DAF marker tightly linked to a major locus for Ascochyta blight resistance in chickpea (Cicer arietinum L.)

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. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetics of resistance to ascochyta blight in chickpea (Cicer arietinum L.)

Summary Six chickpea lines resistant to Ascochyta rabiei (Pass.) Lab. were crossed to four susceptible cultivars. The hybrids were resistant in all the crosses except the crosses where resistant line BRG 8 was involved. Segregation pattern for diseases reaction in F₂, BCP₁, BCP₂ and F₃ generations in field and glasshouse conditions revealed that resistance to Ascochyta blight is under the control of a single dominant gene in EC 26446, PG 82-1, P 919, P 1252-1 and NEC 2451 while a recessive gene is responsible in BRG 8. Allelic tests indicated the presence of three independently segregating genes for resistance; one dominant gene in P 1215-1 and one in EC 26446 and PG 82-1, and a recessive one in BRG 8.Research paper No. 3600     

Genetic and physical mapping of the QTLAR3 controlling blight resistance in chickpea (Cicer arietinum L)

Physical and genetic maps of chickpea a QTL related to Ascochyta blight resistance and located in LG2 (QTL_AR3) have been constructed. Single-copy markers based on candidate genes located in the Ca2 pseudomolecule were for the first time obtained and found to be useful for refining the QTL position. The location of the QTL_AR3 peak was linked to an ethylene insensitive 3-like gene (Ein3). The Ein3 gene explained the highest percentage of the total phenotypic variation for resistance to blight (44.3 %) with a confidence interval of 16.3 cM. This genomic region was predicted to be at the Ca2 physical position 32–33 Mb, comprising 42 genes. Candidate genes located in this region include Ein3, Avr9/Cf9 and Argonaute 4, directly involved in disease resistance mechanisms. However, there are other genes outside the confidence interval that may play a role in the blight resistance pathway. The information reported in this paper will facilitate the development of functional markers to be used in the screening of germplasm collections or breeding materials, improving the efficiency and effectiveness of conventional breeding methods.     

Identification of QTLs for resistance to Fusarium wilt and Ascochyta blight in a recombinant inbred population of chickpea (<Emphasis Type="Italic">Cicer arietinum</Emphasis> L.)

Fusarium wilt (FW; caused by Fusarium oxysporum f. sp. ciceris) and Ascochyta blight (AB; caused by Ascochyta rabiei) are two major biotic stresses that cause significant yield losses in chickpea (Cicer arietinum L.). In order to identify the genomic regions responsible for resistance to FW and AB, 188 recombinant inbred lines derived from a cross JG 62 × ICCV 05530 were phenotyped for reaction to FW and AB under both controlled environment and field conditions. Significant variation in response to FW and AB was detected at all the locations. A genetic map comprising of 111 markers including 84 simple sequence repeats and 27 single nucleotide polymorphism (SNP) loci spanning 261.60 cM was constructed. Five quantitative trait loci (QTLs) were detected for resistance to FW with phenotypic variance explained from 6.63 to 31.55%. Of the five QTLs, three QTLs including a major QTL on CaLG02 and a minor QTL each on CaLG04 and CaLG06 were identified for resistance to race 1 of FW. For race 3, a major QTL each on CaLG02 and CaLG04 were identified. In the case of AB, one QTL for seedling resistance (SR) against ‘Hisar race’ and a minor QTL each for SR and adult plant resistance against isolate 8 of race 6 (3968) were identified. The QTLs and linked markers identified in this study can be utilized for enhancing the FW and AB resistance in elite cultivars using marker-assisted backcrossing.     

Gametophytic selection for wilt resistance and its impact on the segregation of wilt resistance alleles in chickpea (Cicer arietinum L.)

