Fingerprinting environmental conditions and related stress using stable isotopic composition of rice (Oryza sativa L.) grain organic matter

Sea level rise (SLR) is a primary factor responsible for inundation of low-lying coastal regions across the world, which in turn governs the agricultural productivity. In this study, rice (Oryza sativa L.) cultivated seasonally in the Kuttanad Wetland, a SLR prone region on the southwest coast of India, were analysed for oxygen, hydrogen and carbon isotopic ratios (delta O-18, delta H-2 and delta C-13) to distinguish the seasonal environmental conditions prevalent during rice cultivation. The region receives high rainfall during the wet season which promotes large supply of fresh water to the local water bodies via the rivers. In contrast, during the dry season reduced river discharge favours sea water incursion which adversely affects the rice cultivation. The water for rice cultivation is derived from regional water bodies that are characterised by seasonal salinity variation which co-varies with the delta O-18 and delta H-2 values. Rice cultivated during the wet and the dry season bears the isotopic imprints of this water. We explored the utility of a mechanistic model to quantify the contribution of two prominent factors, namely relative humidity and source water composition in governing the seasonal variation in oxygen isotopic composition of rice grain OM. delta C-13 values of rice grain OM were used to deduce the stress level by estimating the intrinsic water use efficiency (WUEi) of the crop during the two seasons. 1.3 times higher WUE, was exhibited by the same genotype during the dry season. The approach can be extended to other low lying coastal agro-ecosystems to infer the growth conditions of cultivated crops and can further be utilised for retrieving paleo-environmental information from well preserved archaeological plant remains. (c) 2015 Elsevier Ltd. All rights reserved.

Phenotypic characters of rice landraces reveal independent lineages of short-grain aromatic indica rice

Rice landraces are lineages developed by farmers through artificial selection during the long-term domestication process. Despite huge potential for crop improvement, they are largely understudied in India. Here, we analyse a suite of phenotypic characters from large numbers of Indian landraces comprised of both aromatic and non-aromatic varieties. Our primary aim was to investigate the major determinants of diversity, the strength of segregation among aromatic and non-aromatic landraces as well as that within aromatic landraces. Using principal component analysis, we found that grain length, width and weight, panicle weight and leaf length have the most substantial contribution. Discriminant analysis can effectively distinguish the majority of aromatic from non-aromatic landraces. More interestingly, within aromatic landraces long-grain traditional Basmati and short-grain non-Basmati aromatics remain morphologically well differentiated. The present research emphasizes the general patterns of phenotypic diversity and finds out the most important characters. It also confirms the existence of very unique short-grain aromatic landraces, perhaps carrying signatures of independent origin of an additional aroma quantitative trait locus in the indica group, unlike introgression of specific alleles of the BADH2 gene from the japonica group as in Basmati. We presume that this parallel origin and evolution of aroma in short-grain indica landraces are linked to the long history of rice domestication that involved inheritance of several traits from Oryza nivara, in addition to O. rufipogon. We conclude with a note that the insights from the phenotypic analysis essentially comprise the first part, which will likely be validated with subsequent molecular analysis.

Fungal flora of rice field soils

Qualitative and quantitative assessment of the fungal flora of rice field soils yielded 102 species of fungi belonging to 44 genera, when dilution plate, soil plate, root-washing and baiting techniques were employed. The order of efficacy of the methods used was: root-washing > soil plate > dilution plate > baiting. Baiting method, used specifically to isolate aquatic and keratinophilic fungi from soils was studied in detail with reference to the former. Qualitatively, corn leaf bait was the most efficient one while pine pollens and hemp seeds were least efficient. A semi-quantitative method was employed to study the statistically significant differences among the different factors used. Among the keratinophilic baits,viz., human hair, fowl’s feather and wool, wool bait was least efficient. The results of this investigation are discussed.

The polycomb group gene EMF2B is essential for maintenance of floral meristem determinacy in rice

Polycomb Repressive Complex 2 (PRC2) represses the transcriptional activity of target genes through trimethylation of lysine 27 of histone H3. The functions of plant PRC2 have been chiefly described in Arabidopsis, but specific functions in other plant species, especially cereals, are still largely unknown. Here we characterize mutants in the rice EMF2B gene, an ortholog of the Arabidopsis EMBRYONIC FLOWER2 (EMF2) gene. Loss of EMF2B in rice results in complete sterility, and mutant flowers have severe floral organ defects and indeterminacy that resemble loss-of-function mutants in E-function floral organ specification genes. Transcriptome analysis identified the E-function genes OsMADS1, OsMADS6 and OsMADS34 as differentially expressed in the emf2b mutant compared with wild type. OsMADS1 and OsMADS6, known to be required for meristem determinacy in rice, have reduced expression in the emf2b mutant, whereas OsMADS34 which interacts genetically with OsMADS1 was ectopically expressed. Chromatin immunoprecipitation for H3K27me3 followed by quantitative (q)RT-PCR showed that all three genes are presumptive targets of PRC2 in the meristem. Therefore, in rice, and possibly other cereals, PRC2 appears to play a major role in floral meristem determinacy through modulation of the expression of E-function genes.