Raveendran Muthurajan

Source–sink dynamics and proteomic reprogramming under elevated night temperature and their impact on rice yield and grain quality

High night temperatures (HNTs) can reduce significantly the global rice (Oryza sativa) yield and quality. A systematic analysis of HNT response at the physiological and molecular levels was performed under field conditions. Contrasting rice accessions, N22 (highly tolerant) and Gharib (susceptible), were evaluated at 22°C (control) and 28°C (HNT). Nitrogen (N) and nonstructural carbohydrate (NSC) translocation from different plant tissues into grains at key developmental stages, and their contribution to yield, grain-filling dynamics and quality aspects, were evaluated. Proteomic profiling of flag leaf and spikelets at 100% flowering and 12 d after flowering was conducted, and their reprogramming patterns were explored. Grain yield reduction in susceptible Gharib was traced back to the significant reduction in N and NSC translocation after flowering, resulting in reduced maximum and mean grain-filling rate, grain weight and grain quality. A combined increase in heat shock proteins (HSPs), Ca signaling proteins and efficient protein modification and repair mechanisms (particularly at the early grain-filling stage) enhanced N22 tolerance for HNT. The increased rate of grain filling and efficient proteomic protection, fueled by better assimilate translocation, overcome HNT tolerance in rice. Temporal and spatial proteome programming alters dynamically between key developmental stages and guides future transgenic and molecular analysis targeted towards crop improvement.

Physiological and Proteomic Responses of Rice Peduncles to Drought Stress

Panicle exsertion, an essential physiological process for obtaining high grain yield in rice is mainly driven by peduncle (uppermost internode) elongation. Drought at heading/panicle emergence prevented peduncle elongation from reaching its maximum length even after re-watering. This inhibitory effect of drought resulted in delayed heading and trapping spikelets lower down the panicle inside the flag-leaf sheath, thus increasing sterility in the lower un-exserted spikelets and also among the upper superior spikelets whose exsertion was delayed. Intermittent drought stress caused a significant reduction in relative water content (RWC) and an increase in the abscisic acid (ABA) level of the peduncles, while both returned to normal levels upon re-watering. Semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis revealed the down-regulation of GA biosynthetic genes during drought. 2D-PAGE analysis of proteins from peduncles collected under well-watered, drought-stressed, and re-watered plants revealed at least twofold differential changes in expression of 31 proteins in response to drought and most of these changes were largely reversed by re-watering. The results indicate that ABA-GA antagonism is a key focal point for understanding the failure of panicle exsertion under drought stress and the consequent increase in spikelet sterility.

Sugarcane proteomics: Establishment of a protein extraction method for 2-DE in stalk tissues and initiation of sugarcane proteome reference map

Sugarcane is an important commercial crop cultivated for its stalks and sugar is a prized commodity essential in human nutrition. Proteomics of sugarcane is in its infancy, especially when dealing with the stalk tissues, where there is no study to date. A systematic proteome analysis of stalk tissue yet remains to be investigated in sugarcane, wherein the stalk tissue is well known for its rigidity, fibrous nature, and the presence of oxidative enzymes, phenolic compounds and extreme levels of carbohydrates, thus making the protein extraction complicated. Here, we evaluated five different protein extraction methods in sugarcane stalk tissues. These methods are as follows: direct extraction using lysis buffer (LB), TCA/acetone precipitation followed by solubilization in LB, LB containing thiourea (LBT), and LBT containing tris, and phenol extraction. Both quantitative and qualitative protein analyses were performed for each method. 2‐DE analysis of extracted total proteins revealed distinct differences in protein patterns among the methods, which might be due to their physicochemical limitations. Based on the 2‐D gel protein profiles, TCA/acetone precipitation‐LBT and phenol extraction methods showed good results. The phenol method showed a shift in pI values of proteins on 2‐D gel, which was mostly overcome by the use of 2‐D cleanup kit after protein extraction. Among all the methods tested, 2‐D cleanup‐phenol method was found to be the most suitable for producing high number of good‐quality spots and reproducibility. In total, 30 and 12 protein spots commonly present in LB, LBT and phenol methods, and LBT method were selected and subjected to eLD‐IT‐TOF‐MS/MS and nESI‐LC‐MS/MS analyses, respectively, and a reference map has been established for sugarcane stalk tissue proteome. A total of 36 nonredundant proteins were identified. This is a very first basic study on sugarcane stalk proteome analysis and will promote the unexplored areas of sugarcane proteome research.