In the present study, the effect of gametophytic selection on the segregation of molecular markers linked and unlinked to wilt resistance loci was investigated. A homozygous resistant genotype WR315 (h₁h₁ h₂h₂) was crossed to two susceptible lines, Karikadle (H₁H₁ H₂H₂) and BG256 (h₁h₁ H₂H₂), to generate two different F₁ populations. Three F₁ plants from each cross were subjected to gametophytic selection by spraying a pathotoxin at flower bud initiation stage, while the remaining F₁ plants in each cross were treated as control by spraying them with water. Both control and treated F₁ plants were selfed to generate respective F₂ populations. The seeds of control and selected F₂ populations of both crosses were sown to raise the plants. The DNA from 60 to 70 plants in each treatment group were isolated and tested for presence of the markers linked and unlinked to wilt resistance loci. Both the linked and unlinked markers showed expected monogenic ratio of 3:1 individually in control population. In the selected F₂ population the markers CS 27₇₀₀ linked to H₁ locus, A07C₄₁₇ and H₄G₁₁ linked to H₂ locus of wilt resistance exhibited significant deviations for monogenic and digenic ratios. The unlinked markers NCPGR93 and NCPGR48 showed expected monogenic ratios in the selected F₂ population. The results demonstrated that the gametophytic selection for wilt resistance increase the frequency of resistance alleles and resistant plants in the progeny. Deviation from the expected segregation ratio of the marker closely linked to resistance loci suggests the presence of linkage drag in gametophytic selection for resistance. The significant deviation from monogenic ratio was also observed for the linked marker A07C₄₁₇ in the selected F₂ population of second cross BG256 × WR315. On the contrary, the segregation of markers in a different linkage not linked to resistance loci was not affected. Thus demonstrating the utility of gamete selection for resistance is increasing the frequency of resistant plant in the progeny independent of the parental genotype. Gametophytic selection can be applied in plant breeding programmes to develop wilt resistant genotypes in a short period.     

Genetic diversity analysis of advanced chickpea (Cicer arietinum L.) genotypes in Ethiopia for identification of high-yielding and novel Fusarium wilt resistance sources

Journal of Crop Science and Biotechnology - Chickpea (Cicer arietinum L.) is one of the most important food legumes in the world. However, Fusarium wilt is one of the major yield limiting factors...     

Inheritance of resistance to Fusarium wilt (race 2) in chickpea

The inheritance of resistance to Fusarium wilt (race 2) of chickpea was studied in a set of three crosses, i.e. ‘WR315’בC104’ (resistant × susceptible), ‘WR315’בK850’ (resistant × tolerant) and ‘K850’בGW5/7’ (tolerant × tolerant) in order to investigate the number of genes involved, their complementation and to find out whether resistant segregants are possible in a cross between two tolerant cultivars. Tests of F₁, F₂ and F₃ generations of these crosses under controlled conditions at ICRISAT, Patancheru, India, indicated involvement of three loci (two recessive and one dominant alleles). The homozygous recessive form at the first two loci conferred resistance whereas susceptibility occurred when the first two loci were in the dominant form. A dominant allele at the third locus can complement the dominant alleles at the other two loci to confer tolerance. Occurrence of resistant segregants in a cross between two tolerant cultivars was observed.     

Molecular mapping of quantitative trait loci for ascochyta blight and botrytis grey mould resistance in an inter-specific cross in chickpea (Cicer arietinum L.) using genotyping by sequencing

Ascochyta blight (AB) and botrytis grey mould (BGM) are the most devastating fungal diseases of chickpea worldwide. The wild relative of chickpea, C. reticulatum acc. ILWC 292 was found resistant to BGM whereas, GPF2 (Cicer arietinum L.) is resistant to AB. A total of 187 F₈ Recombinant Inbred Lines (RILs) developed from an inter-specific cross of GPF2 × C. reticulatum acc. ILWC 292 were used to identify quantitative trait loci (QTLs) responsible for resistance to AB and BGM. RILs along with parents were evaluated under artificial epiphytotic field/laboratory conditions for two years. Highly significant differences (P < 0.001) were observed for reaction to both pathogens in both years. Parents and RILs were genotyped-by-sequencing to identify genome wide single nucleotide polymorphism (SNPs). A total of 1365 filtered and parental polymorphic SNPs were used for linkage map construction, of which, 673 SNPs were arranged on eight linkage groups. Composite interval mapping revealed three QTLs for AB and four QTLs for BGM resistance. Out of which, two QTLs for AB and three QTLs for BGM were consistent in both years. These QTLs can be targeted for further fine mapping for deployment of resistance to AB and BGM in elite chickpea cultivars using marker-assisted-selection.     

Leaf type is not associated with ascochyta blight disease in chickpea (Cicer arietinum L.)

