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. In order to develop a genetic linkage map for tetraploid cultivated groundnut, a total of 1,145 microsatellite or simple sequence repeat (SSR) markers available in public domain as well as unpublished markers from several sources were screened on two genotypes, TAG 24 and ICGV 86031 that are parents of a recombinant inbred line mapping population.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. Therefore, the map should be useful for the community for a variety of applications.

Transpiration efficiency (TE) has been recognized as an important source of yield variation under drought stress in groundnut. Here the variation for TE is evaluated in a set of 318 recombinant inbred lines (RILs) of groundnut at F 8 generation, derived from a cross between a high TE (ICGV 86031) and a low TE (TAG 24) parent, and the value of specific leaf area (SLA), SPAD chlorophyll meter readings (SCMR) and carbon isotope discrimination (D 13 C) as surrogates of TE are measured. Transpiration efficiency was measured gravimetrically in the 318 RILs and parents under progressive soil drying in a pot culture in two post-rainy seasons. Large and consistent variation for TE existed among the RILs across years. The overall distribution of TE among the RILs indicated that TE was governed by dominant and additive genes. Surrogates SLA and SCMR, were measured prior, during and after completion of the drought period, whereas D 13 C was measured on the dried tissue after harvest. Transpiration efficiency was negatively associated with SLA after the completion of stress treatment (r 2 = 0.15) and D 13 C in leaves (r 2 = 0.13) and positively associated with SCMR during stress (r 2 = 0.17). These associations, all fairly weak, were significant only in 2004. None of these relationships was found in 2005. Although the heritability of SCMR during 2005 was relatively higher than that of TE, and although SCMR has previously been used to identify contrasting germplasm for TE, the stress-dependence of the relationship with TE, and the poor regression coefficients (r 2) with that RIL population, do not confer that these surrogates are adequately robust enough in that population. Though more time consuming, a direct gravimetric evaluation for TE appeared to be more reliable.

Peanut plays an important role in the livelihoods of poor farmers and in the rural economy of many developing countries. Aflatoxin contamination in peanut seeds, caused by Aspergillus flavus, hampers international trade and adversely affects health of consumers of peanut and its products. It can occur in the field when the crop is growing, during harvesting and curing, and in storage and transportation. Aflatoxin research on peanut at ICRISAT focuses on identification and utilization of genetic resistance to preharvest seed infection and aflatoxin production by A. flavus and pre and post harvest management practices to minimize contamination. Breeding for aflatoxin resistance has been a contentious issue in peanut for nearly four decades since the first report of host resistance to aflatoxin production by A. flavus. Despite global efforts, progress in aflatoxin resistance breeding has been limited due to the low level of resistance to different components of resistance (preharvest seed infection and aflatoxin production, and in vitro seed colonization by A. flavus), their variable performance due to high G 3 E interaction, lack of reliable screening protocols, and limited understanding of genetics of resistance. Efforts to combine the three independently inherited components of resistance did not produce expected results towards improving the host plant resistance to aflatoxin contamination. Although breeding lines have shown better performance for resistance to aflatoxin contamination at ICRISAT, they need wider evaluation under diverse growing conditions. The search for better sources of resistance in the cultivated and wild Arachis germplasm continues, and recent developments in the area of transgenic research through modification of aflatoxin biosynthesis pathway or use of genes with antifungal and anti-aflatoxin properties appear encouraging. Meanwhile, the available improved breeding lines coupled with pre and post harvest aflatoxin management practices can help to significantly reduce aflatoxin contamination in farmers' fields. It is expected that transgenic resistance against fungal infection and aflatoxin production in combination with conventional breeding efforts may lead to the development of agronomically superior peanuts that are free of aflatoxin contamination.

Grain legumes are important crops for providing key components in the diets of resource-poor people of the semi-arid tropic (SAT) regions of the world. Although there are several grain legume crops grown in SAT, the present chapter deals with three important legumes i.e. groundnut or peanut (Arachis hypogaea), chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan). Production of these legume crops are challenged by serious abiotic stresses e.g. drought, salinity as well as several fungal, viral and nematode diseases. To tackle these constraints through molecular breeding, some efforts have been initiated to develop genomic resources e.g. molecular markers, molecular genetic maps, expressed sequence tags (ESTs), macro-/micro-arrays, bacterial artificial chromosomes (BACs), etc. These genomic resources together with recently developed genetic and genomics strategies e.g. functional molecular markers, linkage-disequilibrium (LD) based association mapping, functional and comparative genomics offer the possibility of accelerating molecular breeding for abiotic and biotic stress tolerances in the legume crops. However, low level of polymorphism present in the cultivated genepools of these legume crops, imprecise phenotyping of the germplasm and the higher costs of development and application of genomic tools are critical factors in utilizing genomics in breeding of these legume crops

The ability to identify genetic variation is indispensable for effective management and use of genetic resources in crop breeding. Genetic variation among 189 groundnut (Arachis hypogaea L.) accessions comprising landraces, cultivars, a mutant, advanced breeding lines and others (unknown genetic background) representing 29 countries and 10 geographical regions was assessed at 25 microsatellite or simple sequence repeat loci. A high number of alleles (265) were detected in the range of 3 (Ah1TC6G09) to 20 (Ah1TC11H06) with an average of 10.6 alleles per locus. The polymorphism information content value at these loci varied from 0.38 (Ah1TC6G09) to 0.88 (Ah1TC11H06) with an average of 0.70. A total of 59 unique alleles and 127 rare alleles were detected at almost all the loci assayed. Cluster analysis grouped 189 accessions into four clusters. In general, genotypes of South America and South Asia showed high level of diversity. Extraordinary level of natural genetic variation reported here provides opportunities to the groundnut community to make better decisions and define suitable strategies for harnessing the genetic variation in groundnut breeding.