Transcriptome analysis of salinity responsiveness in contrasting genotypes of finger millet (Eleusine coracana L.) through RNA-sequencing

Abstract Finger millet (Eleusine coracana L.) is a hardy cereal known for its superior level of tolerance against drought, salinity, diseases and its nutritional properties. In this study, attempts were made to unravel the physiological and molecular basis of salinity tolerance in two contrasting finger millet genotypes viz., CO 12 and Trichy 1. Physiological studies revealed that the tolerant genotype Trichy 1 had lower Na+ to K+ ratio in leaves and shoots, higher growth rate (osmotic tolerance) and ability to accumulate higher amount of total soluble sugar in leaves under salinity stress. We sequenced the salinity responsive leaf transcriptome of contrasting finger millet genotypes using IonProton platform and generated 27.91 million reads. Mapping and annotation of finger millet transcripts against rice gene models led to the identification of salinity responsive genes and genotype specific responses. Several functional groups of genes like transporters, transcription factors, genes involved in cell signaling, osmotic homeostasis and biosynthesis of compatible solutes were found to be highly up-regulated in the tolerant Trichy 1. Salinity stress inhibited photosynthetic capacity and photosynthesis related genes in the susceptible genotype CO 12. Several genes involved in cell growth and differentiation were found to be up-regulated in both the genotypes but more specifically in tolerant genotype. Genes involved in flavonoid biosynthesis were found to be down-regulated specifically in the salinity tolerant Trichy 1. This study provides a genome-wide transcriptional analysis of two finger millet genotypes differing in their level of salinity tolerance during a gradually progressing salinity stress under greenhouse conditions.

The roots of future rice harvests.

Rice production faces the challenge to be enhanced by 50% by year 2030 to meet the growth of the population in rice-eating countries. Whereas yield of cereal crops tend to reach plateaus and a yield is likely to be deeply affected by climate instability and resource scarcity in the coming decades, building rice cultivars harboring root systems that can maintain performance by capturing water and nutrient resources unevenly distributed is a major breeding target. Taking advantage of gathering a community of rice root biologists in a Global Rice Science Partnership workshop held in Montpellier, France, we present here the recent progresses accomplished in this area and focal points where an international network of laboratories should direct their efforts.

Comparative Root Protein Profiles of Korean Ginseng (Panax ginseng) and Indian Ginseng (Withania somnifera)

Ginsenosides and withanolides are the secondary metabolites from Panax ginseng and Withania somnifera, respectively. These compounds have similar biological properties. Two-dimensional electrophoresis (2-DE) analysis was utilized to reveal the protein profile in the roots of both plants, with the aim of clarifying similarly- and differentially-expressed proteins. Total proteins of Korea ginseng (P. ginseng) and Indian ginseng (W. somnifera) roots were separated by 2-DE using a pH 4-7 immobilized pH gradient strip in the first dimension and 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis in the second dimension. The protein spots were visualized by silver staining. Twenty-one P. ginseng proteins and 35 W. somnifera proteins were chosen for identification by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry; of these, functions were ascribed to 14 and 22 of the P. ginseng and W. somnifera proteins, respectively. Functions mainly included general cell metabolism, defense and secondary metabolism. ATPase and alcohol dehydrogenase proteins were expressed in both plants. The results of this study, to our knowledge, are the first to provide a reference 2-DE map for the W. somnifera root proteome, and will aid in the understanding of the expression and functions of proteins in the roots of Korean ginseng and Indian ginseng.

