A consensus genetic map of chickpea (Cicer arietinum L.) was constructed by merging linkage maps from 10 different populations, using STMS (Sequence-tagged Microsatellite Sites) as bridging markers. These populations derived from five wide crosses (C. arietinum × Cicer reticulatum) and five narrow crosses (Desi × Kabuli types) were previously used for mapping genes for several agronomic traits such as ascochyta blight, fusarium wilt, rust resistance, seed weight, flowering time and days to flower. The integrated map obtained from wide crosses consists of 555 loci including, among other markers, 135 STMSs and 33 cross-genome markers distributed on eight linkage groups and covers 652.67 cM. The map obtained from narrow crosses comprises 99 STMSs, 3 SCARs, 1 ASAP, fusarium resistance gene, 5 morphological traits as well as RAPD and ISSR markers distributed on eight linkage groups covering 426.99 cM. Comparison between maps from wide and narrow crosses reflects a general coincidence, although some discrepancies are discussed. Medicago truncatula cross-genome markers were BLASTed against the M. truncatula pseudogenome permitting assignments of chickpea linkage groups LGI, II, III, IV, V and VI on Medicago chromosomes 2, 5, 7, 1, 3 and 4, respectively. A marker detectable on Medicago chromosome 4 were also located on LGVIII, This consensus map is an important progress to assist breeders for selecting suitable markers to be used in marker-assisted selection (MAS).

Resistance of chickpea against the disease caused by the ascomycete Ascochyta rabiei is encoded by two or three quantitative trait loci, QTL1, QTL2 and QTL3. A total of 94 recombinant inbred lines developed from a wide cross between a resistant chickpea line and a susceptible accession of Cicer reticulatum , a close relative of cultivated chickpea, was used to identify markers closely linked to QTL1 by DNA amplification fingerprinting in combination with bulked segregant analysis. Of 312 random 10mer oligonucleotides, 3 produced five polymorphic bands between the parents and bulks. Two of them were transferred to the population on which the recent genetic map of chickpea is based, and mapped to linkage group 4. These markers, OPS06-1 and OPS03-1, were linked at LOD-scores above 5 to markers UBC733B and UBC181A flanking the major ascochyta resistance locus. OPS06-1 mapped at the peak of the QTL between markers UBC733B (distance 4.1 cM) and UBC181A (distance 9.6 cM), while OPS03-1 mapped 25.1 cM away from marker UBC733B on the other flank of the resistance locus. STMS markers localised on this linkage group were transferred to the population segregating for ascochyta resistance. Three of these markers were closely linked to QTL1. Twelve of 14 STMS markers could be used in both populations. The order of STMS markers was essentially similar in both populations, with differences in map distances between them. The availability of flanking STMS markers for the major resistance locus QTL1 will help to elucidate the complex resistance against different Ascochyta pathotypes in future.

Fifty sequence-tagged microsatellite site (STMS) markers and a resistant gene-analog (RGA) locus were integrated into a chickpea ( Cicer arietinum L., 2n = 2 x = 16 chromosomes) genetic map that was previously constructed using 142 F(6)-derived recombinant inbred lines (RILs) from a cross of C. arietinum x Cicer reticulatum Lad. The map covers 1,174.5 cM with an average distance of 7.0 cM between markers in nine linkage groups (LGs). Nine markers including the RGA showed distorted segregation ( P < 0.05). The majority of the newly integrated markers were mapped to marker-dense regions of the LGs. Six co-dominant STMS markers were integrated into two previously reported major quantitative trait loci (QTLs) conferring resistance to Ascochyta blight caused by Ascochyta rabiei (Pass.) Labr. Using common STMS markers as anchors, three maps developed from different mapping populations were joined, and genes for resistance to Ascochyta blight, Fusarium wilt (caused by Fusarium oxysporum Schlechtend.: Fr. f. sp. ciceris), and for agronomically important traits were located on the combined linkage map. The integration of co-dominant STMS markers improves the map of chickpea and makes it possible to consider additional fine mapping of the genome and also map-based cloning of important disease resistance genes.

Resistance gene analog polymorphism (RGAP)is a targeted homology based method, which has been used in different crops to identify tightly linked markers for disease resistance genes and also to enrich the map with a different class of markers. In chickpea, using the RGA primers, which are designed based on the conserved motifs present in characterized R-genes, Bulk Segregant Analysis (BSA) was performed on a resistant bulk and a susceptible bulk along with parents for ascochyta blight resistance. Of all available RGAs and their48 different combinations, only one RGA showed polymorphism during BSA. This marker was evaluated in an F 7:8 population of142 RILs from an interspecific cross of C. arietinum (FLIP 84-92C) × C. reticulatum (PI 599072) and was mapped to Cicer linkage map. The genomic location of chickpea RGA was compared with the locations of mapped chickpea R-genes. This is the first RGA marker mapped to chickpea linkage map.

