Browsing by Author "Rajneesh Paliwal"

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Genetic diversity and population structure analyses using hypervariable microsatellite markers in foxtail millets (Setaria species): Future smart nutri-cereal crop
(Elsevier B.V., 2025) Mula Pratapa Reddy; Ved Prakash Rai; Chagam Venkata Chandra Mohan Reddy; Reetesh Kumar; Rajneesh Paliwal; B. Sinha
Knowledge of genetic diversity in germplasm resources is a prerequisite for crop improvement and successful breeding programs. Foxtail millet (Setaria species), a staple food in certain regions, stands out for its rich content of carbohydrates, proteins, dietary fiber, and essential minerals, contributing to a well-balanced diet. The genetic diversity and population structure of a foxtail millet collection consisting of 107 accessions were measured using 31 class I hypervariable SSR markers (>24 bp). 106 polymorphic alleles were detected, ranging from 2 to 8 alleles per locus, across the entire collection with an average of 3.42 alleles per locus. The average polymorphism information content (PIC), gene diversity (GD) and major allelic frequency (MAF) were 0.49, 0.56 and 0.53, respectively. Unweighted neighbor-joining based cluster analysis classified all the genotypes into four distinct major clusters I, II, III and IV, with 25, 40, 21 and 21 genotypes, respectively. Pair-wise estimates of dissimilarity values ranged from 0.094 to 0.931, with a mean of 0.719. The population structure analysis categorized the entries into four sub-populations, namely SP1, SP2, SP3 and SP4, which have 44, 26, 22, and 15 accessions, respectively. The standardized population distance (Fst) within the populations ranged from SP1 (0.604) to SP4 (0.207) with an average Fst of 0.384. The present study identified eight genotypes based on their genetic distance and favorable phenotypic traits for potential use in future breeding programs. These genotypes include four accessions of Setaria italica (ISe 1387, ISe 1234, ISe 1286, ISe 375), one accession of Setaria viridis (GS 40), one accession of Setaria faberi (SIA 2745), and two landraces (SC 13685 and SC 13653). The genetic insights presented in this study are valuable for the utilization of foxtail millet germplasm in future breeding endeavours. © 2024 SAAB
Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers
(2013) Ved Prakash Rai; Rajesh Kumar; Sanjay Kumar; Ashutosh Rai; Sanjeet Kumar; Major Singh; Sheo Pratap Singh; Awadesh Bahadur Rai; Rajneesh Paliwal
A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2-5). The average polymorphic information content (PIC) was 0.69 (range, 0.29-0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44-0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin. © 2013 Prof. H.S. Srivastava Foundation for Science and Society.
Identification of QTLs for stay green trait in wheat (Triticum aestivum L.) in the 'Chirya 3' × 'Sonalika' population
(2010) Uttam Kumar; Arun K. Joshi; Maya Kumari; Rajneesh Paliwal; Sundeep Kumar; Marion S. Röder
Stay green or delayed senescence is considered to play a crucial role in grain development in wheat when assimilates are limited. We identified three QTLs for stay green on the chromosomes 1AS, 3BS and 7DS using a recombinant inbred (RI) population developed by making crosses between the stay green parent 'Chirya 3' and non-stay green 'Sonalika'. The RI lines were evaluated in natural field conditions for 2 years in replicated trial. The QTL on chromosome 1A was identified in both the years, while the QTLs on 3BS and 7DS were identified only in 1st and 2nd year, respectively. The QTLs explained up to 38.7% of phenotypic variation in a final simultaneous fit. The alleles for higher stay green values derived from the stay green parent 'Chirya 3'. The QTLs were named as QSg.bhu-1A, QSg.bhu-3B and QSg.bhu-7D. The QTL QSg.bhu-3B and QSg.bhu-7D were placed in the 3BS9-0.57-0.78 and 7DS5-0.36-0.61 deletion bins, respectively. © 2010 Springer Science+Business Media B.V.
QTL mapping for important horticultural traits in pepper (Capsicum annuum L.)
