An integrated molecular marker map of the chickpea genome was established using 130 recombinant inbred lines from a wide cross between a cultivar resistant to fusarium wilt caused by Fusarium oxysporum Schlecht. emend. Snyd. &. Hans f. sp. ciceri (Padwick) Snyd & Hans, and an accession of Cicer reticulatum (PI 489777), the wild progenitor of chickpea. A total of 354 markers were mapped on the RILs including 118 STMSs, 96 DAFs, 70 AFLPs, 37 ISSRs, 17 RAPDs, eight isozymes, three cDNAs, two SCARs and three loci that confer resistance against different races of fusarium wilt. At a LOD-score of 4.0, 303 markers cover 2077.9 cM in eight large and eight small linkage groups at an average distance of 6.8 cM between markers. Fifty one markers (14.4%) were unlinked. A clustering of markers in central regions of linkage groups was observed. Markers of the same class, except for ISSR and RAPD markers, tended to generate subclusters. Also, genes for resistance to races 4 and 5 of fusarium wilt map to the same linkage group that includes an STMS and a SCAR marker previously shown to be linked to fusarium wilt race 1, indicating a clustering of several fusarium-wilt resistance genes around this locus. Significant deviation from the expected 1 : 1 segregation ratio was observed for 136 markers (38.4%, P<0.05). Segregation was biased towards the wild progenitor in 68% of the cases. Segregation distortion was similar for all marker types except for ISSRs that showed only 28.5% aberrant segregation. The map is the most extended genetic map of chickpea currently available. It may serve as a basis for marker-assisted selection and map-based cloning of fusarium wilt resistance genes and other agronomically important genes in future.

A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum×C. reticulatum cross: localization of resistance genes for fusarium wilt races 4 and 5

A size-selected genomic library comprising 280,000 colonies and representing ≈18% of the chickpea genome, was screened for (GA)n, (GAA)n and (TAA)n microsatellite-containing clones, of which 389 were sequenced. The majority (∼75%) contained perfect repeats; interrupted, interrupted compound and compound repeats were only present in 6%–9% of cases. (TAA)-microsatellites contained the longest repeats, with unit numbers from 9 to 131. For 218 loci primers could be designed and used for the detection of microsatellite length polymorphisms in six chickpea breeding cultivars, as well as in C. reticulatum and C. echinospermum, wild, intercrossable relatives of chickpea. A total of 174 primer pairs gave interpretable banding patterns, 137 (79%) of which revealed at least two alleles on native polyacrylamide gels. A total of 120 sequence-tagged microsatellite site (STMS) markers were genetically mapped in 90 recombinant inbred lines from an inter-species cross between C. reticulatum and the chickpea cultivar ICC 4958. Markers could be arranged in 11 linkage groups (at a LOD score of 4) covering 613 cM. Clustering as well as random distribution of loci was observed. Segregation of 46 markers (39%) deviated significantly (P ≥ 0.05) from the expected 1:1 ratio. The majority of these loci (73%) were located in three distinct regions of the genome. The present STMS marker map represents the most advanced co-dominant DNA marker map of the chickpea genome.

Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome.

A genetic linkage mapping study was conducted in 93 doubled-haploid lines derived from a cross between Triticum aestivum L. em. Thell 'Arina' and a Norwegian spring wheat breeding line, NK93604, using diversity arrays technology (DArT), amplified fragment length polymorphism (AFLP), and simple sequence repeat (SSR) markers. The objective of this study was to understand the distribution, redundancy, and segregation distortion of DArT markers in comparison with AFLP and SSR markers. The map contains a total of 624 markers with 189 DArTs, 165 AFLPs and 270 SSRs, and spans 2595.5 cM. All 3 marker types showed significant (p 0.98) and multicollinearity among the clustered markers. The present study is the first to compare the utility of DArT with AFLP and SSR markers, and the present map has been successfully used to identify novel QTLs for resistance to Fusarium head blight and powdery mildew and for anther extrusion, leaf segment incubation, and latency.

Distribution of DArT, AFLP, and SSR markers in a genetic linkage map of a doubled-haploid hexaploid wheat population.