Resistance gene analog polymorphism (RGAP)is a targeted homology based method, which has been used in different crops to identify tightly linked markers for disease resistance genes and also to enrich the map with a different class of markers. In chickpea, using the RGA primers, which are designed based on the conserved motifs present in characterized R-genes, Bulk Segregant Analysis (BSA) was performed on a resistant bulk and a susceptible bulk along with parents for ascochyta blight resistance. Of all available RGAs and their48 different combinations, only one RGA showed polymorphism during BSA. This marker was evaluated in an F population of142 RILs from an interspecific cross of (FLIP 84-92C) × (PI 599072) and was mapped to linkage map. The genomic location of chickpea RGA was compared with the locations of mapped chickpea R-genes. This is the first RGA marker mapped to chickpea linkage map.

Ascochyta blight, caused by Ascochyta rabiei (Pass.) Lab., is a devastating disease of chickpea (Cicer arietinum L.) worldwide. Resistant germplasm has been identified and the genetics of resistance has been the subject of numerous studies. The objectives of the present study were to determine the genetics of resistance to ascochyta blight of chickpea and to map and tag the chromosomal regions involved using molecular markers. We used a set of 142 F-5;6 recombinant inbred lines (RILs) obtained from an interspecific cross of C. arietinum (FLIP84-92C, resistant parent) x C. reticulatum Lad. (PI 599072, susceptible parent). The RILs were scored for disease reactions in the,field over 2 yr and were genotyped for polymorphic molecular markers [isozyme, random amplified polymorphic DNA (RAPD), and inter simple sequence repeat (ISSR)] in the laboratory. The disease was scored quantitatively and data were used for QTL analysis. A linkage map was established that comprised nine Linkage groups containing 116 markers covering a map distance of 981.6 centimorgans (cM) with an average distance of 8.4 cM between markers. Two quantitative trait loci (QTLs), QTL-1 and QTL-2, conferring resistance to ascochyta blight, were identified which accounted for 50.3 and 45.0% of the estimated phenotypic variation in 1997 and 1998, respectively, and were mapped to linkage groups 6 and 1, respectively. Two RAPD markers flanked QTL-1 and were 10.9 cM apart while one ISSR marker and an isozyme marker flanked QTL-2 and were 5.9 cM apart. These markers can be used for marker-assisted selection for ascochyta blight resistance in chickpea breeding programs, and to develop durable resistant cultivars through gene pyramiding.

Fusarium oxysporum Schlechtend.: Fr. f. sp. ciceris (Padwick) causes a vascular wilt of chickpea ( Cicer arietinum L.) and significantly limits production worldwide. The objectives of this study were (i) to determine the inheritance of resistance to races 0 and 5 of fusarium wilt and the genetic map positions of the resistance genes and (ii) to assess the linkage relationships between these two genes and other known wilt resistance genes in chickpea. Seedlings of 131 F 6 ‐derived recombinant inbred lines (RILs) were tested for reaction to races 0 and 5. A 1 resistant:1 susceptible segregation ratio was observed for both races, indicating that resistance to each race is controlled by a single gene. Linkage analysis indicated that the genes for resistance to races 4 and 5 were in the same linkage group and were separated by 11.2 centiMorgans (cM). The gene for resistance to race 0 was not linked to the race 4 and 5 resistance genes. In addition, an allele‐specific associated primer (ASAP) product (CS‐27R/CS‐27F), developed from the CS‐27 primer, was located between the two resistance genes and was 7.2 and 4 cM from the genes for resistance to races 4 and 5, respectively. Map positions of these two race‐specific resistance genes and the marker reported to be linked to the genes for resistance to races 1 and 4 support the hypothesis that wilt resistance genes are clustered on the same chromosome. Since the gene conferring resistance to race 0 is found in a different region of the genome, other genomic regions may be responsible for resistance to wilt pathogens. The gene symbols foc‐0 , foc‐4 , and foc‐5 are proposed for the genes for resistance to races 0, 4, and 5 of the pathogen, respectively. Identification and further evaluation of disease resistance gene clusters would improve our understanding of wilt resistance in chickpea and facilitate the transfer of resistance genes to new cultivars.

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.

We describe a simple and new approach, based on inter-simple sequence repeats (ISSRs), for finding markers linked to clusters of disease resistance genes. In this approach, simple sequence repeats (SSR) are used directly in PCR reactions, and markers found to be linked to disease resistance genes provide important information for the selection of other sequences which can be used with PCR to find other linked markers. Based on an ISSR marker linked to a gene of interest, many new markers can be identified in the same region. We previously demonstrated that ISSR markers are useful in gene tagging and identified a marker, UBC-855500, linked to the gene for resistance to fusarium wilt race 4 in chickpea. This ISSR marker provided the information used in the present study for selecting other primers which amplified a region linked to the gene for resistance to fusarium wilt race 4. The primers were based on homology with the (AC)n sequence and were used for PCR amplifications. Changes in the sequence were at the anchor region of the primers. The repeat (AC)8T amplified a marker, UBC-8251200, which was located 5.0 cM from the gene for resistance to fusarium wilt race 4 and was closer than other markers. These results indicated that ISSR markers can provide important information for the design of other primers and that by making changes at the 3′ and 5′ anchors close linkage to the desired gene can be found. The approach allows rapid scanning of the targeted region and may provide important information for genome analysis of plant species.