Mayank Rai

Wide Hybridization and Embryo-Rescue for Crop Improvement in Solanum

Tomato is known in the literature as Solanum lycopersicum, as well as Lycopersicon esculentum. In north eastern region of India, cultivation of tomato in rice fallow is becoming popular and may be helpful in increasing production of vegetables, which will not only increase per capita availability of vegetables, but also improve the economic condition of the farmers through employment generation. Tomato is highly prone to biotic stresses, especially diseases, insects and nematodes. Genes are available in different wild species, but it has not been easy to transfer these genes in cultivated species due to problems in crossability. Solanum lycopersicum was crossed with S. peruvianum and Solanum pimpinellofolium. 25 days after pollination was found to be the optimum time for rescuing the embryos. Murashige and Skoog’s (MS) medium supplemented with 1 mg/l GA3, 0.1 mg/l NAA and 0.5 mg/l BAP was found to be the most effective for germination of the immature putative hybrid embryos. The confirmation of hybridity of the embryo rescued plants from the interspecific crosses of both S. lycopersicum var. MT-3 and S. lycopersicum var. Kashi Amrit with S. peruvianum (WIR-3957) was done using RAPD markers.

Allele mining across two low-P tolerant genes PSTOL1 and PupK20-2 reveals novel haplotypes in rice genotypes adapted to acidic soils

About 40% of the global arable land is acidic, and in India, majority of these acidic soils are in the north-eastern region. Soil acidity leads to high phosphorus (P) fixation that causes P deficiency; therefore, there is a need to characterize the identified potential donors for acidic soils for P-deficiency tolerance. We evaluated rice genotypes for nucleotide variation in two loci reported for low P tolerance, namely PSTOL1 and PupK20-2 . Sequence comparison for PSTOL1 revealed two distinct haplotypes. Genotypes with higher P uptake such as LR 19 and LR 23 had the desired Kasalath-type haplotype, whereas those with lower P uptake such as UR 29 and LR 39 showed a mixed haplotype. A total of four novel nucleotide variations were observed in 3′-UTR (untranslated region). Sequencing of PupK20-2 revealed a total of 28 SNPs and one insertion–deletion, of which 24 SNPs were novel. The discovery of novel SNPs across both PSTOL1 and PupK20-2 suggests the existence of novel haplotypes in genotypes adapted to acidic soil conditions. We reported for the first time the characterization of the donors being used in breeding programmes for acidic soils at the molecular level. The implications in breeding programmes are discussed.

Seedling stage low temperature response in tolerant and susceptible rice genotypes suggests role of relative water content and members of OsSNAC gene family

ABSTRACT Low temperature (LT) severely affects rice growth and grain yield. Recently, we reported contrasting genotypes including ARR 09 and Takyer for seedling stage long duration low temperature response. Here we show that susceptible rice genotypes show an increase in lipid peroxide levels and decrease in relative water content (RWC) to a higher extent in comparison to tolerant genotypes in response to 3 h LT. Stress induced NAC family members (OsNAC1, OsNAC2, OsNAC3, and OsNAC5) showed a higher transcript accumulation in tolerant genotypes than in sensitive genotypes after LT treatment suggesting stress tolerance might be due to higher expression of stress-responsive transcription factors. Furthermore, ARR 09 can be used as an important genetic resource to better understand LT tolerance mechanism.

Looking beyond PsTOL1: marker development for two novel rice genes showing differential expression in P deficient conditions.

With the availability of the full genome sequence of rice, identification and localization of genes related to stress tolerance has become feasible. Using the rice genome information, better alleles of these genes can be identified in the germplasm, which will be useful for breeding. Insufficient plant-available soil phosphorus (P) is a major constraint for rice production and is apparent under conditions which are commonly characterized by infertile, highly acidic and P fixing soils. A few genes such as PHR1, PHR2, OsPTF1, OsSPX1, OsSPX2, OsSPX3, OsIPS1 and OsIPS2 (Hou et al. 2005; Wang et al. 2009) have been reported in P deficiency signalling, but whether they function similarly in different rice genotypes in response to low P is not clear. Only one major quantitative trait loci (QTL) phosphorus uptake1 (Pup1) (Wissuwa et al. 1998) has been identified in rice for better uptake of P under deficiency conditions explaining nearly 30% variation for P uptake and has now been narrowed down to gene level (PsTOL1) (Gamuyao et al. 2012). Molecular genetic understanding of P deficiency tolerance is so far restricted to two genes, i.e. PsTOL1 and PTF1. Phosphorus deficiency tolerance being a complex quantitative trait, where P uptake is only one of the components, it is likely that there would be other molecular mechanisms, loci and genes that contribute to tolerance. Thus, there is a need to generate and evaluate novel molecular breeding resources to capture different molecular mechanisms for P deficiency tolerance. In this study, for the first time, we report the use of rice genotypes adapted to acidic soils of eastern and northeastern India for generating novel molecular tools in terms of characterized germplasm and gene-based markers. These resources will be helpful for understanding molecular mechanism underlying adaptability and performance under acidic soils.

