[Show abstract][Hide abstract] ABSTRACT: Dwarf plant height and tillering ability are two of the most important agronomic traits that determine the plant architecture, and have profound influence on grain yield in rice. To understand the molecular mechanism controlling these two traits, an EMS-induced recessive dwarf and increased tillering1 (dit1) mutant was characterized. The mutant showed proportionate reduction in each internode as compared to wild type revealing that it belonged to the category of dn-type of dwarf mutants. Besides, exogenous application of GA3 and 24-epibrassinolide, did not have any effect on the phenotype of the mutant. The gene was mapped on the long arm of chromosome 4, identified through positional candidate approach and verified by cosegregation analysis. It was found to encode carotenoid cleavage dioxygenase7 (CCD7) and identified as an allele of htd1. The mutant carried substitution of two nucleotides CC to AA in the sixth exon of the gene that resulted in substitution of serine by a stop codon in the mutant, and thus formation of a truncated protein, unlike amino acid substitution event in htd1. The new allele will facilitate further functional characterization of this gene, which may lead to unfolding of newer signalling pathways involving plant development and architecture.. 2014 A substitution mutation in OsCCD7 cosegregates with dwarf and increased tillering phenotype in rice. J. Genet. 93, xx–xx]
[Show abstract][Hide abstract] ABSTRACT: Moth bean (Vigna aconitifolia (Jacq.) Marechal), an important grain-legume crop grown in hot desert regions of Thar, under scorching sun rays, was investigated for heat tolerance at molecular level. In the present study, we constructed a forward suppression subtractive hybridization (SSH) cDNA library of heat tolerant genotype RMO-40 to identify genes expressing under delayed response to elevated temperature. Heat induction was carried out by exposing 14-day-old seedlings to elevated temperature of 42 °C for 30 min. A total of 125 unigenes (33 contigs and 92 singletons) were derived by cluster assembly and sequence alignment of 200 ESTs; out of 125 unigenes, 21 (16 %) were found to be novel to moth bean. Gene ontology functional classification terms were retrieved for 98 (78.4 %) unigenes of which 73 (58.4 %) ESTs were functionally annotated (GO consensus) where 19 unigenes were annotated with 11 enzyme commission (EC) codes and were mapped to 25 different KEGG pathways. We have identified a majority of heat-shock proteins (constituting 35 % of the present library) aiding heat stress tolerance to moth bean. An expression level of 22 ESTs generated from the above SSH cDNA library was studied through semiquantitative RT-PCR assay simultaneously under 5 and 30 min of heat stress at 42 °C.
[Show abstract][Hide abstract] ABSTRACT: Rice (Oryza sativa) is the staple food of more than half of the world‟s population. The
International Rice Genome Sequencing Project (IRGSP) generated very high quality
sequences that were used to predict the number and type of genes, and the non-genic
regions containing repeats and mobile genetic elements. Concerted efforts are required
to understand the function of individual genes, and their interactions among themselves
as well as with environment in relation to variation in traits for a directed genetic
manipulation of this important crop for the benefit of the mankind. One of the
approaches to determine functions of genes employs natural mutants available in the
germplasm or those induced by physical, chemical or biological agents. Mutants
facilitate unveiling the causal relationships between coding/regulatory sequences and
plant performance, and also cloning of the corresponding genes. Therefore a number of
international efforts are underway for generation, collection and characterization of
mutants for providing technological platform for functional genomics. In an indigenous
effort funded by the Department of Biotechnology (DBT), Government of India, a set of
22, 292 EMS mutagenised lines have been generated in the background of an upland
rice variety Nagina-22. EMS was chosen since it gives high point mutation densities by
base substitution either in the transcribed regions or in the regulatory elements of a
gene that might alter gene function leading to creation of a series of alleles of a gene.
