Browsing by Author "Verma, Priyanka"

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Construction of a genetic linkage map and identification of QTLs for seed weight and seed size traits in lentil (Lens culinaris Medik.)
(PLOS, 2015) Verma, Priyanka; Goyal, Richa; Chahota, R.K.; Sharma, Tilak R.; Abdin, M. Z.; Bhatia, Sabhyata
Seed weight and seed size both are quantitative traits and have been considered as important components of grain yield, thus identification of quantitative trait loci (QTL) for seed traits in lentil (Lens culinaris) would be beneficial for the improvement of grain yield. Hence the main objective of this study was to identify QTLs for seed traits using an intraspecific mapping population derived from a cross between L. culinaris cv. Precoz (seed weight-5.1g, seed size-5.7mm) and L. culinaris cv. L830 (seed weight-2.2g, seed size-4mm) comprising 126 F8-RILs. For this, two microsatellite genomic libraries enriched for (GA/CT) and (GAA/CTT) motif were constructed which resulted in the development of 501 new genomic SSR markers. Six hundred forty seven SSR markers (including 146 previously published) were screened for parental polymorphism and 219 (33.8%) were found to be polymorphic among the parents. Of these 216 were mapped on seven linkage groups at LOD4.0 spanning 1183.7cM with an average marker density of 5.48cM. Phenotypic data from the RILs was used to identify QTLs for the seed weight and seed size traits by single marker analysis (SMA) followed by composite interval mapping (CIM) which resulted in one QTL each for the 2 traits (qSW and qSS) that were co-localized on LG4 and explained 48.4% and 27.5% of phenotypic variance respectively. The current study would serve as a strong foundation for further validation and fine mapping for utilization in lentil breeding programs.
Development of an expressed gene catalogue and molecular markers from the de novo assembly of short sequence reads of the lentil (Lens culinaris Medik.) transcriptome
(John Wiley & Sons Ltd, 2013) Verma, Priyanka; Shah, Niraj; Bhatia, Sabhyata
Genomic resources such as ESTs, molecular markers and linkage maps are essential for crop improvement. However, these resources are still limited in important legumes such as lentil (Lens culinaris Medik.), which is valued world wide as a rich source of dietary protein. In this study, the de novo transcriptome assembly of 119,855,798 short reads, generated by Illumina paired-end sequencing, was performed using various assembly programs. This resulted in 42,196 nonredundant high-quality transcripts of average length 810 bases, N50 value of 1,432 and an average expression per transcript of 26.21 rpkm reads per kilobase per million(RPKM). Similarity search with the unigenes and protein sequences of other plants resulted in maximum similarity with soybean. A total of 20,009 nonredundant transcripts showed similarity with the UniProtKB database and of these, 18,064 transcripts were grouped into three main GO categories, that is, biological process (15,126), molecular function (15,505) and cellular component (9,434). Annotated transcripts were mapped to 289 predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 8,893 transcripts were classified into 24 functional categories based on Cluster of Orthologous Groups (COG) of proteins. Mining the data set for the presence of SSRs resulted in 8,722 SSRs with a frequency occurrence of one SSR per 3.92 kb. From these, 5,673 SSR primer pairs were designed, and a subset of these were utilized for diversity analysis. This study, which provides a large data set of annotated transcripts and gene-based SSR markers, would serve as a foundation for various applications in lentil breeding and genetics.
