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Search Results: 1 - 10 of 192184 matches for " Hari D. Upadhyaya "
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Genetic relationships among seven sections of genus Arachis studied by using SSR markers
Ravi Koppolu, Hari D Upadhyaya, Sangam L Dwivedi, David A Hoisington, Rajeev K Varshney
BMC Plant Biology , 2010, DOI: 10.1186/1471-2229-10-15
Abstract: The average transferability rate of 101 SSR markers tested to section Arachis and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, Arachis pusilla exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (A. duranensis) and the B-genome accession ICG 8206 (A. ipa?nsis) were found most closely related to A. hypogaea.A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of Arachis, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of A. monticola and A. hypogaea as well as on the most probable donor of A and B-genomes of cultivated groundnut.The genus Arachis has its origin in South America where the species of this genus are widespread [1]. This genus includes 80 species, 69 species described by Krapovickas and Gregory [1] and 11 species described by Valls and Simpson [2]. Arachis is divided into 9 sections (Arachis, Erectoides, Heteranthae, Caulorrhizae, Rhizomatosae, Extranervosae, Triseminatae, Procumbentes and Trierectoides) based on morphology, geographic distribution and cross compatibility relationships [1]. Species present in sections Erectoides, Extranervosae and Triseminatae and diploid species of section Rhizomatosae are believed to be basal in their divergence when compared to the species in other sections [3,4].
Mini core germplasm collections for infusing genetic diversity in plant breeding programs
Hari D Upadhyaya*, Devvart Yadav, Naresh Dronavalli, CLL Gowda, and Sube Singh
Electronic Journal of Plant Breeding , 2010,
Abstract: Plant genetic resources are essential components to meet future food security needs of world. Crop germplasm diversitycontributes to developing improved crop cultivars aimed at increasing crop productivity. The large size of germplasmcollections, coupled with unavailability of detailed data and information, has resulted in low use (<1%) of germplasmleading to a narrow genetic base in many crops. The miniaturization of crop collections with almost full representation ofgenetic diversity in the form of mini core (~1% of the entire collection) approach is an effective methodology to enrichand enhance crop improvement programs. The concept and process of developing mini core at The International CropsResearch Institute for the Semi-Arid Tropics (ICRISAT) has been recognized worldwide as an “International PublicGood” (IPG). The mini core provides a means for accessing the larger collections for further exploration and also helps inproper assessment of genetic diversity and population structure and for association mapping and targeted gene mining.Use of mini core approach will lead to greater utilization of diverse germplasm for developing broad-based cultivars,especially in the context of climate change. Many national programs have shown immense interest in evaluating minicore as reflected by the supply of 114 sets of mini core of chickpea, groundnut, pigeonpea, sorghum, pearl millet, foxtailmillet and finger millet to researchers in 14 countries. Scientists have been able to identify new and diverse sources ofvariation for morpho-agronomic, quality, biotic, and abiotic stress resistance traits in various crops. The molecularcharacterization of the mini core will further enhance its use in plant breeding programs.
Exploring Germplasm Diversity to Understand the Domestication Process in Cicer spp. Using SNP and DArT Markers
Manish Roorkiwal, Eric J. von Wettberg, Hari D. Upadhyaya, Emily Warschefsky, Abhishek Rathore, Rajeev K. Varshney
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0102016
Abstract: To estimate genetic diversity within and between 10 interfertile Cicer species (94 genotypes) from the primary, secondary and tertiary gene pool, we analysed 5,257 DArT markers and 651 KASPar SNP markers. Based on successful allele calling in the tertiary gene pool, 2,763 DArT and 624 SNP markers that are polymorphic between genotypes from the gene pools were analyzed further. STRUCTURE analyses were consistent with 3 cultivated populations, representing kabuli, desi and pea-shaped seed types, with substantial admixture among these groups, while two wild populations were observed using DArT markers. AMOVA was used to partition variance among hierarchical sets of landraces and wild species at both the geographical and species level, with 61% of the variation found between species, and 39% within species. Molecular variance among the wild species was high (39%) compared to the variation present in cultivated material (10%). Observed heterozygosity was higher in wild species than the cultivated species for each linkage group. Our results support the Fertile Crescent both as the center of domestication and diversification of chickpea. The collection used in the present study covers all the three regions of historical chickpea cultivation, with the highest diversity in the Fertile Crescent region. Shared alleles between different gene pools suggest the possibility of gene flow among these species or incomplete lineage sorting and could indicate complicated patterns of divergence and fusion of wild chickpea taxa in the past.
Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs
Rachit K. Saxena, Eric von Wettberg, Hari D. Upadhyaya, Vanessa Sanchez, Serah Songok, Kulbhushan Saxena, Paul Kimurto, Rajeev K. Varshney
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0088568
Abstract: Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively.
Abundant Microsatellite Diversity and Oil Content in Wild Arachis Species
Li Huang, Huifang Jiang, Xiaoping Ren, Yuning Chen, Yingjie Xiao, Xinyan Zhao, Mei Tang, Jiaquan Huang, Hari D. Upadhyaya, Boshou Liao
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050002
Abstract: The peanut (Arachis hypogaea) is an important oil crop. Breeding for high oil content is becoming increasingly important. Wild Arachis species have been reported to harbor genes for many valuable traits that may enable the improvement of cultivated Arachis hypogaea, such as resistance to pests and disease. However, only limited information is available on variation in oil content. In the present study, a collection of 72 wild Arachis accessions representing 19 species and 3 cultivated peanut accessions were genotyped using 136 genome-wide SSR markers and phenotyped for oil content over three growing seasons. The wild Arachis accessions showed abundant diversity across the 19 species. A. duranensis exhibited the highest diversity, with a Shannon-Weaver diversity index of 0.35. A total of 129 unique alleles were detected in the species studied. A. rigonii exhibited the largest number of unique alleles (75), indicating that this species is highly differentiated. AMOVA and genetic distance analyses confirmed the genetic differentiation between the wild Arachis species. The majority of SSR alleles were detected exclusively in the wild species and not in A. hypogaea, indicating that directional selection or the hitchhiking effect has played an important role in the domestication of the cultivated peanut. The 75 accessions were grouped into three clusters based on population structure and phylogenic analysis, consistent with their taxonomic sections, species and genome types. A. villosa and A. batizocoi were grouped with A. hypogaea, suggesting the close relationship between these two diploid wild species and the cultivated peanut. Considerable phenotypic variation in oil content was observed among different sections and species. Nine alleles were identified as associated with oil content based on association analysis, of these, three alleles were associated with higher oil content but were absent in the cultivated peanut. The results demonstrated that there is great potential to increase the oil content in A. hypogaea by using the wild Arachis germplasm.
Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.)
Hari D Upadhyaya, Sangam L Dwivedi, Michael Baum, Rajeev K Varshney, Sripada M Udupa, Cholenahalli LL Gowda, David Hoisington, Sube Singh
BMC Plant Biology , 2008, DOI: 10.1186/1471-2229-8-106
Abstract: The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection.The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.Chickpea (Cicer arietinum L.) is the 4th most important grain-legume crop after soybean, bean, and pea, but contributes only 3.1% to the world grain legumes production (based on 2001 to 2006 average production of 266.5 million tons of soybean, beans, peas, chickpea, broad beans, cowpea, lentil, and pigeonpea) http://faostat.fao.org/site/408/DesktopDefault.aspx?PageID=408 webcite, assessed on 27th Jan
Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives
Mulualem T. Kassa, R. Varma Penmetsa, Noelia Carrasquilla-Garcia, Birinchi K. Sarma, Subhojit Datta, Hari D. Upadhyaya, Rajeev K. Varshney, Eric J. B. von Wettberg, Douglas R. Cook
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0039563
Abstract: Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe “domestication bottleneck” during pigeonpea domestication.
