Quantitative trait loci associated with drought tolerance at reproductive stage in rice

Drought is a major constraint to rice (Oryza sativa) yield and its stability in rainfed and poorly irrigated environments. Identifying genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and development of more drought tolerant cultivars. Quantitative trait loci (QTL) for grain yield and its components and other agronomic traits were identified using a subset of 154 doubled haploid lines derived from a cross between two rice cultivars, CT9993-510 to 1-M and IR62266-42 to 6-2. Drought stress treatments were managed by use of a line source sprinkler irrigation system, which provided a linearly decreasing level of irrigation coinciding with the sensitive reproductive growth stages. The research was conducted at the Ubon Rice Research Center, Ubon, Thailand. A total of 77 QTL were identified for grain yield and its components under varying levels of water stress. Out of the total of 77 QTL, the number of QTL per trait were: 7-grain yield (GY); 8-biological yield (BY); 6-harvest index (HI); 5-d to flowering after initiation of irrigation gradient (DFAIG); 10-total spikelet number (TSN); 7-percent spikelet sterility (PSS); 23-panicle number (PN); and 11-plant height (PH). The phenotypic variation explained by individual QTL ranged from 7.5% to 55.7%. Under well-watered conditions, we observed a high genetic association for BY, HI, DFAIG, PSS, TSN, PH, and GY. However, only BY and HI were found to be significantly associated with GY under drought treatments. QTL flanked by markers RG104 to RM231, EMP2_2 to RM127, and G2132 to RZ598 on chromosomes 3, 4, and 8 were associated with GY, HI, DFAIG, BY, PSS, and PN under drought treatments. The aggregate effects of these QTL on chromosomes 3, 4, and 8 resulted in higher grain yield. These QTL will be useful for rainfed rice improvement, and will also contribute to our understanding of the genetic control of GY under drought conditions at the sensitive reproductive stage. Close linkage or pleiotropy may be responsible for the coincidence of QTL detected in this experiment. Digenic interactions between QTL main effects for GY, BY, HI, and PSS were observed under irrigation treatments. Most (but not all) DH lines have the same response in measure of productivity when the intensity of water deficit was increased, but no QTL by irrigation treatment interaction was detected. The identification of genomic regions associated with GY and its components under drought stress will be useful for marker-based approaches to improve GY and its stability for farmers in drought-prone rice environments.     

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

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

Morphological phenotyping of enteric neurons using neurofilament immunohistochemistry renders chemical phenotyping more precise in porcine ileum

The aim of the study was: (1) to test the suitability of neurofilament (NF) immunohistochemistry for representing the shapes of morphologically defined neuron types in the pig ileum myenteric plexus, (2) to estimate the proportions of these neuron types as related to the whole myenteric neuron population and (3) to demonstrate the usefulness of a refined morphological classification of enteric neurons on the paradigm of calcitonin gene-related peptide (CGRP)-immunoreactive neurons. So far, immunoreactivity for this peptide was supposed to be present in the pig enteric nervous system only in type II neurons. Ileal whole mounts of two pigs were stained with the cuprolinic blue (CB) method and, thereafter, incubated with an antibody pool against NF proteins (70, 160 and 210 kDa), visualised with a fluorochrome-tagged secondary antibody. The structural representation of morphologically defined myenteric neuron types typical for pig ileum (Stach I, II, IV, V and VI) was equivalent to their silver impregnated image, as demonstrated in previous studies. Counts of CB-stained neurons revealed between 2,526 and 2,662 neurons per square centimetre in one pig and between 2,027 and 2,763 in the other. As related to these total neuron numbers, the proportions of type I neurons were 1.7% and 1.5%, of type II neurons 7.2% and 7.9%, of type IV neurons 1.9% and 2.4%, of type V neurons 1.1% and 1.5%, and of type VI neurons 1.3% each. These values are generally comparable with those estimated earlier on silver impregnated material. Double labelling for NF and CGRP indicated that CGRP-immunoreactive smooth contoured neurons with long processes could be subdivided into two distinct morphological neuron types, i.e. type II and type V. We conclude that NF immunohistochemistry is an appropriate tool for representation of morphologically defined enteric neuron types in the pig. Combination of this technique with immunohistochemistry for neuroactive substances may be useful for making both morphological and chemical classification schemes mutually more precise.     