The three major leaf types in chickpea are normal compound leaf, simple leaf and multipinnate. Simple leaf types are less commonly cultivated worldwide and are often reputed to be susceptible to ascochyta blight disease, whereas other leaf types range from resistant to susceptible. This study determined the association between host plant resistance to ascochyta blight and different leaf types in segregating populations derived from crosses between disease resistant and susceptible chickpea genotypes. In addition, the inheritance of disease resistance and leaf type was investigated in intraspecific progeny derived from crosses between two resistant genotypes with normal leaf type (ICC 3996 and Almaz), one susceptible simple leaf type (Kimberley Large) and one susceptible multipinnate leaf type (24 B-Isoline). Our results showed that, in these segregating populations, susceptibility to ascochyta blight was not linked to multipinnate or simple leaf types; resistance to ascochyta blight depended more on genetic background than leaf shape; leaf type was controlled by two genes with a dihybrid supplementary gene action; normal leaf type was dominant over other leaf types; and inheritance of ascochyta blight resistance was controlled by two major genes, one dominant and one recessive. Since there was no linkage between ascochyta blight susceptibility and leaf type, breeding various leaf types with ascochyta blight resistance is a clear possibility. These results have significant implications for chickpea improvement, as most current extra large seeded kabuli varieties have a simple leaf type.     

Leaf types and their genetics in chickpea (Cicer arietinum L.)

Summary Commonly the chickpea leaf is uni-imparipinnate, having 9–15 leaflets. However, certain variants have been reported; these are available in the chickpea collection at ICRISAT and were re-examined. Based on the lamina differentiation, three major classes of leaf type can be recognized: uni-imparipinnate (normal), multipinnate and simple (leaf). (Certain other leaf forms reported earlier are not classes of leaf type though they are distinct variants). It was determined that the leaf type differences are governed by two genes (mlsl), which show supplementary gene action. The multipinnate leaf is formed when the first gene is dominant (ml⁺sl/.sl). Whereas the simple leaf occurs when the first gene is recessive and the second gene is in either form (ml./ml.), the normal leaf is expressed when both dominant genes are present (ml⁺sl⁺/..).Submitted as J.A. No. 814 by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT).     

Genetics for speed of plumule emergence in chickpea (Cicer arietinum L.)

Summary Genetics for speed of plumule emergence was studied using six generations (P₁, P₂, F₁, BC₁(P₁), BC₂(P₂) and F₂) in three crosses. Two of the crosses which had parents of different emergence speed were controlled by two genes with duplicate epistasis. The third cross which involved parents of little difference for speed, indicated incomplete dominance for one gene of bit fast parent over the slow one. In all the crosses F₂ segregation pattern was confirmed by the segregation pattern of back crosses. The gene symbols were designated as Sp1Sp1 Sp2Sp2 for fast speed parents: sp1sp1 sp2sp2 for slow parent and sp1sp1 Sp2Sp2 for the parent with bit fastness for speed of plumule emergence.     

Methods for screening resistance in chickpea to Ascochyta blight

Summary In Morocco, Ascochyta blight is a major limiting factor in chickpea production. The best long term solution to the problem seems to be the production of chickpea lines with durable resistance to the disease. Because of the nature of durable resistance, screening methods assessing resistance quantitatively had to be developed. Four methods are described: a seedling test, a germination test, a score of the percentage infected pods and a hair density score. With these screening methods a quantitative assessment of resistance in chickpea to blight appeared possible.Mr Pieters is with the FAO Plant Protection and Production division. Mr Tahiri is with the Service de Contrôle des Semences et Plants in Morocco.     

Two major genes for seed size in chickpea (Cicer arietinum L.)

Summary Seed size as determined by seed weight, is an important trait for trade and component of yield and adaptation in chickpea (Cicer arietinum L.). Inheritance of seed size in chickpea was studied in a cross between ICC11255, a normal seed size parent (average 120 mg seed⁻¹) and ICC 5002, a small seed size parent (average 50 mg seed⁻¹). Seed weight observations on individual plants of parents, F₁, F₂, and backcross generations, along with reciprocal cross generations revealed that the normal seed size was dominant over small seed size. No maternal effect was detected for seed size. The numbers of individuals with normal, small and medium (average 150 mg seed⁻¹) seed sizes in F ₂ population were 1237, 323 and 111 fitting well to the expected ratio of 12:3:1 (χ² = 0.923, P = 0.630). The segregation data of backcross generations also indicated that seed size in chickpea was controlled by two genes with dominance epistasis. We designate the genotype of ICC 11255 as Sd ₁ Sd ₁ sd ₂ sd ₂, and ICC 5002 as sd ₁ sd ₁Sd₂ Sd ₂ wherein Sd ₁ is epistatic to Sd ₂ and sd ₂ alleles.     

