[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: 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: 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: 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.
[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: 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: 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: Rice the major staple food crop which feeds more than half of the world’s population but, lacks pathway to synthesize and
accumulate provitamin A in endosperm therefore rice eaters particularly children, and pregnant women suffer due to vitamin
A deficiency. The pathway for provitamin A synthesis in rice endosperm has been engineered and transgenic rice lines have
yellow endosperm, called ‘Golden Rice’. The present study aimed at studying the inheritance of transgene(s) in six transgenic
events of ‘Golden Rice’ and transfer of provitamin A trait from transgenic lines to a widely grown mega rice variety Swarna.
The events E1, R1 and W1 showed normal Mendelian inheritance in F2, BC1F1 and BC1F2 generations. The event W1 was studied in BC1F3 as well and showed normal Mendelian inheritance of 3:1. The inheritance pattern in L1 event in BC1F1 and BC1F2 showed normal Mendelian inheritance following expected ratio 1:1 and 3:1 respectively. The two events G1 and T1 showed distorted
segregation in BC1F2 and BC2F2 respectively in Swarna genetic background. In G1 event, transgene inheritance showed segregation distortion in BC1F2 in favour of transgene negative plants. In T1 event, inheritance followed expected Mendelian segregation in BC1F1, BC2F1 and BC2F2, generations. However, when tested against co-dominant inheritance 1:2:1 pattern in BC2F2, segregation distortion was observed with less than the expected transgene homozygotes. While against 3:1 ratio, it showed
the expected segregation pattern in BC2F2 generation. Segregation distortion probably due to differential transmission of transgene positive/negative gametes through
either/both parents which needs further study.
KeywordsProvitamin A–Transgenic event–Phytoene synthase (psy)
–Phytoene desaturase (crtI)–Transgene inheritance–Segregation distortion
Journal of Plant Biochemistry and Biotechnology 01/2011; 20(1):29-38. · 0.41 Impact Factor
[show abstract][hide abstract] ABSTRACT: Unigene sequences constitute a rich source of functionally relevant microsatellites. The present study was undertaken to mine the microsatellites in the available unigene sequences of sugarcane for understanding their constitution in the expressed genic component of its complex polyploid/aneuploid genome, assessing their functional significance in silico, determining the extent of allelic diversity at the microsatellite loci and for evaluating their utility in large-scale genotyping applications in sugarcane.
The average frequency of perfect microsatellite was 1/10.9 kb, while it was 1/44.3 kb for the long and hypervariable class I repeats. GC-rich trinucleotides coding for alanine and the GA-rich dinucleotides were the most abundant microsatellite classes. Out of 15,594 unigenes mined in the study, 767 contained microsatellite repeats and for 672 of these putative functions were determined in silico. The microsatellite repeats were found in the functional domains of proteins encoded by 364 unigenes. Its significance was assessed by establishing the structure-function relationship for the beta-amylase and protein kinase encoding unigenes having repeats in the catalytic domains. A total of 726 allelic variants (7.42 alleles per locus) with different repeat lengths were captured precisely for a set of 47 fluorescent dye labeled primers in 36 sugarcane genotypes and five cereal species using the automated fragment analysis system, which suggested the utility of designed primers for rapid, large-scale and high-throughput genotyping applications in sugarcane. Pair-wise similarity ranging from 0.33 to 0.84 with an average of 0.40 revealed a broad genetic base of the Indian varieties in respect of functionally relevant regions of the large and complex sugarcane genome.
Microsatellite repeats were present in 4.92% of sugarcane unigenes, for most (87.6%) of which functions were determined in silico. High level of allelic diversity in repeats including those present in the functional domains of proteins encoded by the unigenes demonstrated their use in assay of useful variation in the genic component of complex polyploid sugarcane genome.
[show abstract][hide abstract] ABSTRACT: Large number of well-filled grains per panicle is an important yield component trait in rice. A combination of QTL mapping and transcriptome profiling was used to identify candidate genes for grain number. A framework linkage map was constructed using 166 SSR markers evenly distributed over the 12 rice chromosomes. QTL mapping using 3 years phenotyping data on a set of recombinant inbred lines derived from a cross between Pusa 1266 (high grain number) and Pusa Basmati 1 (low grain number) identified one consistent QTL qGN4-1 on the long arm of chromosome 4 with major effect on grain number. This QTL was co-localized with major QTLs for primary and secondary branches per panicle, and number of panicles per plant. The QTL interval was narrowed down to 11.1 cM (0.78 Mbp) by targeted enrichment of the region with six additional markers. Microarray transcriptome profiling revealed eight genes in the qGN4-1 region differentially expressed between the two parents during early panicle development. Synteny of this QTL and potential candidates was examined in wheat, barley, maize, sorghum, and Brachypodium to further validate the association.
[show abstract][hide abstract] ABSTRACT: Forty-four soybean genotypes with different photoperiod response were selected after screening of 1000 soybean accessions under artificial condition and were profiled using 40 SSR and 5 AFLP primer pairs. The average polymorphism information content (PIC) for SSR and AFLP marker systems was 0.507 and 0.120, respectively. Clustering of genotypes was done using UPGMA method for SSR and AFLP and correlation was 0.337 and 0.504, respectively. Mantel's correlation coefficients between Jaccard's similarity coefficient and the cophenetic values were fairly high in both the marker systems (SSR = 0.924; AFLP = 0.958) indicating very good fit for the clustering pattern. UPGMA based cluster analysis classified soybean genotypes into four major groups with fairly moderate bootstrap support. These major clusters corresponded with the photoperiod response and place of origin. The results indicate that the photoperiod insensitive genotypes, 11/2/1939 (EC 325097) and MACS 330 would be better choice for broadening the genetic base of soybean for this trait.
Genetics and Molecular Biology 04/2010; 33(2):319-24. · 0.74 Impact Factor