The uniqueness of this national effort is phenotyping for a range of traits. Elaborate
phenotyping by different partner institutions has led to identification of mutants for plant
growth and architecture, flowering, maturity, grain number, shape and size, yield,
resistance to blast and bacterial leaf blight diseases, phosphorus use efficiency, and
tolerance to herbicide, drought and salinity. Inheritance of selected mutants has been
carried out using F2 populations developed from the cross of the mutants with wild type
Nagina22. Mutant loci for seed size and plant height have been mapped using SSR
markers on chromosomes 5 and 4, respectively. Transcriptome profiling using rice
microarrays has revealed altered expression of only a limited set of genes in these
mutants. In contrast, hundreds of genes were found differentially regulated in a gain-offunction
mutant having higher level of tolerance to moisture deficit stress. This mutant
also showed longer roots and more of partially closed stomata under stress. Two of the
mutants, one for plant height and the other for seed size were characterized in detail.
The dwarf mutant showed proportionate reduction in each of the internodes as
compared to wild type. The gene, identified through positional candidate approach and
verified by co-segregation analysis, was found to encode Carotenoid Cleavage
Dioxygenase7 (CCD7) and identified as an allele of htd1. The mutant carried
substitution of two nucleotides CC to AA in the sixth exon of the gene that resulted in
substitution of serine by a stop codon in the mutant. The short grain mutant had shorter,
narrower, and lesser cells in as compared to the wild type. The candidate gene region
on the short arm of chromosome 5 includes srs3, which was already reported to control
grain size in rice. It encodes kinesin 13 family proteins with a major role in mediation of
microtubule organisation during mitosis. Sequencing of 11kb srs3 gene region revealed
a substitution of C to T in the coding region of the mutant leading to creation of a stop
codon. Sequencing of the kinesin motor domain region of the gene did not reveal
presence of this mutation in 96 germplasm lines having significant grain size variation.
Results suggested utility of the mutant resource in rice functional genomics including
discovery of new genes for traits agronomic importance and allele mining.
[Show abstract][Hide abstract] ABSTRACT: Maize is an increasingly important food crop in southeast Asia. The elucidation of its genetic architecture, accomplished by exploring quantitative trait loci and useful alleles in various lines across numerous breeding programs, is therefore of great interest. The present study aimed to characterize subtropical maize lines using high-quality SNPs distributed throughout the genome.
We genotyped a panel of 240 subtropical elite maize inbred lines and carried out linkage disequilibrium, genetic diversity, population structure, and principal component analyses on the generated SNP data. The mean SNP distance across the genome was 70 Kb. The genome had both high and low linkage disequilibrium (LD) regions; the latter were dominant in areas near the gene-rich telomeric portions where recombination is frequent. A total of 252 haplotype blocks, ranging in size from 1 to 15.8 Mb, were identified. Slow LD decay (200-300 Kb) at r2 <= 0.1 across all chromosomes explained the selection of favorable traits around low LD regions in different breeding programs. The association mapping panel was characterized by strong population substructure. Genotypes were grouped into three distinct clusters with a mean genetic dissimilarity coefficient of 0.36.
The genotyped panel of subtropical maize lines characterized in this study should be useful for association mapping of agronomically important genes. The dissimilarity uncovered among genotypes provides an opportunity to exploit the heterotic potential of subtropical elite maize breeding lines.
[Show abstract][Hide abstract] ABSTRACT: Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. DNA markers such as microsatellite or simple sequence repeat markers have been widely used to estimate the genetic diversity in rice. The present study was carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of random vis-á-vis QTL linked/gene based simple sequence repeat markers in diversity estimation. A set of 88 rice accessions that included landraces, farmer's varieties and popular Basmati lines were evaluated for agronomic traits and molecular diversity. The random set of SSR markers included 50 diversity panel markers developed under IRRI's Generation Challenge Programme (GCP) and the trait-linked/gene based markers comprised of 50 SSR markers reportedly linked to yield and related components. For agronomic traits, significant variability was observed, ranging between the maximum for grains/panicle and the minimum for panicle length. The molecular diversity based grouping indicated that varieties from a common centre were genetically similar, with few exceptions. The trait-linked markers gave an average genetic dissimilarity of 0.45 as against that of 0.37 by random markers, along with an average polymorphic information constant value of 0.48 and 0.41 respectively. The correlation between the kinship matrix generated by trait-linked markers and the phenotype based distance matrix (0.29) was higher than that of random markers (0.19). This establishes the robustness of trait-linked markers over random markers in estimating genetic diversity of rice germplasm.
