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Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.

Rice is one of the most important food crop drastically affected by drought in lowland rice ecosystem. Dissecting out the traits of importance and genomic regions influencing the response of drought tolerance and yield traits on grain yield will aid the breeders to know the genetic mechanism of drought tolerance of rice leads to the development of drought tolerant varieties. Grain yield and its components on drought situation of recombinant inbred population (IR 58821/IR 52561) were investigated under lowland managed stress situation in 2003 and 2004 by given importance to the relative water content. Water deficit resulted in significant effect on phenology and grain yield. Best lines were selected for further varietal development programme. Variability studies showed the traits viz., days to 70% relative water content, leaf rolling, leaf drying, harvest index, biomass yield and grain yield offer high scope for improvement for drought tolerance by way of simple selection technique. Correlation and path analysis indicated that, to harness high yielding combined with drought tolerance breeders should give selection pressure on relative water content, panicle length, grains per panicle, harvest index, biomass yield, root/shoot ratio and root length in positive direction, and low scores of leaf rolling, leaf drying and drought recovery rate. Analysis of quantitative trait loci for drought tolerance, yield and its components allowed the identification of 38 regions associated with both drought tolerant and yield traits. Out of these, 18 were closely linked with DNA markers could be used for marker assisted selection in breeding for drought tolerance in rice. Pleiotropism and G · E effects interaction were noticed in some of the traits. Parent IR 58821 contributed favorable alleles for the entire drought related and most of the yield component traits. Identification of traits of Ó Springer Science+Business Media B.V. 2006importance and their nature of relationship by morphological and molecular level under lowland condition will be useful to improve drought tolerance of rice.

Key messageGiven recent advances in pulse molecular biology, genomics-driven breeding has emerged as a promising approach to address the issues of limited genetic gain and low productivity in various pulse crops.AbstractThe global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability.

Lentil is one of most important pulse crops in South Asia, and invariably encounters terminal moisture stress, leading to forced maturity and lower yield. A long and prolific root system is known to enhance capacity of the plant to extract water from the lower soil strata and thus help avoid the water stress. We assessed genetic variation for 12 traits among 43 lentil genotypes comprising improved varieties and promising breeding lines. The average root length at the 65-day plant stage ranged from 42 to 83 cm. Two genotypes (EC 208362 and VKS 16/11) with shorter root length and poor dry root weight (DRW) and three genotypes (DPL 53, JL 1, and IPL 98/193) with longer root length and high DRW were identified with stable performance over the years. Relationship of root traits with seed yield under rainfed conditions was non-significant in our study. The SPAD value (chlorophyll content) showed significantly positive correlation with DRW (r = 0.45**) and root length (r = 0.44**) and thus can be used as selection criterion for phenotyping root traits which are otherwise difficult to measure in the field. In drought-prone environments, early flowering and maturity, seedling vigour, and high SPAD value, biological yield, and harvest index were identified as key traits for higher seed yield in lentil. Our results revealed significant genetic variability for these traits in lentil germplasm. Indian genotypes adapted to rainfed conditions were shown to have longer roots and higher DRW. The three genotypes (DPL 53, JL 1, and IPL 98/193) identified with superior root traits either originated from or have in their ancestries at least one parent adapted to rainfed conditions. These genotypes can be utilised for the development of mapping populations to identify QTLs associated with these traits for marker-assisted breeding of drought-tolerant, high-yielding varieties of lentil.

Chickpea (Cicer arietinum L.) is known to be sensitive to many herbicides and, therefore, choices for using post-emergence herbicides for weed control are limited. The present study was aimed at identifying sources of tolerance to two herbicides with different modes of action (imazethapyr—amino acid synthesis inhibitor; and metribuzin—photosynthesis inhibitor) for use in breeding herbicide tolerant cultivars. Screening of 300 diverse chickpea genotypes (278 accessions from the reference set and 22 breeding lines) revealed large genetic variations for tolerance to herbicides imazethapyr and metribuzin. In general, the sensitivity of the genotypes to metribuzin was higher compared to that for imazethapyr. Several genotypes tolerant to metribuzin (ICC 1205, ICC 1164, ICC 1161, ICC 8195, ICC 11498, ICC 9586, ICC 14402 ICC 283) and imazethapyr (ICC 3239, ICC 7867, ICC 1710, ICC 13441, ICC 13461, ICC 13357, ICC 7668, ICC 13187) were identified, based on average herbicide tolerance scores from two experimental locations each. The herbicide tolerant lines identified in this study will be useful resources for development of herbicide tolerant cultivars and for undertaking genetic and physiological studies on herbicide tolerance in chickpea

Genetic diversity was studied among 21 accessions of lentil using SSR markers and morphological traits in order to assess the diversification of Indian gene-pool of lentil through introgression of exotic genes and introduction of germplasm. Among these , 16 genotypes either had 'Precoz' gene, an Argentine line in their pedigree or genes from introduced lines from ICARDA. Sixty five SSR markers and eight phenotypic traits were used to analyse the level of genetic diversity in these genotypes. Forty three SSR markers (66 %) were polymorphic and generated a total of 177 alleles with an average of 4.1 alleles per SSR marker. Alleles per marker ranged from 2 to 6. The polymorphic information content ranged 0.33 to 0.80 with an average of 0.57, suggesting that SSR markers are highly polymorphic among the studied genotypes. Genetic dissimilarity based a dendrogram grouped these accessions into two main clusters (cluster I and cluster II) and it ranged 33 % to 71 %, suggesting high level of genetic diversity among the genotypes. First three components of PCA based morphological traits explained higher variance (95.6 %) compared to PCA components based on SSR markers (42.7 %) of total genetic variance. Thus, more diversity was observed for morphological traits and genotypes in each cluster and sub-cluster showed a range of variability for seed size, earliness, pods/plant and plant height. Molecular and phenotypic diversity analysis thus suggested that use of germplasm of exotic lines have diversified the genetic base of lentil germplasm in India. This diversified gene-pool will be very useful in the development of improved varieties of lentil in order to address the effect of climate change, to adapt in new cropping systems niches such as mixed cropping, relay cropping, etc. and to meet consumers' preference.

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