Hemant Kumar Yadav

EST-derived SSR markers in Jatropha curcas L.: development, characterization, polymorphism, and transferability across the species/genera

A total of 12,080 sequences, including 5,851 transcriptome contigs developed at NBRI and 5,002 singlets and 1,227 contigs assembled from 13,201 expressed sequence tags (ESTs) of Jatropha curcas from National Center for Biotechnology Information database were used to search for simple sequence repeats (SSRs). Seven hundred and two sequences containing 786 SSRs with 93.4% simple and 7.6% compound repeat motifs were identified. Dinucleotide repeats (DNRs) were most abundant, followed by trinucleotide and tetranucleotide repeats. AG/CT was the most common motif (50.0%) followed by AT/AT (38.8%) and AC/GT (10.0%) among the DNRs. Four hundred and six primer pairs were designed out of the 702 SSR-containing sequences. Fifty randomly selected EST-SSR markers were amplified in 25 accessions collected from different geographical regions of India. Twenty-one SSR markers were polymorphic and with allele variation from two to four. Polymorphic information content value ranged between 0.04 and 0.61 with an average of 0.25 ± 0.16, indicating low to moderate level of informativeness within these EST-SSRs. The polymorphic markers showed 57.0% to 95.6% transferability among five species of Jatropha and 47.0% transferability across genera in Ricinus communis. Fifty-one alleles detected by the 21 polymorphic EST-SSRs were used to determine genetic relationships among 25 J. curcas accessions. Genetic similarity coefficient ranged from 0.44 to 0.94. The 25 accessions got grouped to three main clusters, comprising 10, 11, and four accessions. This is the first report of development of EST-SSRs in J. curcas and will be valuable resource for future genetical studies, like construction of linkage maps, diversity analysis, quantitative trait locus/association mapping, and molecular breeding of J. curcas.

Genetic Variability and Interrelationship Among Opium and its Alkaloids in Opium Poppy (Papaver Somniferum L.)

SummaryThe plant species Papaver somniferum L. (opium poppy) is grown commercially in several countries under secure area to produce opium and its major alkaloids i.e. morphine, codeine, thebaine, narcotine and papaverine for pharmaceutical industries. In recent years the global demand for these alkaloids and its derivatives are growing. Seeing the global demand there is urgent need to develop high opium yielding varieties integrated with high specific alkaloids. However, a breeding programme focused on developing improved varieties requires knowledge about the genetic variability for the concern traits. Therefore the present investigation was undertaken to examine phenotypic and genotypic variability, broad sense heritability, genetic advance under selection and interrelationship of traits. A total of 122 accessions were found to be highly variables for all the traits studied. Broad sense heritability ranged from 74.18% (for opium yield/plant) to 99.00% (for papaverine content). Expected genetic advance was varied between 33.91% (for morphine content) and 257.46% (for papaverine content). Genetic correlation analysis revealed that opium yield is negatively correlated with morphine and papaverine content. Among alkaloids codeine, thebaine, narcotine and papaverine showed positive correlation among themselves. The correlations among alklaloids were justified based on the biosynthetic pathway of opium alkaloids.

Development and characterization of genomic and expressed SSRs for levant cotton ( Gossypium herbaceum L.)

Four microsatellite-enriched genomic libraries for CA(15), GA(15), AAG(8) and ATG(8) repeats and transcriptome sequences of five cDNA libraries of Gossypium herbaceum were explored to develop simple sequence repeat (SSR) markers. A total of 428 unique clones from repeat enriched genomic libraries were mined for 584 genomic SSRs (gSSRs). In addition, 99,780 unigenes from transcriptome sequencing were explored for 8,900 SSR containing sequences with 12,471 expressed SSRs. The present study adds 1,970 expressed SSRs and 263 gSSRs to the public domain for the use of genetic studies of cotton. When 150 gSSRs and 50 expressed SSRs were tested on a panel of four species of cotton, 68 gSSRs and 12 expressed SSRs revealed polymorphism. These 200 SSRs were further deployed on 15 genotypes of levant cotton for the genetic diversity assessment. This is the first report on the successful use of repeat enriched genomic library and expressed sequence database for microsatellite markers development in G. herbaceum.