Journal of Genetics 12/2013; 92(3):545-57. · 0.88 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Grain size is one of the three productivity related traits in rice and hence a major target for genetic improvement. Since understanding genetic variation in grain size between Basmati and indica genotypes is important for rice improvement, a recombinant inbred population was developed from a traditional aromatic cultivar ‘Basmati 370’ and a non-aromatic indica genotype ‘IRBB60’. This population was phenotyped in two locations for grain length (GL), grain breadth (GB), GL/GB ratio (LBR) and grain weight (GW). Though the RIL population reported in the current study exhibited segregation distortion (SD) for 54 % of the markers, they were utilized in analysis using an appropriate statistical package, PROC QTL in the SAS environment. Interval mapping revealed a total of 15 QTLs for GL, seven for GB, 15 for LBR and two for GW. Among them 13 were not reported earlier and thus novel. For a known major QTL identified in the study, GW8 for GB, a PCR based functional marker was designed and validated. This is the first report wherein a very high proportion of markers (>50 %) exhibiting SD have been successfully used for QTL mapping.
[Show abstract][Hide abstract] ABSTRACT: Plant height and flowering time are two of the important traits that affect plant architecture. Efforts were made in this study to characterize morphologically the-EMS-induced dwarf and early flowering mutants of rice variety Nagina22 and to study their mode of inheritance. Nine true breeding mutants generated earlier by EMS treatment were analysed for differences in their phenotypic characteristics recorded according to the national guidelines for Distinctness, Uniformity and Stability (DUS). The mutants exhibited variation from Nagina22 for maximum of 11 DUS characteristics to a minimum of 4 DUS descriptors, while retaining majority of the wild type features. Plant height of the dwarf mutants ranged from 69 to 101cm, while tiller number was in the range of 9 to 60. The early flowering mutants were weak in their plant stature, but flowered approximately 20-25 days earlier than Nagina22. Significant correlation among various traits of the selected mutants was observed. The mutant traits exhibited monogenic inheritance giving 3:1 phenotypic segregation ratio in F2 generation. These mutants have potential usage in functional analysis of the traits and in rice improvement programs.
[Show abstract][Hide abstract] ABSTRACT: Genetic improvement of sugar content in sugarcane would benefit from the availability of sufficient DNA markers and a genetic map. Genetic linkage maps were constructed to identify quantitative trait loci (QTLs) for seedling brix (SB), brix (B), sucrose percent in juice (SUC), stalk number (SN), stalk length (SL), stalk diameter (SD), internodes (INT), number of green leaves (NGL), at three crop cycles across seven environments in a segregating population with 207 individuals derived from a bi-parental cross of sugarcane elite cultivars. Linkage analysis led to the construction of eight linkage groups (LGs) for Co86011 and sixteen LGs for CoH70. The combined length of the two linkage maps was 2606.77 cM distributed over 24 LGs. 31 QTLs were identified: 2 for SB, 7 for B, 6 for SUC, 4 for SN, 1 for SL, 3 for SD, 6 for INT and 2 for NGL at LOD scores ranging from 2.69 to 4.75. 7 QTLs (22 %) had stable effect across crop year and locations. Markers from parents were found to be associated with both positive and negative effect on all of the traits analyzed. The most important QTLs intervals identified in this study using single-dose marker, were qB2, qSUC2, qINT2 and qB2, qSUC2, qSL2, qINT2 located between SSR markers UGSM31548 and UGSM31649. These QTLs could be put into use in marker assisted breeding.