Genetic control of plasticity in root morphology and anatomy of rice in response to water-deficit

The genetic analysis of root morphology and anatomy in a rice diversity panel resulted in identification of the genetic loci that regulates the rooting plasticity in response to water deficit. Elucidating the genetic control of rooting behavior under water-deficit stress is essential to breed climate-robust rice (Oryza sativa) cultivars. Using a diverse panel of 274 indica genotypes grown under control and water-deficit conditions during vegetative growth, we phenotyped 35 traits, mostly related to root morphology and anatomy, involving 45,000 root-scanning images and nearly 25,000 cross sections from the root-shoot junction. The phenotypic plasticity of these traits was quantified as the relative change in trait value under water-deficit compared with control conditions. We then carried out a genome-wide association analysis on these traits and their plasticity, using 45,608 high-quality single-nucleotide polymorphisms. One hundred four significant loci were detected for these traits under control conditions, 106 were detected under water-deficit stress, and 76 were detected for trait plasticity. We predicted 296 (control), 284 (water-deficit stress), and 233 (plasticity) a priori candidate genes within linkage disequilibrium blocks for these loci. We identified key a priori candidate genes regulating root growth and development and relevant alleles that, upon validation, can help improve rice adaptation to water-deficit stress.

Is early morning flowering an effective trait to minimize heat stress damage during flowering in rice

Highlights • Early-morning flowering (EMF) helps rice plants to escape heat stress damage under field conditions.• EMF traits and spikelet sterility were estimated from indica cultivars originating from 13 tropical and 20 subtropical countries.• None of the tested 289 cultivars had the EMF trait.• EMF trait introgressed into popular rice cultivar showed high environmental stability.

Pyramiding Genes for Enhancing Tolerance to Abiotic and Biotic Stresses

Biotic stresses and abiotic stress factors such as salt, drought, cold and extreme temperatures severely limit crop productivity. Attempts to improve crop varieties for traits conferring tolerance to these stresses are being made continuously to sustain the food production. Molecular breeding and genetic engineering strategies are serving as efficient tools to accelerate the process of developing stress tolerant genotypes. Developing crop varieties that can withstand incidence of multiple stresses is one of the major breeding objectives nowadays, wherein series of target genes identified in different parents are accumulated into a single genotype (gene pyramiding). Generation of transgenic plants by introducing two or three foreign genes is one of the common means to develop plants exhibiting resistance against multiple stresses. Recently there have been advances in the mapping of genes controlling quantitative traits, through quantitative trait loci (QTL) mapping experiments and analysis of genomic data. Such advancements in genome mapping and high-throughput laboratory genotyping protocols have enabled us to monitor introgression of desired genes/regions from two or three different sources into a single background. In this paper, we have attempted to review the achievements made in the field of generation of improved crop varieties by pyramiding (genetic transformation and marker assisted gene pyramiding) desired genes from different sources.

Starch content and cassava mosaic disease genetic diversity with relation to yield in south Indian cassava (Manihot esculenta Crantz) germplasm

Cassava, family Euphorbiaceae, is the fifth most important staple food crop. The study of variability and diversity present in diverse cassava accessions maintained at the field genebank of TCRS, TNAU is essential to design the breeding program of cassava in TNAU. Hence, a study was carried out to assess the genetic diversity based on morphological traits and Simple Sequence Repeat (SSR) markers, identifying the SSR markers linked to a cassava mosaic disease-resistant QTL region. Genetic diversity among cassava germplasm accessions was estimated using 28 morphological traits and three SSR markers. The polymorphic information content (PIC) result gives high information for all the SSR markers. Morphological traits revealed 10 clusters and the SSR markers revealed 13 clusters at a similarity coefficient of 2.514 and 0.75, respectively. The SSR marker diversity revealed that the most promising clusters (II and XII) possessing accessions with yield attributing traits and cluster IX were grouped together due to low yield and CMD susceptibility. Morphological descriptors revealed variance for yield contributing traits. The first three principle components accounted for 10.8, 9.1, and 8.4%, respectively. Correlation studies showed significant correlation among yield and yield-attributing traits, which in turn influences yield. The morphological traits diversity reveals that cluster VI was the most promising cluster in which genotypes ME209 and ME460 possess higher yield and starch content with cassava mosaic disease (CMD) resistance. Most of the accessions grouped under cluster X belong to selection from International Centre for Tropical Agriculture (CIAT) collections and the cultivars under clusters I and II were true cassava seed (TCS) selections of India. The CMD-linked SSR marker which is reported in the previous studies have generated eight alleles and each were regressed with CMD resistance and resulted in non-significant linkage to CMD resistance.