Large‐scale resource development in Gossypium hirsutum L. by 454 sequencing of genic‐enriched libraries from six diverse genotypes

The sequence information has been proved to be an essential genomic resource in case of crop plants for their genetic improvement and better utilization by humans. To dissect the Gossypium hirsutum genome for large-scale development of genomic resources, we adopted hypomethylated restriction-based genomic enrichment strategy to sequence six diverse genotypes. Approximately 5.2-Gb data (more than 18.36 million reads) was generated which, after assembly, represents nearly 1.27-Gb genomic sequences. We predicted a total of 93,363 gene models (21,399 full length) and identified 35,923 gene models which were validated against already sequenced plant genomes. A total of 1,093 transcription factor-encoding genes, 3,135 promoter sequences and 78 miRNA (including 17 newly identified in Gossypium) were predicted. We identified significant no. of molecular markers including 47,093 novel simple sequence repeats and 66,364 novel single nucleotide polymorphisms. In addition, we developed NBRI-Comprehensive Cotton Genomics database, a web resource to provide access of cotton-related genomic resources developed at NBRI. This study contributes considerable amount of genomic resources and suggests a potential role of genic-enriched sequencing in genomic resource development for orphan crop plants.

Genetic divergence in parental genotypes and its relation with heterosis, F1 performance and general combining ability (GCA) in opium poppy (Papaver somniferum L.)

SummaryGenetic divergence in 110 population (20 parents and 90 F1 hybrids) of opium poppy was studied by multivariate analysis. All the entries were grouped in 14 clusters. Out of 20 parents, ten were accumulated in one cluster and rest 10 distributed over seven clusters. Estimates of cluster distance showed that maximum intra-cluster distance was in -cluster IX (25.62) followed by cluster I (22.41), V (22.23) and IV (21.06). The inter cluster distances varied from 16.62 (between cluster XII and XIV) to 195.10 (between cluster IV and IX). The cluster analysis indicated substantial diversity among the parental genotypes, which had the potential to release considerable variation in their crosses. The first four principal components (PCs) with eigen values >1 accounted for 68% of variation among the population. The first and second components could account for 29 and 20% of the total morphological and alkaloidal variations, respectively. The PC1 was closely related to yield and yield related traits. The characters contributing greatest positive weight on PC1 were opium yield, plant height, stem diameter, capsule weight/plant and seed yield/plant. The possibilities of relationship between genetic divergence, F1 performance, heterosis and GCA of parents have been explored.

Genetic combining ability estimates in the F1 and F2 generations for yield, its component traits and alkaloid content in opium poppy (Papaver somniferum L.)

The F1 and F2 generations of a twenty parent fractional diallel cross of opium poppy (P. somniferum L.) were analyzed for combining ability for ten quantitative and five quality (alkaloids) traits. The results indicated significant differences among the parents for combining ability for all the traits. The GCA and SCA components of variances were significant for all the characters. However, the SCA component of variance (δ2s) was predominant indicating the preponderance of non-additive gene effect for all the traits except for leaves/plant and papaverine in F1 hybrids. The average degree of dominance (δ2s/δ2g) was more than unity indicating over dominance and also confirming non-additive mode of gene action. Among the parents IS-16, IS-13 and NBRI-1 for early flowering, BR226 and BR241 for branches/plant, capsule weight/plant, seed yield/plant and husk yield/plant, BR227 for leaves/plant, UO1285 for capsule size and opium yield/plant, NBRI-5 for husk yield/plant, morphine, codeine, and thebaine and ‘Papline’ for plant height and papaverine content were found good general combiners. Parent ND1001 was good combiner for codeine and narcotine content. Inclusion of good general combiners in a multiple crossing program or an intermating population involving all the possible crosses among them subjected to bi-parental mating may be expected to offer maximum promise in breeding for higher opium, seed yield and alkaloid contents.

Diversity analysis in Indian genotypes of linseed (Linum usitatissimum L.) using AFLP markers.

