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1. CLAVATA signaling pathway genes modulating flowering time and flower number in chickpea

Author:
Tripathi, Shailesh,   et al.   ; Basu, Udita; Narnoliya, Laxmi; Srivastava, Rishi; Sharma, Akash; Bajaj, Deepak; Daware, Anurag; Thakro, Virevol; Malik, Naveen; Upadhyaya, Hari D.; Hegde, V. S.; Tyagi, Akhilesh K.; Parida, Swarup K.;     Show all 13 Authors
Source:
Theoretical and applied genetics 2019 v.132 no.7 pp. 2017-2038
ISSN:
0040-5752
Subject:
agronomic traits; alleles; apical meristems; chickpeas; crops; cultivars; flowering date; flowers; genomics; haplotypes; introgression; loci; messenger RNA; molecular cloning; phylogeny; quantitative trait loci; seed yield; signal transduction; single nucleotide polymorphism
Abstract:
... KEY MESSAGE: A combinatorial genomic strategy delineated functionally relevant natural allele of a CLAVATA gene and its marker (haplotype)-assisted introgression led to development of the early-flowering chickpea cultivars with high flower number and enhanced yield/productivity. Unraveling the genetic components involved in CLAVATA (CLV) signaling is crucial for modulating important shoot apical m ...
DOI:
10.1007/s00122-019-03335-y

2. Transcriptional signatures modulating shoot apical meristem morphometric and plant architectural traits enhance yield and productivity in chickpea

Author:
Tripathi, Shailesh,   et al.   ; Narnoliya, Laxmi; Basu, Udita; Bajaj, Deepak; Malik, Naveen; Thakro, Virevol; Daware, Anurag; Sharma, Akash; Hegde, Venkatraman S.; Upadhyaya, Hari D.; Singh, Ashok K.; Tyagi, Akhilesh K.; Parida, Swarup K.;     Show all 13 Authors
Source:
Theplant journal 2019 v.98 no.5 pp. 864-883
ISSN:
0960-7412
Subject:
agronomic traits; alleles; apical meristems; binding sites; chickpeas; crops; cultivars; farmers; food security; gene expression regulation; genetic improvement; genome-wide association study; genomics; haplotypes; introgression; isogenic lines; land use; messenger RNA; molecular cloning; morphometry; phenotype; plant density; plant height; planting density; population growth; quantitative trait loci; stem cells; transcription (genetics); transcription factors
Abstract:
... Plant height (PH) and plant width (PW), two of the major plant architectural traits determining the yield and productivity of a crop, are defined by diverse morphometric characteristics of the shoot apical meristem (SAM). The identification of potential molecular tags from a single gene that simultaneously modulates these plant/SAM architectural traits is therefore prerequisite to achieve enhanced ...
DOI:
10.1111/tpj.14284

3. Genetic dissection of photosynthetic efficiency traits for enhancing seed yield in chickpea

Author:
Tripathi, Shailesh,   et al.   ; Basu, Udita; Bajaj, Deepak; Sharma, Akash; Malik, Naveen; Daware, Anurag; Narnoliya, Laxmi; Thakro, Virevol; Upadhyaya, Hari D.; Kumar, Rajendra; Bharadwaj, Chellapilla; Tyagi, Akhilesh K.; Parida, Swarup K.;     Show all 13 Authors
Source:
Plant, cell and environment 2019 v.42 no.1 pp. 158-173
ISSN:
0140-7791
Subject:
alleles; chickpeas; chromosome mapping; cultivars; gene expression regulation; genome-wide association study; genomics; germplasm; haplotypes; homozygosity; leaves; loci; marker-assisted selection; photosynthesis; protein-protein interactions; quantitative trait loci; seed yield; single nucleotide polymorphism
Abstract:
... Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics‐assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene‐based association mapping, genome‐wide association study, quantitative trait loci (QTL) mapping, and expression profiling. Th ...
DOI:
10.1111/pce.13319