Effect of low light intensity on key traits and genotypes of hilly rice (Oryza sativa) germplasm

Low light intensity stress is a critical abiotic stress that reduces rice yield and quality. Present study has been carried out with a set of hill rice germplasm under ambient light and low light condition. Results related to principal components analysis (PCA) revealed that grain yield, plant height and pollen viability are the most informative components accounted for 63.95 % variance among the genotypes studied under low light condition. The three main traits contributing to PCA was. IRCTN 91-84, IRCTN 91-94 and RCPL 1-9C were found to be the most tolerant genotype to low light intensity under this study. * Corresponding author KEYWORDS

Understanding Fe2+ toxicity and P deficiency tolerance in rice for enhancing productivity under acidic soils

Abstract Plants experience low phosphorus (P) and high iron (Fe) levels in acidic lowland soils that lead to reduced crop productivity. A better understanding of the relationship between these two stresses at molecular and physiological level will lead to development of suitable strategies to increase crop productivity in such poor soils. Tolerance for most abiotic stresses including P deficiency and Fe toxicity is a quantitative trait in rice. Recent studies in the areas of physiology, genetics, and overall metabolic pathways in response to P deficiency of rice plants have improved our understanding of low P tolerance. Phosphorous uptake and P use efficiency are the two key traits for improving P deficiency tolerance. In the case of Fe toxicity tolerance, QTLs have been reported but the identity and role played by underlying genes is just emerging. Details pertaining to Fe deficiency tolerance in rice are well worked out including genes involved in Fe sensing and uptake. But, how rice copes with Fe toxicity is not clearly understood. This review focuses on the progress made in understanding these key environmental stresses. Finally, an opinion on the key genes which can be targeted for this stress is provided.

In silico characterisation of novel rice transcripts differentially expressed in phosphorus dificient conditions suggests a role of these transcripts in multiple abiotic stresses

Phosphorus deficiency adversely affects crop productivity. The mechanism of tolerance in plants is not well understood. The current study successfully annotated a set of highly significant (Log2 RPKM ≥3) nine novel sequences up-regulated in P deficient condition identified from a low P tolerant rice genotype. Sequence annotation identified two transcripts (Os01g37260 and Os02g11060) carrying known domains, F-box and WD, respectively. Multiple Expectation maximization for Motif Elicitation (MEME) revealed presence of conserved domains like D[LP][HY][CL]D[CM][DT]C[AP][DQ][IQ]C, [EH][DN]HN[HS] [ER][FY][EP]I[HN]H which might play a role in phosphorus deficiency tolerance. Analysis of the upstream regions indicated presence of stress responsive elements like E Box, ABRE, and MYBCORE suggesting regulation of the novel transcripts by DNA binding. Protein localization prediction tool suggests that these novel proteins might be targeted to nucleus, chloroplast and cell wall. Transcripts Os02g03640 and Os02g10250 revealed potential target sites for microRNA binding suggesting role of novel miRNAs in low phosphorus response. Our analysis suggests that an F-box protein, Os01g37260 (OSFBx14) might be a promising candidate gene playing a role in multiple abiotic stresses including P deficiency.

Quantitative evaluation of lentil (Lens culinaris Medikus.) germplasm under low-input acidic upland soil conditions of North-East India

The present investigation was carried out to assess genetic diversity in 88 lentil genotypes and to identify desirable genotypes under low-input acidic upland soil conditions. Shoot weight, number of pods/plant number of primary branches showed highest association with yield. All the lentil genotypes were grouped into eight distinct clusters. The maximum contribution towards divergence was due to seed thickness followed by plant height and root biomass. Principal components analysis performed on quantitative traits revealed that the first three most informative components accounted for 78.83% variance among the genotypes studied. Genotypes IPL325, LRIC560812 and PL-04, were found suitable for lowinput acidic upland conditions.