Development, characterization and cross-species transferability of genomic SSR markers in berseem (Trifolium alexandrinum L.), an important multi-cut annual forage legume
(Springer, 2015) Verma, Priyanka; Chandra, Amaresh; Roy, Ajoy Kumar; Malaviya, Devendra Ram; Kaushal, Pankaj; Pandey, Dinesh; Bhatia, Sabhyata
Egyptian clover (Trifolium alexandrinum), a multi-cut forage legume, is widely grown as an annual feed crop. Genetic improvement in this legume is largely hampered due to limited availability of genomic resources. Hence, a genomic library enriched for GA/CT motif was constructed to develop SSR primers. As a result, 667 SSR primer pairs were developed and 111 were validated in T. alexandrinum cv. Wardan s-99-1. Among these, 45 primer pairs were used for the analysis of genetic diversity among 86 Trifolium accessions, resulting in 220 alleles with an average of 4.88 alleles per locus. Polymorphic information content for these markers ranged from 0.040 to 0.819 with an average of 0.445. The observed and expected heterozygosity for individual loci ranged from 0.39 to 0.89 and 0.368 to 0.80 with an average of 0.675 and 0.659, respectively. The markers exhibited varied levels of cross-species transferability ranging from 93.33 % across T. resupinatum to 40.0 % across T. balansae. Phylogenetic relationships were analyzed using the unweighted pair group method with arithmetic averages (UPGMA)-based dendrogram which was able to establish the uniqueness of each genotype and grouped them into two major clusters. To the best of our knowledge, the SSR markers reported here are among the first to be reported in this important yet neglected forage legume. They were assessed to be highly efficient and polymorphic and found to be useful for distinguishing the closely related genotypes of Trifolium. This large resource of SSR markers would therefore facilitate new avenues for T. alexandrinum genomics.
Expanding the repertoire of microsatellite markers for polymorphism studies in Indian accessions of mung bean (Vigna radiata L. Wilczek)
(Springer, 2014) Shrivastava, Divya; Verma, Priyanka; Bhatia, Sabhyata
Limited availability of validated, polymorphic microsatellite markers in mung bean (Vigna radiata), an important food legume of India, has been a major hurdle towards its improvement and higher yield. The present study was undertaken in order to develop a new set of microsatellite markers and utilize them for the analysis of genetic diversity within mung bean accessions from India. A GA/CT enriched library was constructed from V. radiata which resulted in 1,250 putative recombinant clones of which 850 were sequenced. SSR motifs were identified and their flanking sequences were utilized to design 328 SSR primer pairs. Of these, 48 SSR markers were employed for assessing genetic diversity among 76 mung bean accessions from various geographical locations in India. Two hundred and thirty four alleles with an average of 4.85 alleles per locus were detected at 48 loci. The polymorphic information content (PIC) per locus varied from 0.1 to 0.88 (average: 0.49 per locus). The observed and expected heterozygosities ranged from 0.40 to 0.95 and 0.40 to 0.81 respectively. Based on Jaccard's similarity matrix, a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA) analysis which revealed that one accession from Bundi, Rajasthan was clustered out separately while remaining accessions were grouped into two major clusters. The markers generated in this study will help in expanding the repertoire of the available SSR markers thereby facilitating analysis of genetic diversity, molecular mapping and ultimately broadening the scope for genetic improvement of this legume.
Exploring genetic variability within lentil (Lens culinaris Medik.) and across related legumes using a newly developed set of microsatellite markers
(Springer, 2014) Verma, Priyanka; Sharma, Tilak R.; Srivastava, Prem S.; Abdin, M. Z.; Bhatia, Sabhyata
Lentil (Lens culinaris Medik.) is an economically important grain legume, yet the genetic and genomic resources remain largely uncharacterized and unexploited in this crop. Microsatellites have become markers of choice for crop improvement applications. Hence, simple sequence repeat (SSR) markers were developed for lentil through the construction of genomic library enriched for GA/CT motifs. As a result 122 functional SSR primer pairs were developed from 151 microsatellite loci and validated in L. culinaris cv. Precoz. Thirty three SSR markers were utilized for the analysis of genetic relationships between cultivated and wild species of Lens and related legumes. A total of 123 alleles were amplified at 33 loci ranging from 2-5 alleles with an average of 3.73 alleles per locus. Polymorphic information content (PIC) for all the loci ranged from 0.13 to 0.99 with an average of 0.66 per locus. Varied levels of cross genera transferability were obtained ranging from 69.70 % across Pisum sativum to 12.12 % across Vigna radiata. The UPGMA based dendrogram was able to establish the uniqueness of each genotype and grouped them into two major clusters clearly resolving the genetic relationships within lentil and related species. The new set of SSR markers reported here were efficient and highly polymorphic and would add to the existing repertoire of lentil SSR markers to be utilized in molecular breeding. Moreover, the improved knowledge about intra- and inter-specific genetic relationships would facilitate germplasm utilization for lentil improvement.