Genetic basis of drought resistance at reproductive stage in rice: separation of drought tolerance from drought avoidance

Drought tolerance (DT) and drought avoidance (DA) are two major mechanisms in drought resistance of higher plants. In this study, the genetic bases of DT and DA at reproductive stage in rice were analyzed using a recombinant inbred line population from a cross between an indica lowland and a tropical japonica upland cultivar. The plants were grown individually in PVC pipes and two cycles of drought stress were applied to individual plants with unstressed plants as the control. A total of 21 traits measuring fitness, yield, and the root system were investigated. Little correlation of relative yield traits with potential yield, plant size, and root traits was detected, suggesting that DT and DA were well separated in the experiment. A genetic linkage map consisting of 245 SSR markers was constructed for mapping QTL for these traits. A total of 27 QTL were resolved for 7 traits of relative performance of fitness and yield, 36 QTL for 5 root traits under control, and 38 for 7 root traits under drought stress conditions, suggesting the complexity of the genetic bases of both DT and DA. Only a small portion of QTL for fitness- and yield-related traits overlapped with QTL for root traits, indicating that DT and DA had distinct genetic bases.     

Drought-responsive mechanisms in rice genotypes with contrasting drought tolerance during reproductive stage

Water status is the main factor affecting rice production. In order to understand rice strategies in response to drought condition in the field, the drought-responsive mechanisms at the physiological and molecular levels were studied in two rice genotypes with contrasting susceptibility to drought stress at reproductive stage. After 20 d of drought treatment, the osmotic potential of leaves reduced 78% and 8% in drought susceptible rice cultivar Zhenshan97B and tolerant rice cultivar IRAT109, respectively. The panicle lengths had no obvious changes in drought stressed Zhenshan97B and IRAT109, suggesting that drought stress impose less effect on assimilate translocation from leaf to vegetative growth of panicles. IRAT109 showed more extensive deeper root growth that could be considered a second line of defense against drought stress. The C_i/C_a ratio exhibited enhancement over reduction of g_s in both cultivars, reflecting the non-stomatal limitation to photosynthesis occurred during drought stress. Orthophosphate dikinase, glycine dehydrogenase, ribulose bisphosphate carboxylase (Rubisco), glycine hydroxymethyltransferase and ATP synthase were down-regulated for Zhenshan97B in response to drought stress, suggesting the reduction of capacity of carbon assimilation in this rice cultivar. In drought-stressed IRAT109, transketolase, Rubisco were down-regulated, however, Rubisco activase and peptidyl-prolyl cis-trans isomerase, which might alleviate the damage on Rubisco by drought stress, were up-regulated. The increased abundances of chloroplastic superoxide dismutase [Cu-Zn] and dehydroascorbate reductase might provide antioxidant protection for IRAT109 against damage by dehydration.     

A protocol for high-throughput phenotyping, suitable for quantitative trait analysis in mice

Whole-genome genetic association studies in outbred mouse populations represent a novel approach to identifying the molecular basis of naturally occurring genetic variants, the major source of quantitative variation between inbred strains of mice. Measuring multiple phenotypes in parallel on each mouse would make the approach cost effective, but protocols for phenotyping on a large enough scale have not been developed. In this article we describe the development and deployment of a protocol to collect measures on three models of human disease (anxiety, type II diabetes, and asthma) as well as measures of mouse blood biochemistry, immunology, and hematology. We report that the protocol delivers highly significant differences among the eight inbred strains (A/J, AKR/J, BALBc/J, CBA/J, C3H/HeJ, C57BL/6 J, DBA/2 J, and LP/J), the progenitors of a genetically heterogeneous stock (HS) of mice. We report the successful collection of multiple phenotypes from 2000 outbred HS animals. The phenotypes measured in the protocol form the basis of a large-scale investigation into the genetic basis of complex traits in mice designed to examine interactions between genes and between genes and environment, as well as the main effects of genetic variants on phenotypes.     

