Rajender Singh

Bio: Rajender Singh is an academic researcher from Indian Council of Agricultural Research. The author has contributed to research in topics: Population & Germplasm. The author has an hindex of 16, co-authored 94 publications receiving 718 citations. Previous affiliations of Rajender Singh include Indian Agricultural Research Institute & University of Saskatchewan.

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat

Abstract: Drought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is first sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refinement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For effective future use of findings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under field drought conditions along with genomic resources, warranted in endeavour of wheat productivity.

Uncovering Genomic Regions Associated With 36 Agro-Morphological Traits in Indian Spring Wheat Using GWAS.

Abstract: Wheat genetic improvement by integration of advanced genomic technologies is one way of improving productivity. To facilitate the breeding of economically important traits in wheat, SNP loci and underlying candidate genes associated with the 36 agro-morphological traits were attempted in a diverse panel of 404 genotypes. Using Breeders’ 35K Axiom Array in a comprehensive genome-wide association study covering 4364.79 cM of the wheat genome and compressed mixed linear model, a total of 146 SNPs (-log10 P ≥ 4) were found associated with 23 traits out of 36 traits studied explaining 3.7-47.0% phenotypic variations. To reveal this a subset of 260 genotypes was characterized phenotypically for six quantitative traits [days to heading (DTH), days to maturity (DTM), plant height (PH), spike length (SL), awn length (Awn_L) and leaf length (Leaf_L)] under five environments. Gene annotations mined ~38 putative candidate genes which were confirmed using tissue and stage specific gene expression data from RNA Seq. We observed strong co-localized loci for four traits (glume pubescence, spike length, plant height and awn color) on chromosome 1B (24.64 cM) annotated five putative candidate genes. This study led to the discovery of hitherto unreported loci for some less explored traits (such as leaf sheath wax, awn attitude, glume pubescence) besides the refined chromosomal regions of known loci associated with the traits..This study provides valuable information of the genetic loci and their potential genes underlying the traits such as awn characters which are being considered as important contributors towards yield enhancement.

Identification of genomic regions associated with seed dormancy in white-grained wheat

Abstract: Pre-harvest sprouting (PHS) in developing wheat (Triticum aestivum L.) spikes is stimulated by cool and wet weather and leads to a decline in grain quality. A low level of harvest-time seed dormancy is a major factor for PHS, which generally is a larger problem in white-grained as compared to red-grained wheat. We have in this study analyzed seed dormancy levels at the 92nd Zadok growth stage of spike development in a doubled-haploid (DH) white wheat population and associated variation for the trait with regions on the wheat genome. The phenotypic data was generated by growing the parent lines Argent (non-dormant) and W98616 (dormant) and 151 lines of the DH population in the field during 2002 and 2003, at two locations each year, followed by assessment of harvest-time seed dormancy by germination tests. A genetic map of 2681 cM was constructed for the population upon genotyping 90 DH lines using 361 SSR, 292 AFLP, 252 DArT and 10 EST markers. Single marker analysis of the 90 genotyped lines associated regions on chromosomes 1A, 2B, 3A, 4A, 5B, 6B, and 7A with seed dormancy in at least two out of the four trials. All seven putative quantitative trait loci (QTLs) were contributed by alleles of the dormant parent, W98616. The strongest QTLs positioned on chromosomes 1A, 3A, 4A and 7A were confirmed by interval mapping and markers at these loci have potential use in marker-assisted selection of PHS resistant white-grained wheat.

Mapping quantitative trait loci associated with grain filling duration and grain number under terminal heat stress in bread wheat (Triticum aestivum L.)

Abstract: Terminal heat stress has the potential negative impact on wheat production across the world, especially in South Asia. Under the threat of terminal heat stress, wheat genotypes with stay green trait would suffer from high temperature stress during their long grain filling duration (GFD). The genotypes with short GFD would be advantageous. To identify quantitative trait loci (QTL) for heat tolerance, a RIL population of K 7903 (heat tolerant) and RAJ 4014 (heat sensitive) wheat genotypes was investigated under timely and late-sown conditions. Heat susceptibility index of GFD, yield components and traits under late-sown condition were used as phenotypic data for QTL identification. Stable QTLs associated with these traits were identified on chromosomes 1B, 2B, 3B, 5A and 6B. The LOD value ranged from 2.9 to 5.0 and the corresponding phenotyping variation explained ranged from 12.0–22%. QTL for heat susceptibility index for the grain filling duration were colocalized with QTL for productive tillers under late sown and GFD under late-sown condition on chromosomes 1B and 5A, respectively. These genomic regions could be exploited for molecular wheat breeding programmes targeting heat tolerance.

Genome-Wide Association Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance.

Abstract: Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Abstract: The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated. It is found that the correlation between these two estimates is large when the sample size is small, and decreases slowly as the sample size increases. Using the relationship obtained, a statistical method for testing the neutral mutation hypothesis is developed. This method needs only the data of DNA polymorphism, namely the genetic variation within population at the DNA level. A simple method of computer simulation, that was used in order to obtain the distribution of a new statistic developed, is also presented. Applying this statistical method to the five regions of DNA sequences in Drosophila melanogaster, it is found that large insertion/deletion (greater than 100 bp) is deleterious. It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

In vitro: Response of plant growth regulators and antimalformins on conidia germination of Fusarium mangiferae and incidence of mango malformation

Abstract: Mango malformation is the most important and threatening disease of recent times, primarily because of persistent lacuna in complete understanding of its nature. Diverse Fusarium spp, including F. mangiferae, were found to be associated with the disease. Here, F. mangiferae from mango cv Dashehri was morphologically characterized. Typically, oval-shaped microconidia without septum and crescent-shaped macroconidia with 3-septate were more often observed, whereas not a single chlamydospore was detected. The length and width of micro- and macro-conidia were 7.5, 55, 3.2, and 3.5, respectively. The plant growth regulators such as NAA, GA3, BAP and ethrel were found to induce in vitro germination of conidia of F. mangiferae after 12 h. In contrast, antimalformin silver nitrate (AgNO3) inhibits conidial germination in vitro and none of conidia was germinated beyond 500 ppm, however antimalformin glutathione was highly effective in stimulating conidial germination of F. mangiferae in vitro at > 1000 ppm after 24 h. We observed that the response of F. mangiferae to germinate the conidia in vitro under influence of plant growth regulators and antimalformins is not coincided with earlier findings of reduced disease incidence by exogenous application of these compounds. The present findings do not authenticate the involvement of F. mangiferae in the disease, however hormonal imbalance, most probably ethylene, might be responsible for deformed functional morphology of panicle. Further, a signal transduction mechanism of stress-stimulated ethylene imbalance causing physio-morphological changes in reproductive organs of mango flower and thereby failure of fertilization and fruit set, which needs to be investigated.