Dutta S.,Indian Agricultural Research Institute |
Dutta S.,Kalyani University |
Kumawat G.,Indian Agricultural Research Institute |
Singh B.P.,Indian Agricultural Research Institute |
And 15 more authors.
BMC Plant Biology | Year: 2011
Background: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping.Results: In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population.Conclusion: We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea. © 2011 Dutta et al; licensee BioMed Central Ltd.
Singh N.K.,Indian Agricultural Research Institute |
Gupta D.K.,Indian Agricultural Research Institute |
Jayaswal P.K.,Indian Agricultural Research Institute |
Mahato A.K.,Indian Agricultural Research Institute |
And 27 more authors.
Journal of Plant Biochemistry and Biotechnology | Year: 2012
Pigeonpea (Cajanus cajan) is an important grain legume of the Indian subcontinent, South-East Asia and East Africa. More than eighty five percent of the world pigeonpea is produced and consumed in India where it is a key crop for food and nutritional security of the people. Here we present the first draft of the genome sequence of a popular pigeonpea variety 'Asha'. The genome was assembled using long sequence reads of 454 GS-FLX sequencing chemistry with mean read lengths of >550 bp and >10-fold genome coverage, resulting in 510,809,477 bp of high quality sequence. Total 47,004 protein coding genes and 12,511 transposable elements related genes were predicted. We identified 1,213 disease resistance/defense response genes and 152 abiotic stress tolerance genes in the pigeonpea genome that make it a hardy crop. In comparison to soybean, pigeonpea has relatively fewer number of genes for lipid biosynthesis and larger number of genes for cellulose synthesis. The sequence contigs were arranged in to 59,681 scaffolds, which were anchored to eleven chromosomes of pigeonpea with 347 genic-SNP markers of an intra-species reference genetic map. Eleven pigeonpea chromosomes showed low but significant synteny with the twenty chromosomes of soybean. The genome sequence was used to identify large number of hypervariable 'Arhar' simple sequence repeat (HASSR) markers, 437 of which were experimentally validated for PCR amplification and high rate of polymorphism among pigeonpea varieties. These markers will be useful for fingerprinting and diversity analysis of pigeonpea germplasm and molecular breeding applications. This is the first plant genome sequence completed entirely through a network of Indian institutions led by the Indian Council of Agricultural Research and provides a valuable resource for the pigeonpea variety improvement. © 2011 Society for Plant Biochemistry and Biotechnology.
Sharma K.L.,Indian Central Research Institute for Dryland Agriculture |
Grace J.K.,Indian Central Research Institute for Dryland Agriculture |
Mishra P.K.,Indian Central Research Institute for Dryland Agriculture |
Venkateswarlu B.,Indian Central Research Institute for Dryland Agriculture |
And 11 more authors.
Communications in Soil Science and Plant Analysis | Year: 2011
Rainfed semi-arid tropical Vertisols of the Indian subcontinent encounter many problems on account of the physical, chemical, and biological soil qualities and consequently have poor crop yields. To ensure sustainable crop production, there is a need to improve and periodically assess the quality of these soils by adopting suitable soil and nutrient-management practices on a long-term basis. Hence, soil quality assessment studies were conducted at the Central Research Institute for Dryland Agriculture, Hyderabad, India, by adopting an ongoing long-term experiment from Akola Centre (Maharashtra) of All-India Coordinated Research Project for Dryland Agriculture (AICRPDA) for the rainfed Vertisol. This long-term experiment was initiated in 1987 with six soil and nutrient management treatments: T1, control; T2, 50 kg nitrogen (N) + 25 kg phosphorus pentoxide (P2O5) ha-1; T3, 25 kg N ha-1 through leuceana; T4, 25 kg N ha-1 through farmyard manure (FYM); T5, 25 kg N + 25 kg P2O5 + 25 kg N ha-1 through FYM; and T6, 25 kg P2O5 ha-1 + 50 kg N ha-1 through leuceana under cotton + greengram intercropping (1:1). Out of the 19 soil quality parameters studied, significant influence of the soil and