AFLP fingerprinting of 45 Indian genotypes of linseed was carried out to determine the genetic relationship among them. Sixteen primer combinations produced 1142 fragments with 1129 as polymorphic and 13 as monomorphic fragments. Polymorphic fragments varied from 44 (E-ACA/M-CTA) to 94 (E-AGC/M-CAC) with an average of 70.6 fragments per primer combination. The frequency of polymorphism varied from 93.7% to 100% with an average of 98.8% across all the genotypes. The PIC value ranged from 0.19 to 0.31 with an average of 0.23 per primer combination. The primer pair E-AGC/M-CAC showed the maximum PIC value (0.31) followed by E-AGC/M-CAG (0.29), E-AAC/M-CAG (0.26) and E-AGC/M-CTA (0.25). Resolving power (RP) and marker index (MI) varied from 13.73 to 43.50 and 8.81 to 28.91 respectively. The Jaccards similarity coefficient varied from 0.16 to 0.57 with an average of 0.26 ± 0.05. The maximum genetic similarities (57%) were detected between genotypes Him Alsi-1 and Him Alsi-2, followed by Him Alsi-1 and GS41 and GS41 and LC-54. The genotypes R-552, Himani, RKY-14, Meera, Indira Alsi-32 and Suyog were found to be more divergent genotypes. The NJ clustering grouped all the 45 genotypes into three major clusters. In general the genotypes of cluster III had high oil content and those of cluster I had low oil content. At the population level, within population variance was much higher than between populations variance.

Assessment of genetic diversity and population structure in gladiolus (Gladiolus hybridus Hort.) by ISSR markers

ISSR (Inter simple sequence repeat) markers were used to assess the genetic diversity and population structure in 53 indigenous and exotic genotypes of gladiolus (Gladiolus hybridus Hort.). Molecular markers analysis showed PIC ranges from 0.42 (ISSR 861) to 0.99 (ISSR 855, ISSR 856 and ISSR 889) with an average 0.812, marker index ranged from 0.99 (ISSR 889) to 9.26 (ISSR 851) with an average 4.66 and resolving power of the primers ranged from 0.03 (ISSR 889) to 11.58 (ISSR 861) with an average value 3.80. The dendrogram based UPGMA clustering showed that all the 53 genotypes grouped into three main clusters. Nei’s gene diversity (Na) varied from 0.929 to 1.717, effective number of alleles (Ne) varied from 1.262 to 1.369, Shannon’s information index (I) ranged from 0.251 to 0.359 and gene diversity (He) was in the range from 0.167 to 0.229. Population structure analysis revealed three groups in which 32 genotypes were admixture types.

Mediastinal neurenteric cysts in children: A case series

Background: Foregut duplication cysts associated with vertebral anomalies are referred to as neurenteric cyst. About 30 cases have been reported in the literature so far. Posterior mediastinal neurenteric cysts are very rare and a few studies could be found in the literature even after extensive search. Because of rarity we are prompted to present 7 cases of posterior mediastinal neurenteric cysts to further add on to the literature. Study design: All the details of the patients of neurenteric cysts operated in department of paediatric surgery over a period of 2010-15 were taken from patient case files. Results: There were 7 pateints of neurenteric cyst including 3 males and 4 females with age ranged from 4 months to 8 years. Patients presented with recurrent chest infection along with two case having dysphasia also. In 5 cases there were right sided cysts while two had cyst on left side in posterior mediastinum. In 2 cases the cysts were extending to abdomen while one patient had separate ileal duplication cyst. Another case had mediastinal cyst which was communicating with ileum. All the mediastinal cysts were excised through posterior thoracotomy and subsequently confimed on histolpathology. Conclusion: Neurenteric cysts should be considered in the differential diagnosis of mediastinal cysts of paediatric age group. Key words: mediastinal, neurenteric cyst, paediatric.

Primary salivary gland lymphomas:A case series

Background: Primary lymphoma of the salivary gland is not often encountered in routine practice. About 5–10% of Non-Hodgkins lymphomas (NHLs) are found in the salivary gland, most frequently involving parotid gland. Henceforth, it is necessary to understand the distinct clinical presentations and course of primary salivary gland lymphomas as this may help guide the proper diagnosis and management of patients with these tumors. Materials and Methods: We retrospectively reviewed primary NHL diagnosed at our medical institute over a period of 2 years. Results: Five cases of primary salivary gland lymphoma were found, two involving parotid gland while other three affecting submandibular gland. None of the cases had a clinical suspicion of lymphoma. However, they were diagnosed as having NHL B-cell type on histopathology. Conclusion: Since primary salivary gland NHL is an uncommon finding, it is often overlooked as the differential diagnosis. Methods of diagnosing and treating lymphoma are different from those of other benign pathologies of the salivary gland. Therefore, a high index of suspicion is warranted to provide a quick and efficient diagnosis and treatment without subjecting the patient to unnecessary tests and procedures.