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.

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.

/pdf/transcriptional-profiling-of-chickpea-genes-differentially-4z6k7rhds2.pdf

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

Cicer arietinum L. (chickpea) and Vicia faba L. (faba bean, broad bean or horse bean) were found in late 10th millennium b.p. levels at Tell el-Kerkh, in north-west Syria. They are the earliest well preserved archaeobotanical finds of these two species. Over a hundred C. arietinum specimens were recovered which showed a wide morphological diversity varying from C. arietinum ssp. reticulatum to the more rounded shape as seen in cultivated varieties. For Vicia faba, 29 complete and 119 half seeds, as well as many fragments were recovered. Tell el-Kerkh is one of the few early PPNB Near Eastern sites situated in the Mediterranean zone which could have been the habitat of the unknown wild progenitor of the faba bean. The wild progenitor of chickpea, C. a. reticulatum, is found in a limited area of southeast Turkey, at a considerable distance from Tell el-Kerkh. These finds suggest that the use and domestication of these pulses is perhaps earlier than was previously supposed.

http://g.willcox.pagesperso-orange.fr/archaeobotanical%20images/PDF/WillTannoWillcox%20pulses.pdf

The origins of cultivation of Cicer arietinum L. and Vicia faba L.: early finds from Tell el-Kerkh, north-west Syria, late 10th millennium b.p.

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

A study was conducted to quantify the effect of elevated carbon dioxide (CO2) and temperature on soil organic nitrogen (N) fractions and enzyme activities in rice rhizosphere. Rice crop was grown inside the open top chambers in the ICAR-Indian Agricultural Research Institute. The N was applied in four different doses. Grain yield and aboveground N uptake by rice significantly reduced under elevated temperature. However, elevated CO2 along with elevated temperature was able to compensate this loss. Principal component analysis clearly indicated that microbial biomass carbon, microbial biomass N, amino acid N, total hydrolysable N, ammonia N and serine–threonine N contributed significantly to rice grain yield. Combined effect of elevated CO2 and elevated temperature decreased the total hydrolysable N, especially for lower N doses. The N-acetyl-glucosaminidase and leucine aminopeptidase enzyme activities were negatively correlated with the organic N pools. Higher activities of these enzymes under limited N supply may accelerate the decomposition of organic N in soil. When N was applied in super-optimal dose, plant N demand was met thereby causing lesser depletion of total hydrolysable N. Better nitrogen management will alleviate faster depletion of native soil N under future scenario of climate change and thus might cause N sequestration in soil.

Do elevated CO2 and temperature affect organic nitrogen fractions and enzyme activities in soil under rice crop

Pharmacophore modeling studies on xanthones as monoamine oxidase-a inhibitors

Restriction fragment length polymorphism (RFLP) analysis of Brassica juncea genome using 39 random homologous genomic DNA clones and chlorophyll a, b binding polypeptide (cab-3c) cDNA of tomato as probes revealed high degree of sequence duplication. The average number of hybridizing fragments per probe (8) was much higher than that earlier reported using cDNA probes in B. juncea. Null alleles observed for majority (56.2%) of the polymorphic duplicate loci suggested a significant role of insertion/deletion events in evolution of mustard genome. Distortion in segregation was evident in respect of only 9.6% of the segregating loci indicating that the mapping population used was relatively unbiased and thus can be used efficiently for genome mapping as well as for location of genes. Forty-nine polymorphic duplicate loci could be mapped to 15 linkage groups. Arrangement of these loci on different linkage groups revealed intra and inter-chromosomal duplications as well as duplication of chromosome blocks.Three of the eight cab loci could be mapped on three different linkage groups. Null allelic situation for seven of the cab loci suggested the role of DNA rearrangement in evolution of this multigene family in B. juncea.

Anuradha Sharma

Papers

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

Do elevated CO2 and temperature affect organic nitrogen fractions and enzyme activities in soil under rice crop

Pharmacophore modeling studies on xanthones as monoamine oxidase-a inhibitors

Detection and Mapping of Duplicate Loci in Brassica juncea

RFLP mapping in Indian Mustard (Brassica juncea)