The effects of enhanced UV-B radiation on photosynthetic and biochemical activities in super-high-yield hybrid rice Liangyoupeijiu at the reproductive stage

We investigated the light reactions, CO₂ assimilation, but also the chloroplast ultrastructure in the upper three functional leaves (flag, 2^nd, and 3^rd leaves) of the Chinese super-high-yield hybrid rice (Oryza sativa L.) Liangyoupeijiu (LYPJ) with ultraviolet-B (UV-B) treatment during reproductive development. Photosynthetic parameters showed that the upper 3 functional leaves of LYPJ entered into senescence approximately 15 days after flag leaf emergence (DAE). Leaves in UV-B treatment exhibited greater efficiency in absorbing and utilizing light energy of photosystem II (PSII), characterized by higher chlorophyll (Chl) content and the whole chain electron transport rate (ETR). However, UV-B radiation reduced activities of Ca²⁺-ATPase and photophosphorylation. The significantly decreased activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was greatly associated with the decline in photosynthetic efficiency. The net photosynthetic rate (P _N) and stomatal conductance (g _s) suffered strong reductions before 25 DAE, and afterwards showed no significant difference between control and treatment. UV-B treatment delayed chloroplasts development of flag leaves. Chloroplast membranes later swelled and disintegrated, and more stromal thylakoids were parallel to each other and were arranged in neat rows, which might be responsible for better performance of the primary light reaction. It is likely that accumulation of starch and an increase in the number of lipid droplet and translucent plastoglobuli were results of an inhibition of carbohydrate transport. Our results suggest that long-term exposure to enhanced UV-B radiation was unlikely to have detrimental effects on the absorption flux of photons and the transport of electrons, but it resulted in the decrease of photophosphorylation and Rubisco activation of LYPJ. The extent of the damage to the chloroplast ultrastructure was consistent with the degree of the inhibition of photosynthesis.     

A protocol for Agrobacterium-mediated transformation in rice

Agrobacterium-mediated transformation of rice is an important method that has been widely adopted by many laboratories. However, because current approaches rely on culture systems, routine protocols have been established only in japonica rice, especially those varieties with higher regeneration potential. Some very efficient methods have been developed for japonica varieties that enable high-throughput functional analysis in rice; however, many elite japonica, and most indica, varieties are difficult to regenerate, leading to low transformation efficiencies. Much effort has been devoted to improving transformation efficiency for all rice genotypes. Here, we describe an Agrobacterium-mediated rice transformation method that is applicable to easily cultured varieties in addition to elite japonica varieties that are more difficult to culture. Using this method, transgenic rice plants can be obtained in about 2-3 months with a transformation frequency of 30-50%, both in easily cultured varieties and recalcitrant elite japonica rice.     

Effect of nitrogen,phosphorus and potassium on spikelet sterility induced by low temperature at the reproductive stage of rice

Spikelet sterility induced by low temperature at the reproductive stage of rice increased further with the increase of nitrogen supply. Spikelet sterility in Fujisaka-5 did not increase due to low temperature when nitrogen supply was increased from 10 to 40 ppm and at 80 ppm nitrogen supply it was less affected than IR36. Total nitrogen content in the leaves increased with the increase of nitrogen supply and was forced to be associated with the spikelet sterility induced by low temperature. Based on auricle distance between the last two leaves, the most sensitive stage to low temperature damage differed in Fujisaka-5 and IR36. Spikelet sterility induced by low temperature for 10 days was very high in both the varieties and the effect of nitrogen was not clear.The effect of phosphorus on the spikelet sterility induced by low temperature at reproductive stage was not clear except that at the highest phosphorus (P) level (10 ppm) the spikelet sterility increased both in Fujisaka-5 and IR36.Spikelet sterility induced by low temperature at the reproductive stage of rice decreased with the increase of Potassium (K) supply in both Fujisaka-5 and IR36. With an increase of potassium supply, nitrogen (N) content decreased in the leaves and panicles and spikelet sterility induced by low temperature decreased with an increase of the K to N ratio in the leaves and panicles. The results suggest that potassium might play a major role to counteract the low temperature damage at the reproductive stage of rice.     