Inheritance of resistance to Ascochyta blight in chickpea

Summary The mode of inheritance of resistance to Ascochyta blight (Ascochyta rabiei) isolate G-52 in chickpea was studied in three cross combinations and their reciprocals. It was found that resistance variety I-13 was controlled by a single dominant gene pair.     

A consensus genetic map of chickpea (Cicer arietinum L.) based on 10 mapping populations

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).     

Mapping and validation of QTLs for resistance to an Indian isolate of Ascochyta blight pathogen in chickpea

Ascochyta blight (AB) caused by Ascochyta rabiei, is globally the most important foliar disease that limits the productivity of chickpea (Cicer arietinum L.). An intraspecific linkage map of cultivated chickpea was constructed using an F₂ population derived from a cross between an AB susceptible parent ICC 4991 (Pb 7) and an AB resistant parent ICCV 04516. The resultant map consisted of 82 simple sequence repeat (SSR) markers and 2 expressed sequence tag (EST) markers covering 10 linkage groups, spanning a distance of 724.4 cM with an average marker density of 1 marker per 8.6 cM. Three quantitative trait loci (QTLs) were identified that contributed to resistance to an Indian isolate of AB, based on the seedling and adult plant reaction. QTL1 was mapped to LG3 linked to marker TR58 and explained 18.6% of the phenotypic variance (R ²) for AB resistance at the adult plant stage. QTL2 and QTL3 were both mapped to LG4 close to four SSR markers and accounted for 7.7% and 9.3%, respectively, of the total phenotypic variance for AB resistance at seedling stage. The SSR markers which flanked the AB QTLs were validated in a half-sib population derived from the same resistant parent ICCV 04516. Markers TA146 and TR20, linked to QTL2 were shown to be significantly associated with AB resistance at the seedling stage in this half-sib population. The markers linked to these QTLs can be utilized in marker-assisted breeding for AB resistance in chickpea.     

Induction and inheritance of determinate growth habit in chickpea (Cicer arietinum L.)

Summary The character of determinate plant growth has not been reported for chickpea and has not been observed in the world germplasm collection at ICRISAT, Patancheru, India. A determinate growth habit would be desirable where growing conditions often lead to excessive vegetative growth. We attempted to generate this trait by mutation breeding. Seeds of the cultivar ICCV 6 were exposed to varying irradiation treatments, M₁ and M₂ populations were raised, and in the latter one plant was detected that showed the determinate growth habit and female sterility. The character of determinate growth segregated in a postulated digenic epistatic 3:13 fashion in the F₂ and confirmed its digenic mode of inheritance in the F₃ and F₄. The symbol cd is proposed for the allele conditioning for determinancy and Dt for the allele expressing the determinate trait. Continued mutation breeding with this and other material may result in identifying fully fertile, determinate plant types.Abbreviations DT - determinate - IDT - indeterminate ICRISAT Journal Article No. 1396.     

Integrated breeding approaches for improving drought and heat adaptation in chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is a dry season food legume largely grown on residual soil moisture after the rainy season. The crop often experiences moisture stress towards end of the crop season (terminal drought). The crop may also face heat stress at the reproductive stage if sowing is delayed. The breeding approaches for improving adaptation to these stresses include the development of varieties with early maturity and enhanced abiotic stress tolerance. Several varieties with improved drought tolerance have been developed by selecting for grain yield under moisture stress conditions. Similarly, selection for pod set in the crop subjected to heat stress during reproductive stage has helped in the development of heat‐tolerant varieties. A genomic region, called QTL‐hotspot, controlling several drought tolerance‐related traits has been introgressed into several popular cultivars using marker‐assisted backcrossing (MABC), and introgression lines giving significantly higher yield than the popular cultivars have been identified. Multiparent advanced generation intercross (MAGIC) approach has been found promising in enhancing genetic recombination and developing lines with enhanced tolerance to terminal drought and heat stresses.