanomaterials for agriculture is relatively new as compared to their use in biomedical and industrial sectors. In order to promote sustainable nanoagriculture, biocompatible silver nanoparticles (AgNPs) have been synthesized through green route using kaffir lime leaf extract for use as nanopriming agent for enhancing seed germination of rice aged seeds. Results of various characterization techniques showed the successful formation of AgNPs which were capped with phytochemicals present in the plant extract. Rice aged seeds primed with phytosynthesized AgNPs at 5 and 10 ppm significantly improved germination performance and seedling vigor compared to unprimed control, AgNO3 priming, and conventional hydropriming. Nanopriming could enhance α-amylase activity, resulting in higher soluble sugar content for supporting seedlings growth. Furthermore, nanopriming stimulated the up-regulation of aquaporin genes in germinating seeds. Meanwhile, more ROS production was observed in germinating seeds of nanopriming treatment compared to unprimed control and other priming treatments, suggesting that both ROS and aquaporins play important roles in enhancing seed germination. Different mechanisms underlying nanopriming-induced seed germination were proposed, including creation of nanopores for enhanced water uptake, rebooting ROS/antioxidant systems in seeds, generation of hydroxyl radicals for cell wall loosening, and nanocatalyst for fastening starch hydrolysis.

Environmentally benign synthesis of phytochemicals-capped gold nanoparticles as nanopriming agent for promoting maize seed germination.

Application of nanotechnology in agriculture is moving towards to improve the cultivation and growth of crop plants. The present study is the first attempt to propose a simple, yet cost-effective and ecofriendly synthesis of phytochemicals-capped GNPs using rhizome extract of galanga plant at room temperature. The synthesized GNPs were characterized by various characterization techniques. To promote the green nanotechnology applications in agriculture, GNPs solution at environmentally realistic dose (5 to 15ppm) as nanopriming agent was used to activate the germination and early seedling growth of maize aged seeds. Priming with 5ppm GNPs showed the best effects on promoting emergence percentage (83%) compared to unprimed control (43%) and hydroprimed groups (56%). Seed priming at both 5 and 10ppm GNPs also enhanced seedling vigor index by 3 times over the control. Priming with GNPs at 10ppm was found to enhance the best physiological and biochemical properties of maize seedlings. Internalization studies by inductively coupled plasma atomic emission spectroscopy (ICP-OES) and transmission electron microscopy (TEM) strongly supported that GNPs can internalize into seeds. However, ICP-OES analysis revealed that GNPs were not present in both shoot and root parts, suggesting that nanopriming approach minimizes the Au translocation from seeds into plant vegetative organs. Phytosynthesized GNPs were found to be less toxic than chemically synthesized GNPs. This is the first report showing phytochemicals-capped GNPs as a promising nanopriming agent for activating the germination of naturally aged seeds of crop plant.

Physiological and biochemical parameters for evaluation and clustering of rice cultivars differing in salt tolerance at seedling stage.

Salinity tolerance levels and physiological changes were evaluated for twelve rice cultivars, including four white rice and eight black glutinous rice cultivars, during their seedling stage in response to salinity stress at 100 mM NaCl. All the rice cultivars evaluated showed an apparent decrease in growth characteristics and chlorophyll accumulation under salinity stress. By contrast an increase in proline, hydrogen peroxide, peroxidase (POX) activity and anthocyanins were observed for all cultivars. The K(+)/Na(+) ratios evaluated for all rice cultivars were noted to be highly correlated with the salinity scores thus indicating that the K(+)/Na(+) ratio serves as a reliable indicator of salt stress tolerance in rice. Principal component analysis (PCA) based on physiological salt tolerance indexes could clearly distinguish rice cultivars into 4 salt tolerance clusters. Noteworthy, in comparison to the salt-sensitive ones, rice cultivars that possessed higher degrees of salt tolerance displayed more enhanced activity of catalase (CAT), a smaller increase in anthocyanin, hydrogen peroxide and proline content but a smaller drop in the K(+)/Na(+) ratio and chlorophyll accumulation.

Salt-responsive mechanisms in chromosome segment substitution lines of rice (Oryza sativa L. cv. KDML105).

Two chromosome segment substitution lines of Khao Dawk Mali 105 (KDML105) rice that carry quantitative trait loci for drought tolerance located on chromosome 8 (DT-QTL8) designated CSSL8-94 and CSSL8-116 were investigated for co-expression network and physiological responses to salinity compared to their parents (KDML105; drought and salt sensitive recurrent parent, and DH103; drought tolerant QTL donor). These CSSL lines show different salt-response traits under salt stress (CSSL8-94 shows higher tolerance than CSSL8-116) and possess different segments of DT-QTL8. To identify specific biological process(es) associated with salt-stress response, co-expression network analysis was constructed from each DT-QTL segment. To evaluate differential physiological mechanisms responding to salt stress, all rice lines/cultivar were grown for 21 d in soils submerged in nutrient solutions, then subjected to 150 mM NaCl for 7 d. Physiological parameters related to co-expression network analysis (photosynthetic parameters) and salt responsive parameters (Na(+)/K(+) ratio, proline content, malondialdehyde and ascorbate peroxidase activity; EC1.11.1.1) were investigated along with the expression analysis of related genes. Physiological responses under salt stress particularly photosynthesis-related parameters of CSSL8-94 were similar to DH103, whereas those of CSSL8-116 were similar to KDML105. Moreover, expression levels of photosynthesis-related genes selected from the co-expression networks (Os08g41460, Os08g44680, Os06g01850, Os03g07300 and Os02g42570) were slightly decreased or stable in CSSL8-94 and DH103 but were dramatically down-regulated in CSSL8-116 and KDML105. These differential responses may contribute to the photosynthesis systems of CSSL8-94 being less damaged under salt stress in comparison to those of CSSL8-116. It can be concluded that the presence of the specific DT-QTL8 segment in CSSL8-94 not only confers drought tolerant traits but also enhances its salt tolerant ability.