Cutting and other forms of derma-abuse in adolescents  [PDF]
Hari D. Maharajh, Rainah Seepersad
Health (Health) , 2010, DOI: 10.4236/health.2010.24055
Abstract: Cutting or self inflicted epidermal damage (derma-abuse) describes a number of blood- letting behaviours among adolescents. Unlike suicidal behaviour, it is associated with low lethality and the absence of suicidal attempts. The purpose of this study is two-fold: Firstly, to present and discuss vignettes of four young adolescents and secondly, to study the dynamics and characteristics of six derma-abusers who have attended Dual Group Therapy (DGT) concurrently with their parents for a six month period. Our findings suggest that patients involved in derma-abuse are generally non-suicidal but engage in comfort cutting for the psychological release of pain, tension reduction and anger management. There is a preponderance of females (80%) with an over-representation of mixed origin and borderline cultural states. In this small group, males amounted to 20% and were more bizarre, gruesome and brutal in their self-abuse. Of the total sample, 10% were of African origin, 60% were of Indian descent and 30% were of mixed ancestry. Psy- chodynamic factors explored in Dual Group Therapy (DGT) are the emphasis on non-suicidal intent, association with tension reduction, reclaiming power and mastery over self and others, life and death instincts, the significance of bloodletting in a socio-cultural context, trans- generational conflicts, dysfunctional family dynamics frequently with parental separation and sexual abuse and early sexual induction.
Ethics in mental Health in resource poor setting: experiences from Nepal
KD Upadhyaya,D Joshi
Journal of Psychiatrists' Association of Nepal , 2011, DOI: 10.3126/jpan.v1i1.9919
Abstract: DOI: http://dx.doi.org/10.3126/jpan.v1i1.9919 Journal of Psychiatrists' Association of Nepal Vol.1(1) 2011: 5-10
Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.)
Abhishek Bohra, Anuja Dubey, Rachit K Saxena, R Varma Penmetsa, KN Poornima, Naresh Kumar, Andrew D Farmer, Gudipati Srivani, Hari D Upadhyaya, Ragini Gothalwal, S Ramesh, Dhiraj Singh, Kulbhushan Saxena, PB Kavi Kishor, Nagendra K Singh, Christopher D Town, Gregory D May, Douglas R Cook, Rajeev K Varshney
BMC Plant Biology , 2011, DOI: 10.1186/1471-2229-11-56
Abstract: A set of 88,860 BAC (bacterial artificial chromosome)-end sequences (BESs) were generated after constructing two BAC libraries by using HindIII (34,560 clones) and BamHI (34,560 clones) restriction enzymes. Clustering based on sequence identity of BESs yielded a set of >52K non-redundant sequences, comprising 35 Mbp or >4% of the pigeonpea genome. These sequences were analyzed to develop annotation lists and subdivide the BESs into genome fractions (e.g., genes, retroelements, transpons and non-annotated sequences). Parallel analysis of BESs for microsatellites or simple sequence repeats (SSRs) identified 18,149 SSRs, from which a set of 6,212 SSRs were selected for further analysis. A total of 3,072 novel SSR primer pairs were synthesized and tested for length polymorphism on a set of 22 parental genotypes of 13 mapping populations segregating for traits of interest. In total, we identified 842 polymorphic SSR markers that will have utility in pigeonpea improvement. Based on these markers, the first SSR-based genetic map comprising of 239 loci was developed for this previously uncharacterized genome. Utility of developed SSR markers was also demonstrated by identifying a set of 42 markers each for two hybrids (ICPH 2671 and ICPH 2438) for genetic purity assessment in commercial hybrid breeding programme.In summary, while BAC libraries and BESs should be useful for genomics studies, BES-SSR markers, and the genetic map should be very useful for linking the genetic map with a future physical map as well as for molecular breeding in pigeonpea.Pigeonpea [Cajanus cajan (L.) Millsp.], also known as tuar or arhar, is an economically important legume crop with an annual production of 3.65 Mt. Cultivation of pigeonpea occurs on ~5 million hectares, primarily in Asia and countries of eastern and southern Africa, and to a lesser extent in countries of Latin America and the Caribbean. As a member of the sub tribe Cajaninae, pigeonpea is contained in an early diverging lineage
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