Novel throughput phenotyping platforms in plant genetic studies

Unraveling the genetic basis of complex traits in plants is limited by the lack of appropriate phenotyping platforms that enable high-throughput screening of many genotypes in multilocation field trials. Near-infrared spectroscopy on agricultural harvesters and spectral reflectance of plant canopies have recently been reported as promising components of novel phenotyping platforms. Understanding the genetic basis of complex traits is now within reach with the use of these new techniques.     

Mapping of quantitative trait loci for salt tolerance at the seedling stage in rice

Salt tolerance was evaluated at the young seedling stage of rice (Oryza sativa L.) using recombinant inbred lines (MG RILs) from a cross between Milyang 23 (japonica/indica) and Gihobyeo (japonica). 22 of 164 MG RILs were classified as tolerant with visual scores of 3.5-5.0 in 0.7% NaCl. Interval mapping of QTLs related to salt tolerance was conducted on the basis of the visual scores at the young seedling stage. Two QTLs, qST1 and qST3, conferring salt tolerance, were detected on chromosome 1 and 3, respectively, and the total phenotypic variance explained by the two QTLs was 36.9% in the MG RIL population. qST1 was the major QTL explaining 27.8% of the total phenotypic variation. qST1 was flanked by Est12-RZ569A, and qST3 was flanked by RG179-RZ596. The detection of new QTLs associated with salt tolerance will provide important information for the functional analysis of rice salt tolerance.     

Elucidation of salt-tolerance metabolic pathways in contrasting rice genotypes and their segregating progenies

Key message

Differentially expressed antioxidant enzymes, amino acids and proteins in contrasting rice genotypes, and co-location of their genes in the QTLs mapped using bi-parental population, indicated their role in salt tolerance.

Abstract

Soil salinity is a major environmental constraint limiting rice productivity. Salt-tolerant ‘CSR27’, salt-sensitive ‘MI48’and their extreme tolerant and sensitive recombinant inbred line (RIL) progenies were used for the elucidation of salt stress tolerance metabolic pathways. Salt stress-mediated biochemical and molecular changes were analyzed in the two parents along with bulked-tolerant (BT) and bulked-sensitive (BS) extreme RILs. The tolerant parent and BT RILs suffered much lower reduction in the chlorophyll as compared to their sensitive counterparts. Activities of antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD) and non-enzymatic antioxidant ascorbic acid were much higher in salt-stressed CSR27 and BT RILs than MI48 and BS RILs. Further, the tolerant lines showed significant enhancement in the levels of amino acids methionine and proline in response to salt stress in comparison to the sensitive lines. Similarly, the tolerant genotypes showed minimal reduction in cysteine content whereas sensitive genotypes showed a sharp reduction. Real time PCR analysis confirmed the induction of methionine biosynthetic pathway (MBP) enzymes cystathionine-β synthase (CbS), S-adenosyl methionine synthase (SAMS), S-adenosyl methionine decarboxylase (SAMDC) and serine hydroxymethyl transferase (SHMT) genes in tolerant lines, suggesting potential role of the MBP in conferring salt tolerance in rice variety CSR27. Proteome profiling also confirmed higher expression of SOD, POD and plastidic CbS and other proteins in the tolerant lines, whose genes were co-located in the QTL intervals for salt tolerance mapped in the RIL population. The study signifies integrated biochemical-molecular approach for identifying salt tolerance genes for genetic improvement for stress tolerant rice varieties.

