http://oar.icrisat.org/6408/7/BiotecAdv_31_1120-1134_2013.pdf

Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics

This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago.

/pdf/integration-of-novel-ssr-and-gene-based-snp-marker-loci-in-1brg0d142m.pdf

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome.

Yield stability of legume crops is constrained by a number of pest and diseases Major diseases are rusts, powdery and downy mildews, ascochyta blights, botrytis gray molds, anthracnoses, damping-off, root rots, collar rots, vascular wilts and white molds Parasitic weeds, viruses, bacteria, nematodes and damages caused by chewing and sap-sucking insects add to this long list of constraints for legume production Their incidence and relative importance together with current understanding of their interactions with the host plants are presented State of the art of current achievements and limitations for breeding for biotic stress resistance are listed and critically discussed The recent development of large scale phenotyping, genome sequencing and analysis of gene, protein and metabolite expressions can be of great help to further decipher plant-pathogen interactions and identify key resistance components that may be introgressed into crop plants through breeding

https://digital.csic.es/bitstream/10261/160300/1/legume_breeding_Rubiales.pdf

Achievements and Challenges in Legume Breeding for Pest and Disease Resistance

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thu​di/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes.

/pdf/novel-ssr-markers-from-bac-end-sequences-dart-arrays-and-a-jx905uoecj.pdf

Novel SSR Markers from BAC-End Sequences, DArT Arrays and a Comprehensive Genetic Map with 1,291 Marker Loci for Chickpea (Cicer arietinum L.)

The major abiotic and biotic stresses that adversely affect yield of chickpea (Cicer arietinum L.) include drought, heat, fusarium wilt, ascochyta blight and pod borer. Excellent progress has been made in developing short-duration varieties with high resistance to fusarium wilt. The early maturity helps in escaping terminal drought and heat stresses and the adaptation of chickpea to short-season environments. Ascochyta blight continues to be a major challenge to chickpea productivity in areas where chickpea is exposed to cool and wet conditions. Limited variability for pod borer resistance has been a major bottleneck in the development of pod borer resistant cultivars. The use of genomics technologies in chickpea breeding programs has been limited, since available genomic resources were not adequate and limited polymorphism was observed in the cultivated chickpea for the available molecular markers. Remarkable progress has been made in the development of genetic and genomic resources in recent years and integration of genomic technologies in chickpea breeding has now started. Marker-assisted breeding is currently being used for improving drought tolerance and combining resistance to diseases. The integration of genomic technologies is expected to improve the precision and efficiency of chickpea breeding in the development of improved cultivars with enhanced resistance to abiotic and biotic stresses, better adaptation to existing and evolving agro-ecologies and traits preferred by farmers, industries and consumers.

https://www.mdpi.com/2073-4395/2/3/199/pdf

Impact of Genomic Technologies on Chickpea Breeding Strategies

Resistance of chickpea against the disease caused by the ascomycete Ascochyta rabiei is encoded by two or three quantitative trait loci, QTL1, QTL2 and QTL 3 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 41 cM) and UBC181A (distance 96 cM), while OPS03-1 mapped 251 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

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

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