[Show abstract][Hide abstract] ABSTRACT: Moth bean ( Vigna aconitifolia (Jacq.) Marechal) is an important grain legume crop grown in rain fed areas of hot desert regions of Thar, India, under scorching sun rays with very little supplementation of water. An SSH cDNA library was generated from leaf tissues of V. aconitifolia var. RMO-40 exposed to an elevated temperature of 42 °C for 5 min to identify early-induced genes. A total of 488 unigenes (114 contigs and 374 singletons) were derived by cluster assembly and sequence alignment of 738 ESTs; out of 206 ESTs (28%) of unknown proteins, 160 ESTs (14%) were found to be novel to moth bean. Only 578 ESTs (78%) showed significant BLASTX similarity (<1 × 10(-6)) in the NCBI non-redundant database. Gene ontology functional classification terms were retrieved for 479 (65%) sequences, and 339 sequences were annotated with 165 EC codes and mapped to 68 different KEGG pathways. Four hundred and fifty-two ESTs were further annotated with InterProScan (IPS), and no IPS was assigned to 153 ESTs. In addition, the expression level of 27 ESTs in response to heat stress was evaluated through semiquantitative RT-PCR assay. Approximately 20 different signaling genes and 16 different transcription factors have been shown to be associated with heat stress in moth bean for the first time.
[Show abstract][Hide abstract] ABSTRACT: BACKGROUND: Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice. RESULTS: Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species. CONCLUSIONS: SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice.
[Show abstract][Hide abstract] ABSTRACT: Rice is staple food for more than half of the world's population including two billion Asians, who obtain 60-70% of their energy intake from rice and its derivatives. To meet the growing demand from human population, rice varieties with higher yield potential and greater yield stability need to be developed. The favourable alleles for yield and yield contributing traits are distributed among two subspecies i.e., indica and japonica of cultivated rice (Oryza sativa L.). Identification of novel favourable alleles in indica/japonica will pave way to marker-assisted mobilization of these alleles in to a genetic background to break genetic barriers to yield.
A new plant type (NPT) based mapping population of 310 recombinant inbred lines (RILs) was used to map novel genomic regions and QTL hotspots influencing yield and eleven yield component traits. We identified major quantitative trait loci (QTLs) for days to 50% flowering (R2 = 25%, LOD = 14.3), panicles per plant (R2 = 19%, LOD = 9.74), flag leaf length (R2 = 22%, LOD = 3.05), flag leaf width (R2 = 53%, LOD = 46.5), spikelets per panicle (R2 = 16%, LOD = 13.8), filled grains per panicle (R2 = 22%, LOD = 15.3), percent spikelet sterility (R2 = 18%, LOD = 14.24), thousand grain weight (R2 = 25%, LOD = 12.9) and spikelet setting density (R2 = 23%, LOD = 15) expressing over two or more locations by using composite interval mapping. The phenotypic variation (R2) ranged from 8 to 53% for eleven QTLs expressing across all three locations. 19 novel QTLs were contributed by the NPT parent, Pusa1266. 15 QTL hotpots on eight chromosomes were identified for the correlated traits. Six epistatic QTLs effecting five traits at two locations were identified. A marker interval (RM3276-RM5709) on chromosome 4 harboring major QTLs for four traits was identified.
The present study reveals that favourable alleles for yield and yield contributing traits were distributed among two subspecies of rice and QTLs were co-localized in different genomic regions. QTL hotspots will be useful for understanding the common genetic control mechanism of the co-localized traits and selection for beneficial allele at these loci will result in a cumulative increase in yield due to the integrative positive effect of various QTLs. The information generated in the present study will be useful to fine map and to identify the genes underlying major robust QTLs and to transfer all favourable QTLs to one genetic background to break genetic barriers to yield for sustained food security.
