Map Development

Specific goal: Public availability of genomic resources eg. molecular markers, ESTs, reference maps and identified linked molecular markers for traits/genes of interest in ICRISAT's crop species.

Outputs:

1. Genomic resources such as SSRs, SNPs, ESTs, BACs, and reference maps.
2. Linked molecular markers for traits/genes of interest.
3. Global, public database with map and population information.
4. Large phenotyping platform for complex traits such as roots.

A major application of genomics is the use of molecular markers as indirect selection tools in a breeding program. Essentially, the goal is a better prediction of a particular phenotype from a determined genotype. To accomplish this, it is necessary to determine molecular markers that have a high predictive value for a particular phenotype or trait. Development of such markers requires:

• Priority traits to be identified,
• Phenotyping methods well established to accurately quantify the traits,
• Dissecting the physiological mechanisms underlying complex traits.
• Contrasting germplasm sources available,
• Molecular markers available,
• Segregating populations produced, and
• Statistical methods available.

Priority traits have been identified in collaboration with the Global Theme on Crop Improvement. In most cases, adequate phenotyping methods are available, although for some traits such as drought and salinity, these will be firmly established. In the case of drought, the priority will be given to component traits of drought tolerance, namely transpiration efficiency to contribute to intermittent drought, and root traits to contribute to terminal drought tolerance. The dissection of the physiological mechanisms involved in the target traits will help progress toward the identification of the genes involved in that specific trait. Contrasting germplasm for use in developing segregating populations are available and in many instances, the required populations at various levels of inbreeding are available. Statistical packages for analyzing the molecular and phenotypic data are available and are being incorporated into a bioinformatics system (iMAS) to allow efficient handling of these datasets.

Genetic linkage maps:

Construction of comprehensive genetic map of chickpea: Low levels of polymorphism and lack of sufficient number of molecular markers such as microsatellites or simple sequence repeats (SSRs) are the main constraints in molecular mapping of traits of interest in chickpea. Hence, to increase the number of genetic resources, a total of 1,655 novel SSRs were developed from (i) SSR-enriched genomic library (311), and (ii) mining the BAC-end sequences (1,344). With an objective to enhance the density of chickpea genetic maps, the developed set of markers was tested for polymorphism on parental genotypes of an interspecific mapping population (Cicer arietinum L. ICC 4958 × C. reticulatum PI 489777) comprising of 131 RILs. A total of 305 markers (52 from SSR enriched library and 253 markers from BAC- end sequences) were found polymorphic in this cross and marker genotyping data were obtained. Apart from these novel SSR markers, genotyping data for several hundred published/ unpublished markers as well as novel gene based SNP markers from many laboratories were assembled. In total, genotyping information has become available for about 1,000 markers on this interspecific mapping population. A comprehensive chickpea genetic map comprising of 873 marker loci has been developed. The high density genetic map will be useful for trait mapping, gene cloning and linking with (future) physical map.

Groundnut

The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.): Molecular markers and genetic linkage maps are pre-requisites for molecular breeding in any crop spe­cies. In case of peanut or groundnut (Arachis hypogaea L.), an amphidiploid (4X) species, not a single genetic map is, however, available based on a mapping population derived from cultivated genotypes. A genetic linkage map was developed for tetraploid cultivated groundnut, using a total of 1,145 microsatellite or simple sequence repeat (SSR) markers that available in public domain as well as unpublished markers from several sources were screened on two genotypes, TAG 24 and ICGV 86031 that are parents of a recombinant inbred line mapping population. As a result, 144 (12.6%) polymorphic markers were identified and these amplified a total of 150 loci. A total of 135 SSR loci could be mapped into 22 linkage groups (LGs). While six LGs had only two SSR loci, the other LGs contained 3 (LG_AhXV) to 15 (LG_AhVIII) loci. As the mapping population used for developing the genetic map segregates for drought tolerance traits, phenotyping data obtained for transpiration, transpiration efficiency, specific leaf area and SPAD chlorophyll meter reading (SCMR) for 2 years were analyzed together with genotyping data. Although, 2–5 QTLs for each trait mentioned above were identified, the phenotypic variation explained by these QTLs was in the range of 3.5–14.1%. In addition, alignment of two linkage groups (LGs) (LG_AhIII and LG_AhVI) of the developed genetic map was shown with available genetic maps of AA diploid genome of groundnut and Lotus and Medicago. The present study reports the construction of the first genetic map for cultivated groundnut and demonstrates its utility for molecular mapping of QTLs controlling drought tolerance related traits as well as establishing relationships with diploid AA genome of groundnut and model legume genome species. The map should be useful for the community for a variety of applications.

For further information, contact: Rajeev Varshney, Tom Hash