Exogenous proline and trehalose promote recovery of rice seedlings from salt-stress and differentially modulate antioxidant enzymes and expression of related genes.

Proline (Pro) and Trehalose (Tre) function as compatible solutes and are upregulated in plants under abiotic stress. They play an osmoprotective role in physiological responses, enabling the plants to better tolerate the adverse effects of abiotic stress. We investigated the effect of exogenous Pro and Tre (10 mM) in seedlings of Thai aromatic rice (cv. KDML105; salt-sensitive) during salt stress and subsequent recovery. Salt stress (S, NaCl) resulted in growth reduction, increase in the Na(+)/K(+) ratio, increase in Pro level and up-regulation of Pro synthesis genes (pyrroline-5-carboxylatesynthetase, P5CS; pyrroline-5-carboxylate reductase, P5CR) as well as accumulation of hydrogen peroxide (H(2)O(2)), increased activity of antioxidative enzymes (superoxide dismutase, SOD; peroxidase, POX; ascorbate peroxidase, APX; catalase, CAT) and transcript up-regulation of genes encoding antioxidant enzymes (Cu/ZnSOD, MnSOD, CytAPX, CatC). Under salt stress, exogenous Pro (PS; Pro+NaCl) reduced the Na(+)/K(+) ratio, further increased endogenous Pro and transcript levels of P5CS and P5CR, but decreased the activity of the four antioxidant enzymes. The transcription of genes encoding several antioxidant enzymes was upregulated. Exogenous Tre (TS; Tre+NaCl) also reduced the Na(+)/K(+) ratio and strongly decreased endogenous Pro. Transcription of P5CS and P5CR was upregulated, the activities of SOD and POX decreased, the activity of APX increased and the transcription of all antioxidant enzyme genes upregulated. Although exogenous osmoprotectants did not alleviate growth inhibition during salt stress, they exhibited a pronounced beneficial effect during recovery period showing higher percentage of growth recovery in PS (162.38%) and TS (98.43%) compared with S (3.68%). During recovery, plants treated with PS showed a much greater reduction in endogenous Pro than NaCl-treated (S) or Tre-treated plants (TS). Increase in CAT activity was most related to significant reduction in H(2)O(2), particularly in the case of PS-treated plants. Advantageous effects of Pro were also associated with increase in APX activity during recovery.

Effect of shading on yield, sugar content, phenolic acids and antioxidant property of coffee beans (Coffea Arabica L. cv. Catimor) harvested from north-eastern Thailand.

BACKGROUND: Environmental conditions, including shading, generally influence the physical and chemical qualities of coffee beans. The present study assessed the changes in some phenolic compounds, antioxidant activity and agronomic characters of coffee beans (Coffea arabica L. cv. Catimor) as affected by different shading conditions including full sun, three artificial shading conditions using a saran covering (50% shade, 60% shade, and 70% shade) and lychee shade. RESULTS: Bean weight and bean size increased significantly (P < 0.05) when the shade level was progressively increased. The coffee beans grown under lychee shade exhibited superior bean yield, 1000-bean weight, total phenolic content and antioxidant activity compared to all other beans. Chlorogenic acid was the most predominant phenolic acid in all samples studied, being the highest in the beans grown under lychee shade, followed by 60% shade, 70% shade, 50% shade and full sun, respectively. In contrast, bean grown under full sun had the highest amount of vanillic acid and caffeic acid. CONCLUSIONS: Antioxidant activity was highly positively associated with chlorogenic acid content. The content of total sugar (fructose, glucose and sucrose) was found highest in coffee beans grown in 60% shade, with fructose the predominant sugar. Under climatic conditions similar to this experiment, it is advisable that growers provide shade to the coffee crop to reduce heat from direct sunlight and promote yield as well as obtain good quality coffee beans.

Genetic diversity analysis of rice cultivars (Oryza sativa L. ) differing in salinity tolerance based on RAPD and SSR markers

Thirty rice cultivars were evaluated for salinity tolerance during the seedling stage and were divided into five tolerance groups including tolerant (T), moderately tolerant (MT), moderately susceptible (MS), susceptible (S) and highly susceptible (HS) which comprised 5, 10, 9, 4 and 2 cultivars respectively. Genetic diversity of all rice cultivars was evaluated using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) markers. The cultivars were evaluated for polymorphisms after amplification with 20 random decamer primers and 20 SSR primer pairs. A total of 161 RAPD markers and 190 SSR alleles were produced which revealed 68.94 percent and 89.47 percent polymorphism respectively. Mean genetic similarity coefficient was 0.82 for RAPD and 0.70 for SSR. Cluster analysis based on RAPD markers was effective in grouping cultivars based on their salt tolerance ability. Group IA1, IB and IV contained three T, three S and two HS rice cultivars respectively. The MT and MS cultivars which showed similar physiological responses to salinity were resolved into two groups: Group IA2 and Group II comprising ten and eight MT/MS cultivars respectively. Cluster analysis based on SSR markers separated rice cultivars into groups based on genetic relatedness which did not correspond to salinity tolerance level. The results from this study provided some useful implications for salt tolerance breeding programs. The evaluation of genetic similarity and cluster analysis together with salt tolerance ability provides some useful guides for assisting plant breeders in selecting suitable genetically diverse parents for the crossing program.