Two small-insert genomic libraries of chickpea (Cicer arietinum L.) were screened with a set of microsatellite-specific oligonucleotide probes. A total of 121 positive clones were identified among 13 000 plated colonies. Thirty-nine clones were recognized by (TAA)5, 26 by (GA)8, 18 by (GT)8, 27 by a pool of AT-rich trinucleotide repeats [(CAA)5, (CAT)5, and (GAA)5], and 11 by a pool of GC-rich trinucleotides [(TCC)5, (CAC)5, (CAG)5, and (CGA)5]. Of 53 clones selected for sequencing, 43 carried a microsatellite. Flanking primer pairs were designed for 28 loci, and used on a small test-set comprising one C. reticulatum and four C. arietinum accessions. Separation of the PCR products on agarose or polyacrylamide gels revealed single bands of the expected size with 22 of the primer pairs. Sixteen of these "Cicer arietinum sequence-tagged microsatellite site" (CaSTMS) markers were polymorphic at an intraspecific level, detecting 2-4 alleles within the four accessions examined. Primer pairs CaSTMS10 and CaSTMS1...

Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.).

Cultivated chickpea (Cicer arietinum) has a narrow genetic base making it difficult for breeders to produce new elite cultivars with durable resistance to major biotic and abiotic stresses. As an alternative to genome mapping, microarrays have recently been applied in crop species to identify and assess the function of putative genes thought to be involved in plant abiotic stress and defence responses. In the present study, a cDNA microarray approach was taken in order to determine if the transcription of genes, from a set of previously identified putative stress-responsive genes from chickpea and its close relative Lathyrus sativus, were altered in chickpea by the three abiotic stresses; drought, cold and high-salinity. For this, chickpea genotypes known to be tolerant and susceptible to each abiotic stress were challenged and gene expression in the leaf, root and/or flower tissues was studied. The transcripts that were differentially expressed among stressed and unstressed plants in response to the particular stress were analysed in the context of tolerant/susceptible genotypes. The transcriptional change of more than two fold was observed for 109, 210 and 386 genes after drought, cold and high-salinity treatments, respectively. Among these, two, 15 and 30 genes were consensually differentially expressed (DE) between tolerant and susceptible genotypes studied for drought, cold and high-salinity, respectively. The genes that were DE in tolerant and susceptible genotypes under abiotic stresses code for various functional and regulatory proteins. Significant differences in stress responses were observed within and between tolerant and susceptible genotypes highlighting the multiple gene control and complexity of abiotic stress response mechanism in chickpea. The annotation of these genes suggests that they may have a role in abiotic stress response and are potential candidates for tolerance/susceptibility.

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Transcriptional profiling of chickpea genes differentially regulated in response to high-salinity, cold and drought

A subgenomic library constructed from small Pstl restriction fragments (0.4 to 2.0 kb) yielded 83.18% low-copy clones. Using 17 random genomic and 5 heterologous probes in 65 probe-enzyme combinations, Restriction Fragment Length Polymorphism (RFLP) for nuclear DNA was studied in five desi and five kabuli type chickpea cultivars. Only two clones revealed polymorphism in the cultivars tested. No polymorphism in chickpea varieties was detected with four Random Amplified Polymorphic DNA (RAPD) markers studied. However, some degree of polymorphism between C. arietinum and its wild relative C. reticulatum was detected. The RFLP analysis of chloroplast and mitochondrial genomes showed no polymorphism.

Narrow Genetic Variability in Cicer arietinum L. as Revealed by RFLP Analysis

RAPD markers were employed for construction of a linkage map and localization of QTLs for oleic acid level using a set of 94 recombinant inbred lines (RILs) of mustard (Brassica juncea L.) as a mapping population. Only 30% of the 235 random primers used were useful in terms of polymorphism detected and the reproducibility of those patterns. Normal Mendelian segregation was observed for the majority of the 130 markers obtained with 71 informative primers; only 13.1% deviated (P < 0.01) from the expected 1:1 ratio. One-hundred and fourteen markers were assigned to 21 linkage groups (LGs) covering a total length of 790.4 cM with an average distance of 6.93 cM between markers. Two quantitative trait loci (QTL) for oleic acid level were mapped to 14- and 10.6-cM marker intervals on two different LGs. Both loci together explained 32.2% of phenotypic variance. One major QTL explained 28.5% of the trait variance observed in this species.

Construction of an RAPD linkage map and localization of QTLs for oleic acid level using recombinant inbreds in mustard (Brassica juncea).