[Show abstract][Hide abstract] ABSTRACT: Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
[Show abstract][Hide abstract] ABSTRACT: In a combined approach of phenotypic and genotypic characterization, 28 indigenous rhizobial isolates obtained from different chickpea growing regions in peninsular and northern India were analyzed for diversity. The field isolates were compared to two reference strains TAL620 and UPM-Ca142 representing M. ciceri and M. mediterraneum respectively. Phenotypic markers such as resistance to antibiotics, tolerance to salinity, temperature, pH, phosphate solubilization ability, growth rate and also symbiotic efficiency showed considerable diversity among rhizobial isolates. Their phenotypic patterns showed adaptations of rhizobial isolates to abiotic stresses such as heat and salinity. Two salt tolerant strains (1.5% NaCl by T1 and T4) with relatively high symbiotic efficiency and two P-solubilising strains (66.7 and 71 microg/ml by T2 and T5) were identified as potential bioinoculants. Molecular profiling by 16S ribosomal DNA Restriction Fragment Length Polymorphism (RFLP) revealed three clusters at 67% similarity level. Further, the isolates were differentiated at intraspecific level by 16S rRNA gene phylogeny. Results assigned all the chickpea rhizobial field isolates to belong to three different species of Mesorhizobium genus. 46% of the isolates grouped with Mesorhizobium loti and the rest were identified as M. ciceri and M. mediterraneum, the two species which have been formerly described as specific chickpea symbionts. This is the first report on characterization of chickpea nodulating rhizobia covering soils of both northern and peninsular India. The collection of isolates, diverse in terms of species and symbiotic effectiveness holds a vast pool of genetic material which can be effectively used to yield superior inoculant strains.
Indian journal of experimental biology 05/2012; 50(5):340-50. · 1.20 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Declining availability of water for irrigation remains one of the major impediments to sustaining the current
level of production. Further enhancement in productivity has to meet the challenge of limited water availability.In the present study, screening of forty genotypes of Brassica, Eruca sativa and Sinapis alba in one meter-long tubes under controlled net-house experimental set-up identified S. alba as highly tolerant. The tolerant genotypes of B. juncea included RGN73 and RH30. The popular mustard cultivar Varuna was moderately tolerant, while genotypes Bio-YSR and RLM619 gave highly sensitive response. Libraries were constructed through suppression subtractive hybridization (SSH) using 29 day stressed plants of S. alba, RGN73, Varuna and Bio-YSR. A total of 3500 recombinant clones were obtained. Sequences of the clones were subjected to BLAST analysis with EST database of Arabidopsis and Brassica which revealed 492 differentially expressed genes belonging to different functional categories. A subset of NAC14, NAC19, AREB1, SHN1, CBP20, HD2C, SOS4, ROP10, PLDa genes showing differential expression under drought stress were validated by semi-quantitative RT-PCR. Full length cDNAs of NAC14 and NAC19 showing up-regulation in S. alba, RGN73, Varuna, BEC-144 and Bio-YSR and down regulation in RLM619 were amplified from above six genotypes, cloned and sequenced. The nucleotide and deduced amino acid sequence of the two genes were used to establish their phylogenic relationship with the other members of this transcription factor gene family. Functional validation of the gene in transgenic Brassica is in progress.
International Conference on Plant Biotechnology for food security: new frontiers; 01/2012
[Show abstract][Hide abstract] ABSTRACT: Basmati rice grown in the Indian subcontinent is highly valued for its unique culinary qualities. Production is, however, often constrained by diseases such as bacterial blight (BB), blast and sheath blight (ShB). The present study developed Basmati rice with inbuilt resistance to BB, blast and ShB using molecular marker-assisted selection.
The rice cultivar 'Improved Pusa Basmati 1' (carrying the BB resistance genes xa13 and Xa21) was used as the recurrent parent and cultivar 'Tetep' (carrying the blast resistance gene Pi54 and ShB resistance quality trait loci (QTL), qSBR11-1) was the donor. Marker-assisted foreground selection was employed to identify plants possessing resistance alleles in the segregating generations along with stringent phenotypic selection for faster recovery of the recurrent parent genome (RPG) and phenome (RPP). Background analysis with molecular markers was used to estimate the recovery of RPG in improved lines.
Foreground selection coupled with stringent phenotypic selection identified plants homozygous for xa13, Xa21 and Pi54, which were advanced to BC(2)F(5) through pedigree selection. Marker-assisted selection for qSBR11-1 in BC(2)F(5) using flanking markers identified seven homozygous families. Background analysis revealed that RPG recovery was up to 89.5%. Screening with highly virulent isolates of BB, blast and ShB showed that the improved lines were resistant to all three diseases and were on a par with 'Improved Pusa Basmati 1' for yield, duration and Basmati grain quality.