4. Assessment of background gamma radiation levels using airborne gamma ray spectrometer data over uranium deposits, Cuddapah Basin, India – A comparative study of dose rates estimated by AGRS and PGRS

Author:
Tripathi, Shailesh,   et al.   ; Srinivas, D.; Ramesh Babu, V.; Patra, I.; Ramayya, M.S.; Chaturvedi, A.K.;     Show all 6 Authors
Source:
Journal of environmental radioactivity 2017 v.167 pp. 1-12
ISSN:
0265-931X
Subject:
United Nations; air; basins; data collection; gamma radiation; governance; milling; minerals; mining; potassium; radioactivity; spectrometers; surveys; thorium; uranium; India
Abstract:
... The Atomic Minerals Directorate for Exploration and Research (AMD) has conducted high-resolution airborne gamma ray spectrometer (AGRS), magnetometer and time domain electromagnetic (TDEM) surveys for uranium exploration, along the northern margins of Cuddapah Basin. The survey area includes well known uranium deposits such as Lambapur-Peddagattu, Chitrial and Koppunuru. The AGRS data collected fo ...
DOI:
10.1016/j.jenvrad.2016.11.027

5. Bromodomain and extra-terminal (BET) family proteins: New therapeutic targets in major diseases

Author:
Tripathi, Shailesh,   et al.   ; Padmanabhan, Balasundaram; Mathur, Shruti; Manjula, Ramu;     Show all 4 Authors
Source:
Journal of biosciences 2016 v.41 no.2 pp. 295-311
ISSN:
0250-5991
Subject:
chromatin; gene expression; histones; inflammation; neoplasms; nervous system diseases; obesity; promoter regions; protein synthesis
Abstract:
... The bromodomains and extra-terminal domain (BET) family proteins recognize acetylated chromatin through their bromodomains (BDs) and help in regulating gene expression. BDs are chromatin ‘readers’: by interacting with acetylated lysines on the histone tails, they recruit chromatin-regulating proteins on the promoter region to regulate gene expression and repression. Extensive efforts have been emp ...
DOI:
10.1007/s12038-016-9600-6

6. Organic manures a convincing source for quality production of Japanese mint (Mentha arvensis L.)

Author:
Tripathi, Shailesh,   et al.   ; Bajeli, Jyoti; Kumar, Ajit; Tripathi, Arunima; Upadhyay, R.K.;     Show all 5 Authors
Source:
Industrial crops and products 2016 v.83 pp. 603-606
ISSN:
0926-6690
Subject:
Mentha arvensis; agricultural colleges; forage; mineral fertilizers; mint; oils; pH; poultry manure; sandy loam soils; soil fertility; soil quality; vegetative growth; vermicomposts; India; United States
Abstract:
... Indiscriminate use of inorganic fertilizers is deleterious to soil health. Application of organic manures helps to maintain soil microbial population, soil fertility as well as enhance the oil quality of Japanese mint. Keeping in view, an experiment was conducted at G.B. Pant University of Agriculture and Technology, Pantnagar, district U.S. Nagar (Uttarakhand), India during 2013–2014 to study the ...
DOI:
10.1016/j.indcrop.2015.12.064

7. Genetic dissection of plant growth habit in chickpea

Author:
Tripathi, Shailesh,   et al.   ; Upadhyaya, Hari D.; Bajaj, Deepak; Srivastava, Rishi; Daware, Anurag; Basu, Udita; Bharadwaj, Chellapilla; Tyagi, Akhilesh K.; Parida, Swarup K.;     Show all 9 Authors
Source:
Functional & integrative genomics 2017 v.17 no.6 pp. 711-723
ISSN:
1438-793X
Subject:
Cicer arietinum; alleles; artificial selection; chickpeas; chromosome mapping; crops; cultivars; domestication; gene pool; genetic background; genetic improvement; genome-wide association study; genomics; genotyping by sequencing; germplasm; growth habit; homozygosity; inbred lines; loci; phenotypic variation; plant architecture; regulator genes; selection pressure; single nucleotide polymorphism; transcription (genetics); transcription factors
Abstract:
... A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and ...
DOI:
10.1007/s10142-017-0566-8

8. samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

Author:
Tripathi, Shailesh,   et al.   ; Stupnikov, Alexey; de Matos Simoes, Ricardo; McArt, Darragh; Salto-Tellez, Manuel; Glazko, Galina; Dehmer, Matthias; Emmert-Streib, Frank;     Show all 8 Authors
Source:
Bioinformatics 2016 v.32 no.21 pp. 3345-3347
ISSN:
1460-2059
Subject:
bioinformatics; computer software; cost effectiveness; experimental design; gene expression regulation; genes; sequence analysis
Abstract:
... Motivation: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (i) a cost efficient and (ii) an optimal experimental design leading to a comprom ...
DOI:
10.1093/bioinformatics/btw475

9. Allelic relationships of flowering time genes in chickpea

Author:
Tripathi, Shailesh,   et al.   ; Gaur, Pooran M.; Samineni, Srinivasan; Varshney, Rajeev K.; Gowda, C. L. Laxmipathi;     Show all 5 Authors
Source:
Euphytica 2015 v.203 no.2 pp. 295-308
ISSN:
0014-2336
Subject:
Cicer arietinum; chickpeas; correlation; crossing; early development; flowering; genes; grain yield; parents; pedigree; phenology; plant breeding; pods; seed yield; seeds; yield components
Abstract:
... Flowering time and crop duration are the most important traits for adaptation of chickpea (Cicer arietinum L.) to different agro-climatic conditions. Early flowering and early maturity enhance adaptation of chickpea to short season environments. This study was conducted to establish allelic relationships of the early flowering genes of ICC 16641, ICC 16644 and ICCV 96029 with three known early flo ...
DOI:
10.1007/s10681-014-1261-7

10. Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea

Author:
Tripathi, Shailesh,   et al.   ; Srivastava, Rishi; Bajaj, Deepak; Sayal, Yogesh K.; Meher, Prabina K.; Upadhyaya, Hari D.; Kumar, Rajendra; Bharadwaj, Chellapilla; Rao, Atmakuri R.; Parida, Swarup K.;     Show all 10 Authors
Source:
Plant science 2016 v.252 pp. 374-387
ISSN:
0168-9452
Subject:
phylogeny; genes; Cicer arietinum; genetic markers; quantitative trait loci; genotyping; yield components; gene expression regulation; databases; transcription factors; seeds; chromosomes; genetic improvement; transcription (genetics); chickpeas; chromosome mapping; stress tolerance; cost effectiveness; agronomic traits; agarose; genetic variation
Abstract:
... The discovery and large-scale genotyping of informative gene-based markers is essential for rapid delineation of genes/QTLs governing stress tolerance and yield component traits in order to drive genetic enhancement in chickpea. A genome-wide 119169 and 110491 ISM (intron-spanning markers) from 23129 desi and 20386 kabuli protein-coding genes and 7454 in silico InDel (insertion-deletion) (1–45-bp) ...
DOI:
10.1016/j.plantsci.2016.08.013

11. A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea

Author:
Tripathi, Shailesh,   et al.   ; Upadhyaya, Hari D.; Bajaj, Deepak; Das, Shouvik; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Gowda, C. L. L.; Sharma, Shivali; Tyagi, Akhilesh K.; Parida, Swarup K.;     Show all 11 Authors
Source:
Plant molecular biology 2015 v.89 no.4-5 pp. 403-420
ISSN:
0167-4412
Subject:
Arabidopsis; alleles; binding proteins; chickpeas; chromosome mapping; domestication; flowering; gene expression regulation; genetic improvement; genome-wide association study; genotyping; haplotypes; loci; quantitative trait loci; single nucleotide polymorphism
Abstract:
... A combinatorial approach of candidate gene-based association analysis and genome-wide association study (GWAS) integrated with QTL mapping, differential gene expression profiling and molecular haplotyping was deployed in the present study for quantitative dissection of complex flowering time trait in chickpea. Candidate gene-based association mapping in a flowering time association panel (92 diver ...
DOI:
10.1007/s11103-015-0377-z