India Meteorological Department (IMD) introduced the objective tropical cyclone (TC) track forecast valid for next 24 hrs over the North Indian Ocean (NIO) in 2003. It further extended the validity period up to 72 hrs in 2009. Here an attempt is made to evaluate the TC landfall forecast issued by IMD during 2003–2013 (11 years) by calculating the landfall point forecast error (LPE) and landfall time forecast error (LTE). The average LPE is about 67, 95, and 124 km and LTE is about 4, 7, and 2 hrs, respectively for 24, 48, and 72-hr forecasts over the NIO as a whole during 2009–2013. The accuracy of TC landfall forecast has been analysed with respect to basin of formation (Bay of Bengal, Arabian Sea, and NIO as a whole), specific regions of landfall, season of formation (pre-monsoon and post-monsoon seasons), intensity of TCs (cyclonic storm (CS), and severe cyclonic storm (SCS) or higher intensities) at the time of initiation of forecast and type of track of TCs (climatological/straight moving and recurving/looping type). The LPE is less over the BOB than over the AS for all forecast lengths up to 72 hrs. Similarly, the LPE is less during the post-monsoon season than during pre-monsoon season. The LPEs are less for climatologically moving/straight moving TCs than for the recurving/looping TCs. The LPE over the NIO has decreased at the rate of about 14.5 km/year during 2003–2013 for 24-hr forecasts. The LTE does not show any significant improvement for 24-hr forecast during the same period. There is significant decrease in LPE and LTE during 2009–2013 compared to 2003–2008 due to the modernisation programme of IMD. The 24-hr LPE and LTE have decreased from 157.5 to 66.5 km and 7.8 to 4.1 hrs, respectively. However, there is still scope for further reduction in 48 and 72-hr forecast errors over the NIO to about 50 and 100 km respectively based on the latest technology including aircraft reconnaissance, deployment of buoys, and assimilation of more observational data from satellite and Doppler weather radars, etc., in the numerical weather prediction (NWP) models during the next five years.

Evaluation of official tropical cyclone landfall forecast issued by India Meteorological Department

For molecular mapping and character tagging in Indian mustard (Brassica juncea), cultivar Varuna and exotic collection BEC 144 were chosen on the basis of morphological and molecular differences. High degree of RFLP was detected between them using genomic DNA clones of Pst! subgenomic library as probes. Of the 48 probe — enzyme combinations, 89.5% were polymorphic. Majority of the probes revealed duplicate loci and a high frequency of null alleles (71.4%). Segregation analysis in the F2 population revealed significant deviation from expected 1:2:1 ratio for 32% of the markers. Using the computer package MAPMAKER, 15 markers could be placed in six linkage groups which covered a total length of 173.9 eM. Based on single factor analysis of variance, three significant marker-quantitative trait associations viz. BJG 59a primary branches/plant, BJG 42Gb - secondary branches/plant and BJG 433-days to f1owering could be identified. The BEC 144 alleles at the quantitative trait loci (QTL) in the marked genomic regions enhanced the trait expression. The putative gene action at these loci was found to be non-additive.

Molecular Mapping and Character Tagging in Brassica juncea—I. Degree, Nature and Linkage Relationship of RFLPs and Their Association With Quantitative Traits

An experiment was conducted in naturally ventilated polyhouse in rainy season during 2007-08 and 2008-09 at Rajasthan College of Agriculture, Udaipur (Raj.) to identify the most suitable cultivar, plant geometry and method of fertilizer applicator in cucumber. The results revealed that cultivar’ Hilton’ was significantly superior to enhance wive length (3.29 m), leaf area (500,99 cm2) , days to first harvest (44.40 days), fruit set (51.04 %), number of fruits per vine (30.89), average weight of fruit (105.28 g), fruit length(18.22 cm) and fruit width (3.62 cm) which ultimately gave maximum yield per vine (3.49kg) during rainy season. Significantly higher yield along with the growth and quality parameters were obtained in spacing 60 x 50cm. The fruit yield per plant was significantly more at 60 x 50 cm, whereas significantly higher yield per square meter was recorded at 60 x 30cm and least yield was recorded at 60 x 50cm. Fustigation practice recorded significantly higher yield (14.49 kg! m2) as compared to conventional method (13.22 kg/rn2).

Response to cultivars, plant geometry and methods of fertilizer application on parthenocarpic cucumber (Cucumis sativus L.) under zero energy polyhouse condition during rainy season

R. P. Sharma

Papers

Narrow Genetic Variability in Cicer arietinum L. as Revealed by RFLP Analysis

Construction of an RAPD linkage map and localization of QTLs for oleic acid level using recombinant inbreds in mustard (Brassica juncea).

Evaluation of official tropical cyclone landfall forecast issued by India Meteorological Department

Molecular Mapping and Character Tagging in Brassica juncea—I. Degree, Nature and Linkage Relationship of RFLPs and Their Association With Quantitative Traits

Response to cultivars, plant geometry and methods of fertilizer application on parthenocarpic cucumber (Cucumis sativus L.) under zero energy polyhouse condition during rainy season