nutrient-management treatments was observed on almost all the parameters except exchangeable calcium (Ca), available iron (Fe), labile carbon (LC), and bulk density (BD). A standard methodology using principal component analysis (PCA) and linear scoring technique (LST) was adopted to identify the key indicators and for computation of soil quality indices. The various key soil quality indicators identified for these Vertisols under cotton + green gram system were pH, electrical conductivity (EC), organic carbon (OC), available K, exchangeable magnesium (Mg), dehydrogenase assay (DHA), and microbial biomass carbon (MBC). The soil quality indices as influenced by different long-term soil and nutrient management treatments varied from 1.46 to 2.10. Among the treatments, the conjunctive use of 25 kg P2O5 ha-1 + 50 kg N ha-1 through leuceana green biomass (T6) maintained significantly higher soil quality index with a value of 2.10 followed by use of 25 kg N +25 kg P2O5 + 25 kg N ha-1 through FYM (T5) (2.01). The order of percent contribution of these identified indicators to soil quality indices was OC (28%) > MBC (25%) > available K (24%) > EC (7%) > pH (6%) = DHA (6%) > exchangeable Mg (4%). Thus, the findings of the present study could be of immense use to the researchers, land managers, farmers, non government organizations (NGOs) and other stakeholders for making periodical assessment of key indicators of soil quality, identifying the best soil and nutrient-management treatments and practices, and planning for improving soil quality to achieve higher productivity goals on a sustainable basis in rainfed semi-arid tropical Vertisol regions. The methodology of the study could also be useful for other rainfed semi-arid tropical Vertisol regions of the world. © Taylor & Francis Group, LLC.
Wakode A.,Panjabrao Deshmukh Krishi Vidyapeeth |
Gangde C.N.,Panjabrao Deshmukh Krishi Vidyapeeth |
Khambalkar V.P.,Panjabrao Deshmukh Krishi Vidyapeeth
AMA, Agricultural Mechanization in Asia, Africa and Latin America | Year: 2013
This study was conducted to determine the influence of various factors on the cotton crop production as yield and output energy. The factors considered were area under crop, irrigation, input energy, hoeing, power sources and FYM application. The influence and relation of these factors were determined for the output energy and the yield of the cotton crop for the small, medium and large farmers. The data were collected from the farmers of the Akola district. Crop yield and output energy were greatly influenced by the power sources, hoeing application and the total input energy. The input-output energy analysis, source-wise energy use and the various energy coefficients of the field operation were determined to identify the energy use in small, medium and large farmers of the studied area. The cost of energy for production of cotton crop was estimated. The cost of energy was more in small farming and minimum in large farming. The economics of the cotton crop showed that the small farmers have benefit-cost ratio more than the larger farmer.
Bhalerao P.D.,Panjabrao Deshmukh Krishi Vidyapeeth |
Gaikwad G.S.,Panjabrao Deshmukh Krishi Vidyapeeth
Indian Journal of Agronomy | Year: 2010
Field experiments were conducted for 3 years at Akola during kharif 2006-07 to 2008-09, to find out the impact of plant geometry and levels of N, P and K fertilization on performance of Bt cotton. From the pooled analysis of 3 years data, it was observed that 90 cm × 45 cm spacing recorded 50.5 and 17.7% higher seed cotton yield than 90 cm x 90 cm and 90 cm × 60 cm spacing, respectively. Wider spacing plants had more boll/plants (23.1) than closer spaced (20.8 bolls/plant). Application of 125% recommended dose of fertilizer/ha was at par with recommended dose of fertilizer (RDF) i.e. 50-25-25 kg N-P-K/ha and significantly higher than 75% RDF. Increase in yield was due to improvement in bolls/plant. There was increasing trend in N, M and R with increasing N, P and K levels. Monetary returns showed increasing trend with decreasing intra row spacing. Consequently spacing of 90cm × 45 cm and recommended dose of fertilizer of non Bt (50-25-25 kg N-P-K/ha) were found suitable for RCH-2 Bt cotton also under rainfed conditions.