12. An efficient and cost-effective approach for genic microsatellite marker-based large-scale trait association mapping: identification of candidate genes for seed weight in chickpea

Author:
Tripathi, Shailesh,   et al.   ; Kujur, Alice; Bajaj, Deepak; Saxena, Maneesha S.; Upadhyaya, Hari D.; Gowda, C. L. L.; Singh, Sube; Tyagi, Akhilesh K.; Jain, Mukesh; Parida, Swarup K.;     Show all 10 Authors
Source:
Molecular breeding 2014 v.34 no.1 pp. 241-265
ISSN:
1380-3743
Subject:
chickpeas; chromosome mapping; gene expression regulation; gene frequency; genes; genetic polymorphism; genotype; genotyping; linkage disequilibrium; microsatellite repeats; phenotypic variation; quantitative trait loci; quantitative traits; screening; transcription factors
Abstract:
... The large-scale validation and high-throughput genotyping of numerous informative genic microsatellite markers are required for association mapping to identify candidate genes for complex quantitative traits in chickpea. However, the screening and genotyping of such informative markers in individual genotypes/whole association panels for trait association mapping involves massive costs in terms of ...
DOI:
10.1007/s11032-014-0033-3

13. Genetic variability and interrelationships of phenological, physicochemical and cooking quality traits in chickpea

Author:
Tripathi, Shailesh,   et al.   ; Sridhar, Vindla; Jukanti, Aravind K.; Suresh, Kamatam; Rao, B. V.; Gowda, C. L. L.; Gaur, Pooran M.;     Show all 7 Authors
Source:
Plant genetic resources 2012 v.10 no.3 pp. 194-201
ISSN:
1479-263X
Subject:
Cicer arietinum; chickpeas; cooking; cooking quality; cultivars; flowering; genetic improvement; genetic variation; genotype; heritability; phenology; physicochemical properties; pods; seed yield; seeds
Abstract:
... Eighty-six chickpea (Cicer arietinum L.) genotypes, including 44 Kabuli type and 42 Desi type, were evaluated for their phenological, physicochemical and cooking quality traits. There were significant differences among the genotypes for days to 50% flowering (34–81 d), days to maturity (85–122 d), number of pods per plant (13–66), number of seeds per plant (15–85), 100-seed weight (10.5–58.6 g), s ...
DOI:
10.1017/S1479262112000251

14. Genomics-assisted breeding for drought tolerance in chickpea

Author:
Tripathi, Shailesh,   et al.   ; Thudi, Mahendar; Gaur, Pooran M.; Krishnamurthy, Lakshmanan; Mir, Reyazul R.; Kudapa, Himabindu; Fikre, Asnake; Kimurto, Paul; Soren, Khela R.; Mulwa, Richard; Bharadwaj, Chellapilla; Datta, Subhojit; Chaturvedi, Sushil K.; Varshney, Rajeev K.;     Show all 14 Authors
Source:
Functional plant biology 2014 v.41 no.11 pp. 1178-1190
ISSN:
1445-4408
Subject:
Cicer arietinum; backcrossing; chickpeas; chromosome mapping; clones; drought; drought tolerance; genetic background; genome; genomics; genotyping; introgression; marker-assisted selection; microsatellite repeats; quantitative trait loci; recurrent selection; single nucleotide polymorphism; stress tolerance; transcriptome
Abstract:
... Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomics-assisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73Mb of sequence data were assembled, capturing of 73.8% of the geno ...
DOI:
10.1071/FP13318