This is the first report of marker-assisted transfer of genes conferring resistance to three different diseases in rice wherein genes xa13 and Xa21 for BB resistance, Pi54 for blast resistance, and a major QTL qSBR11-1 have been combined through marker-assisted backcross breeding. In addition to offering the potential for release as cultivars, the pyramided lines will serve as useful donors of gene(s) for BB, blast and ShB in future Basmati rice breeding programmes.
[Show abstract][Hide abstract] ABSTRACT: Pusa RH10, a popular high yielding superfine grain aromatic rice hybrid and its parents Pusa6A and PRR78 are highly susceptibility to blast disease. Marker assisted backcross breeding (MABB) approach was employed to incorporate blast resistance genes viz., Piz-5 and Pi54, from the donor lines C101A51 and Tetep into the genetic background of PRR78 to develop Pusa1602 (PRR78 + Piz5) and Pusa1603 (PRR78 + Pi54), respectively. Foreground selection for the genes Piz-5 and Pi54 was effected using tightly linked molecular markers, AP5930 and RM206, respectively in two independent backcross series. Further, foreground selection was coupled with stringent phenotypic selection for agronomic, grain and cooking quality traits, to accelerate recurrent parent phenome recovery. Five superior BC2F2 plants homozygous from each of the backcross series were selected and advanced to BC2F5 generation through pedigree selection to develop improved versions of PRR78 with blast resistance. Background analysis revealed the recurrent parent genome recovery up to 89.01% and 87.88% in Pusa1602 and Pusa1603 lines, respectively. The hybrids produced by crossing Pusa6A with improved lines of PRR78, were on par with original Pusa RH10 in terms of yield, grain and cooking quality traits with an added advantage of blast resistance.
Field Crops Research 01/2012; 128(1):8-16. · 2.47 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: An AFLP linkage map of Brassica juncea (L.) Czern and Coss was constructed using 88 recombinant inbred lines (RILs) from a cross between an Indian cultivar 'Varuna' and an accession from Poland 'BEC-144'. The map included 91 AFLP markers organized on 19 linkage groups covering a total map distance of 1679.1 cM. A total of 14 QTLs were detected for oil content (2 QTLs), erucic acid (2 QTLs), eicosenoic acid (2 QTLs), linolenic acid (3 QTLs), linoleic acid (3 QTLs) and palmitic acid (2 QTLs). A specific genomic region on LG2 was associated with contents of three fatty acids: erucic acid, eicosenoic acid and linoleic acid. Some of the markers showed absolute linkage with the QTLs associated with the levels of linolenic acid, linoleic acid and oil content. These markers may be used for improvement of fatty acid profile of B. juncea. Keywords Indian Mustard . AFLP . Fatty acid . Oil content . QTL mapping Abbreviations AFLP Amplified fragment length polymorphism LOD log likelihood odds ratio QTL quantitative trait loci RIL recombinant inbred lines
Journal of Plant Biochemistry and Biotechnology 01/2012; · 0.41 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The small hairpin RNAs (shRNA) are useful in many ways like identification of trait specific molecular markers, gene silencing and characterization of a species. In public domain, hardly there exists any standalone software for shRNA prediction. Hence, a software shRNAPred (1.0) is proposed here to offer a user-friendly Command-line User Interface (CUI) to predict 'shRNA-like' regions from a large set of nucleotide sequences. The software is developed using PERL Version 5.12.5 taking into account the parameters such as stem and loop length combinations, specific loop sequence, GC content, melting temperature, position specific nucleotides, low complexity filter, etc. Each of the parameters is assigned with a specific score and based on which the software ranks the predicted shRNAs. The high scored shRNAs obtained from the software are depicted as potential shRNAs and provided to the user in the form of a text file. The proposed software also allows the user to customize certain parameters while predicting specific shRNAs of his interest. The shRNAPred (1.0) is open access software available for academic users. It can be downloaded freely along with user manual, example dataset and output for easy understanding and implementation. AVAILABILITY: The database is available for free at http://bioinformatics.iasri.res.in/EDA/downloads/shRNAPred_v1.0.exe.