(Springer India, 2015) Neeraj Dwivedi; Rajesh Kumar; Rajneesh Paliwal; Uttam Kumar; Sanjeet Kumar; Major Singh; Rakesh Kumar Singh
Quantitative trait loci (QTLs) for plant height (PHT) and other yield-related traits including number of fruits per plant (NFP), ten fruits weight (TFW), fruit length (FL), fruit width (FW), total fruit weight (ToFW) and pericarp thickness (PT) were mapped in intraspecific advanced recombinant inbred line (RIL) populations of pepper. The RILs were evaluated for 2 years (F8 and F9) for plant height and seven other yield-related traits. Three types of molecular markers; simple sequence repeat (SSR), sequenced characterized amplified region (SCAR) and random amplified polymorphic DNA (RAPD)—were used to generate linkage maps. A total of 10 QTLs for yield-related traits were mapped on four linkage groups (LG). QTLs for plant height were mapped on LG5. The phenotypic contribution of these QTLs ranged from 8 % to 51 % in mean over environments. Out of 10 QTLs detected, nine were stable in both environments except the QTL for fruit length (Qfl.iivr.3.4) on LG3. The five QTLs; Qfw.iivr-2.1, Qtfw.iivr-2.1, Qtofw.iivr-2.1, Qnfp.iivr-2.1 and Qpt.iivr-2.1 were on the same marker interval on LG2 and one QTL, Qtofw.iivr-3.1 were tightly linked on LG3, which suggests that these genomic regions play an important role in enhancing pepper production. The genomic regions of all stable QTLs identified may serve as potential target regions for fine mapping and development of molecular markers for manipulation of yield and morphological traits in pepper. © 2013, Society for Plant Biochemistry and Biotechnology.
QTL mapping for some grain traits in bread wheat (Triticum aestivum L.)
(Springer, 2018) Supriya Kumari; Vandana Jaiswal; Vinod Kumar Mishra; Rajneesh Paliwal; Harindra Singh Balyan; Pushpendra Kumar Gupta
Grain traits are important agronomic attributes with the market value as well as milling yield of bread wheat. In the present study, quantitative trait loci (QTL) regulating grain traits in wheat were identified. Data for grain area size (GAS), grain width (GWid), factor form density (FFD), grain length-width ratio (GLWR), thousand grain weight (TGW), grain perimeter length (GPL) and grain length (GL) were recorded on a recombinant inbred line derived from the cross of NW1014 × HUW468 at Meerut and Varanasi locations. A linkage map of 55 simple sequence repeat markers for 8 wheat chromosomes was used for QTL analysis by Composite interval mapping. Eighteen QTLs distributed on 8 chromosomes were identified for seven grain traits. Of these, five QTLs for GLWR were found on chromosomes 1A, 6A, 2B, and 7B, three QTLs for GPL were located on chromosomes 4A, 5A and 7B and three QTLs for GAS were mapped on 5D and 7D. Two QTLs were identified on chromosomes 4A and 5A for GL and two QTLs for GWid were identified on chromosomes 7D and 6A. Similarly, two QTLs for FFD were found on chromosomes 1A and 5D. A solitary QTL for TGW was identified on chromosome 2B. For several traits, QTLs were also co-localized on chromosomes 2B, 4A, 5A, 6A, 5D, 7B and 7D. The QTLs detected in the present study may be validated for specific crosses and then used for marker-assisted selection to improve grain quality in bread wheat. © 2018, Prof. H.S. Srivastava Foundation for Science and Society.
QTL mapping of terminal heat tolerance in hexaploid wheat (T. aestivum L.)
(Springer Verlag, 2012) Rajneesh Paliwal; Marion S. Röder; Uttam Kumar; J.P. Srivastava; Arun Kumar Joshi
High temperature (>30 °C) at the time of grain filling is one of the major causes of yield reduction in wheat in many parts of the world, especially in tropical countries. To identify quantitative trait loci (QTL) for heat tolerance under terminal heat stress, a set of 148 recombinant inbred lines was developed by crossing a heat-tolerant hexaploid wheat (Triticum aestivum L.) cultivar (NW1014) and a heat-susceptible (HUW468) cultivar. The F5, F6, and F7 generations were evaluated in two different sowing dates under field conditions for 2 years. Using the trait values from controlled and stressed trials, four different traits (1) heat susceptibility index (HSI) of thousand grain weight (HSITGW); (2) HSI of grain fill duration (HSIGFD); (3) HSI of grain yield (HSIYLD); and (4) canopy temperature depression (CTD) were used to determine heat tolerance. Days to maturity was also investigated. A linkage map comprising 160 simple sequence repeat markers was prepared covering the whole genome of wheat. Using composite interval mapping, significant genomic regions on 2B, 7B and 7D were found to be associated with heat tolerance. Of these, two (2B and 7B) were co-localized QTL and explained more than 15 % phenotypic variation for HSITGW, HSIGFD and CTD. In pooled analysis over three trials, QTL explained phenotypic variation ranging from 9. 78 to 20. 34 %. No QTL × trial interaction was detected for the identified QTL. The three major QTL obtained can be used in marker-assisted selection for heat stress in wheat. © 2012 Springer-Verlag.