     

Polymorphism in rice amylases at an early stage of seed germination

A polymorphism in rice amylases at an early stage of seed germination is analyzed by zymogram. In non-glutinous cultivars of rice, alpha-amylase isozymes are mainly confirmed in germinating seeds. However, in glutinous cultivars, beta-amylase isozymes, which are not confirmed in nonglutinous cultivars, make up the major part of the total amylase activity and the expression of alpha-amylases are repressed.     

Point stresses during reproductive stage rather than warming seasonal temperature determine yield in temperate rice

Climate change is predicted to shift temperature regimes in most agricultural areas with temperature changes expected to impact yields of most crops, including rice. These temperature‐driven effects can be classified into point stresses, where a temperature event during a sensitive stage drives a reduction in yield, or seasonal warming losses, where raised temperature is thought to increase maintenance energy demands and thereby decrease available resources for yield formation. Simultaneous estimation of the magnitude of each temperature effect on yield has not been well documented due to the inherent difficulty in separating their effects. We simultaneously quantified the magnitude of each effect for a temperate rice production system using a large data set covering multiple locations with data collected from 1995 to 2015, combined with a unique probability‐based modeling approach. Point stresses, primarily cold stress during the reproductive stages (booting and flowering), were found to have the largest impact on yield (over 3 Mg/ha estimated yield losses). Contrary to previous reports, yield losses caused by increased temperatures, both seasonal and during grain‐filling, were found to be small (approximately 1–2% loss per °C). Occurrences of cool temperature events during reproductive stages were found to be persistent over the study period, and within season, the likelihood of a cool temperature event increased when flowering occurred later in the season. Short and medium grain types, typically recommended for cool regions, were found to be more tolerant of cool temperatures but more sensitive to heat compared to long grain cultivars. These results suggest that for temperate rice systems, the occurrence of periodic stress events may currently overshadow the impacts of general warming temperature on crop production.     

Proteome analysis of rice uppermost internodes at the milky stage

Uppermost internodes, which connect the part between the ear and lower stem, form an important pathway transporting mineral nutrition from roots and photosynthates from leaves (especially the flag leaf) to the ear. The milky stage is the first stage of seed ripening. The uppermost internodes of rice at the milky stage are critical for seed quality and yield. Total soluble proteins of the uppermost internodes of rice (Oryza sativa L. ssp. indica) at the milky stage were analyzed using proteomic methods. Using 2-DE, 762 reproducible protein spots were detected. Among them, 132 abundant proteins were analyzed using MALDI-TOF-MS. Searching in the National Center for Biotechnology Information database, we could identify 98 proteins, which represent 80 gene products. These proteins belong to 11 functional groups with energy production-associated proteins in the first place. The large accumulation of proteins involved in metabolism, signaling, and stress resistance indicated that the uppermost internodes of rice have a high physiological and stress-resistant activity. In addition, our results will also enrich the database of the rice proteome.     

陆地棉萌发至三叶期不同生育阶段耐盐特性

摘要：土壤盐渍化是一个世界性的资源问题和生态问题,盐分胁迫几乎会影响棉花所有重要的生命活动, 造成棉花的减产或其他不利影响。本试验通过对14个品棉花种（系）的萌发期耐盐性、芽期耐盐性以及两个耐盐性不同的品种（系）三叶期的耐盐性,对棉花不同时期的耐盐特性进行了研究,结果表明：棉花在不同生育阶段耐盐能力是不同的,棉花盐敏感时间是在萌发出苗期。随着生育期的延长,棉花的耐盐性是逐步提高的,进行耐盐性鉴定的最佳时期在是萌发出苗期。在三叶期,随着盐分浓度的提高,棉花苗受伤害程度逐渐增加,盐敏感性品种受伤害大于耐盐品种,在同样盐浓度胁迫条件下,耐盐性不同的品种各部分受到的伤害不同,耐盐品种（系）中棉所35受伤害程度由高到低依次为：真叶>上胚轴>子叶;盐敏感品种（系）Tamcot CAB-CS受伤害程度由高到低依次为：真叶> 子叶>上胚轴。