Wricha Tyagi

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

Background The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers. Methodology/Principal Findings In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations. Conclusions/Significance Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.

Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.).

We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype–genotype associations in rice. These resources include a diversity panel of 400 Oryza sativa and 100 Oryza rufipogon accessions that have been purified by single seed descent, a custom-designed Affymetrix array consisting of 44,100 SNPs, an Illumina GoldenGate assay consisting of 1,536 SNPs, and a suite of low-resolution 384-SNP assays for the Illumina BeadXpress Reader that are designed for applications in breeding, genetics and germplasm management. Our long-term goal is to empower basic research discoveries in rice by linking sequence diversity with physiological, morphological, and agronomic variation. This research platform will also help increase breeding efficiency by providing a database of diversity information that will enable researchers to identify useful DNA polymorphisms in genes and germplasm of interest and convert that information into cost-effective tools for applied plant improvement.

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.

Functional properties of an alternative, tissue-specific promoter for rice NADPH-dependent dihydroflavonol reductase

NADPH-dependent dihydroflavonol reductase (DFR) plays an important role in both anthocyanin biosynthesis and proanthocyanidin synthesis in plants. A specific and quantitative RT-PCR assay for transcription from the DFR promoter detected high expression with limited variability in rice tissues. A 440 bp minimal promoter region was identified by transfection of β-glucuronidase (GUS) reporter constructs into Jeokjinju variety. Alignment of the region with orthologous promoters revealed three conserved segments containing both bHLH (-386 to -381) and Myb (-368 to -362) binding sites. Transfection of β-glucuronidase constructs with targeted point mutations in the minimal promoter defined two sites important for promoter function to the transcription factor binding consensus sequences. The expression study showed that the bHLH binding domain (-386 to -381) is essential for DFR expression, and that a Myb binding domain (-368 to -362) is also required for full expression of the DFR gene, while the two bHLH binding domains (-104 to -99 and -27 to -22) nearest to the transcriptional start site are not necessary for DFR expression.

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.