15. Large Genetic Variability in Chickpea for Tolerance to Herbicides Imazethapyr and Metribuzin

Author:
Tripathi, Shailesh,   et al.   ; Gaur, Pooran M.; Jukanti, Aravind K.; Samineni, Srinivasan; Chaturvedi, Sushil K.; Singh, Sarvjeet; Singh, Inderjit; Singh, Guriqbal; Das, Tapas K.; Aski, Muraleedhar; Mishra, Neelu; Nadarajan, Nagasamy; Gowda, C. L. Laxmipathi;     Show all 13 Authors
Source:
Agronomy 2013 v.3 no.3 pp. 524-536
ISSN:
2073-4395
Subject:
Cicer arietinum; amino acids; breeding lines; chickpeas; cultivars; genetic variation; genotype; herbicide resistance; imazethapyr; mechanism of action; metribuzin; plant breeding; screening; weed control
Abstract:
... Chickpea (Cicer arietinum L.) is known to be sensitive to many herbicides and, therefore, choices for using post-emergence herbicides for weed control are limited. The present study was aimed at identifying sources of tolerance to two herbicides with different modes of action (imazethapyr—amino acid synthesis inhibitor; and metribuzin—photosynthesis inhibitor) for use in breeding herbicide toleran ...
DOI:
10.3390/agronomy3030524

16. Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.).

Author:
Tripathi, Shailesh,   et al.   ; Varshney, Rajeev K.; Thudi, Mahendar; Nayak, Spurthi N.; Gaur, Pooran M.; Kashiwagi, Junichi; Krishnamurthy, Lakshmanan; Jaganathan, Deepa; Koppolu, Jahnavi; Bohra, Abhishek; Rathore, Abhishek; Jukanti, Aravind K.; Jayalakshmi, Veera; Vemula, Anilkumar; Singh, S. J.; Yasin, Mohammad; Sheshshayee, M. S.; Viswanatha, K. P.;     Show all 18 Authors
Source:
Theoretical and applied genetics 2014 v.127 no.2 pp. 445-462
ISSN:
0040-5752
Subject:
Cicer arietinum; chickpeas; chromosome mapping; crop yield; cultivars; drought; drought tolerance; genomics; introgression; loci; microsatellite repeats; phenotypic variation; quantitative trait loci; semiarid zones; India
Abstract:
... Analysis of phenotypic data for 20 drought tolerance traits in 1-7 seasons at 1-5 locations together with genetic mapping data for two mapping populations provided 9 QTL clusters of which one present on CaLG04 has a high potential to enhance drought tolerance in chickpea improvement. Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in the ...
DOI:
10.1007/s00122-013-2230-6
PubMed:
24326458
PubMed Central:
PMC3910274

17. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics

Author:
Tripathi, Shailesh,   et al.   ; Varshney, Rajeev K.; Mohan, S. Murali; Gaur, Pooran M.; Gangarao, N.V.P.R.; Pandey, Manish K.; Bohra, Abhishek; Sawargaonkar, Shrikant L.; Chitikineni, Annapurna; Kimurto, Paul K.; Janila, Pasupuleti; Saxena, K.B.; Fikre, Asnake; Sharma, Mamta; Rathore, Abhishek; Pratap, Aditya; Datta, Subhojit; Chaturvedi, S.K.; Mallikarjuna, Nalini; Anuradha, G.; Babbar, Anita; Choudhary, Arbind K.; Mhase, M.B.; Bharadwaj, Ch.; Mannur, D.M.; Harer, P.N.; Guo, Baozhu; Liang, Xuanqiang; Nadarajan, N.; Gowda, C.L.L.;     Show all 30 Authors
Source:
Biotechnology Advances 2013 v.31 pp. 1120-1134
ISSN:
0734-9750
Subject:
Ascochyta; Fusarium wilt; Nematoda; backcrossing; blight; chickpeas; crops; cultivars; developing countries; drought tolerance; food security; genetic background; genetic markers; genomics; genotyping; high-throughput nucleotide sequencing; hybrids; introgression; leaf rust; leaf spot; marker-assisted selection; nucleotide sequences; peanuts; pigeon peas; population; quantitative trait loci; recurrent selection; transcriptome; tropics
Abstract:
... Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. ...
DOI:
10.1016/j.biotechadv.2013.01.001