Papers by Bikram Pratap Singh
Key message Three coding SNPs and one haplotype identified in the OsDREB1F gene have potential to... more Key message Three coding SNPs and one haplotype identified in the OsDREB1F gene have potential to be associated with drought tolerance in rice. Abstract Drought is a serious constraint to rice production worldwide, that can be addressed by deployment of drought tolerant genes. OsDREB1F, one of the most potent drought tolerance transcription activator genes, was re-sequenced for allele mining and association study in a set of 136 wild rice accessions and four cultivated rice. This analysis led to identify 22 SNPs with eight haplotypes based on allelic variations in the accessions used. The nucleotide variation-based neutrality tests suggested that the OsDREB1F gene has been subjected to purifying selection in the studied set of rice germplasm. Six different OsDREB1F protein variants were identified on the basis of translated amino acid residues amongst the orthologues. Five protein variants were truncated due to deletions in coding region and found susceptible to drought stress. Association study revealed that three coding SNPs of this gene were significantly associated with drought tolerance.
Assessment of genetic diversity is essential for germplasm characterization, utilization and cons... more Assessment of genetic diversity is essential for germplasm characterization, utilization and conservation. Genetic diversity in a set of 132 Indian wild rice accessions belonging to Oryza nivara and Oryza rufipogon and eight cultivated rice varieties was evaluated with 25 highly variable simple sequence repeat (HvSSR) markers using agarose gels and 36 genome-wide SNP markers using Sequenom MassARRAY system. A total of 106 SSR alleles were amplified with an average of 4.24 allele per locus, but only 72 alleles with SNP markers because of its bi-allelic nature. PIC values for HvSSR markers ranged from 0.27 (HvSSR 11-24) to 0.71(HvSSR 05-39) with an average of 0.52 and for SNP it ranged from 0.01(11-3935) to 0.39 (09-209) with an average of 0.19, suggesting more allelic diversity for SSRs over SNP markers. Principal coordinate analysis with SSR and SNP markers revealed that the accessions were uniformly distributed across the two axes in both the plots with 66.53% and 77.65% of cumulative variation, respectively. The analysis of the population structure with SNP markers revealed three sub populations. The comprehensive molecular characterization of the selected set of rice germplasm contributes to the knowledge about levels and distribution of genetic diversity in the Indian wild rice.
Background: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food
legumes of ... more Background: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.
Background: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food
legumes of ... more Background: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.
Background: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food
legumes of ... more Background: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.
Background: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food
legumes of ... more Background: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.
Understanding the distribution of genetic diversity among individuals, populations and gene pools... more Understanding the distribution of genetic diversity among individuals, populations and gene pools is crucial for the efficient management of germplasm collections and breeding programs. Diversity analysis is routinely carried out using sequencing of selected gene(s) or molecular marker technologies. Here we report on the development of Diversity Arrays Technology (DArT) for pigeonpea (Cajanus cajan) and its wild relatives. DArT tests thousands of genomic loci for polymorphism and provides the binary scores for hundreds of markers in a single hybridization-based assay. We tested eight complexity reduction methods using various combinations of restriction enzymes and selected PstI/HaeIII genomic representation with the largest frequency of polymorphic clones (19.8%) to produce genotyping arrays. The performance of the PstI/HaeIII array was evaluated by typing 96 accessions representing nearly 20 species of Cajanus. A total of nearly 700 markers were identified with the average call rate of 96.0% and the scoring reproducibility of 99.7%. DArT markers revealed genetic relationships among the accessions consistent with the available information and systematic classification. Most of the diversity was among the wild relatives of pigeonpea or between the wild species and the cultivated C. cajan. Only 64 markers were polymorphic among the cultivated accessions. Such narrow genetic base is likely to represent a serious impediment to breeding progress in pigeonpea. Our study shows that DArT can be effectively applied in molecular systematics and biodiversity studies
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Papers by Bikram Pratap Singh
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.
legumes of semi-arid tropical and subtropical regions, has limited genomic resources,
particularly expressed sequence based (genic) markers. We report a comprehensive set of
validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing,
and its application in genetic diversity analysis and mapping.