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Key message We identified markers associated with GRD resistance after screening an Africa-wide core collection across three seasons in Uganda Abstract Groundnut is cultivated in several African countries where it is a major source of food, feed and income. One of the major constraints to groundnut production in Africa is groundnut rosette disease (GRD), which is caused by a complex of three agents: groundnut rosette assistor luteovirus, groundnut rosette umbravirus and its satellite RNA. Despite several years of breeding for GRD resistance, the genetics of the disease is not fully understood. The objective of the current study was to use the African core collection to establish the level of genetic variation in their response to GRD, and to map genomic regions responsible for the observed resistance. The African groundnut core genotypes were screened across two GRD hotspot locations in Uganda (Nakabango and Serere) for 3 seasons. The Area Under Disease Progress Curve combined with 7523 high quality SNPs were analyzed to establish marker-trait associations (MTAs). Genome-Wide Association Studies based on Enriched Compressed Mixed Linear Model detected 32 MTAs at Nakabango: 21 on chromosome A04, 10 on B04 and 1 on B08. Two of the significant markers were localised on the exons of a putative TIR-NBS-LRR disease resistance gene on chromosome A04. Our results suggest the likely involvement of major genes in the resistance to GRD but will need to be further validated with more comprehensive phenotypic and genotypic datasets. The markers identified in the current study will be developed into routine assays and validated for future genomics-assisted selection for GRD resistance in groundnut.

Peanut (Arachis hypogaea L.) yield and financial returns are often low for smallholder farmers in Ghana. Additionally, aflatoxin concentration in foods derived from peanut can be high enough to adversely affect human health. Eight experiments were conducted in 2016 and 2017 in northern Ghana to compare yield, financial returns, pest reaction, and aflatoxin contamination at harvest with traditional farmer versus improved practices. Relative to the farmer practice, the improved practice consisted of weeding one extra time, applying local potassium-based soaps to suppress arthropods and pathogens, and application of either homogenized oyster shells or a commercial blend of fertilizer containing calcium. Each of these field treatments were followed by either drying peanut on the soil surface and storing in traditional poly bags or drying peanut on tarps and storing in hermetically-sealed bags for 4 months. Peanut yield and financial returns were significantly greater when a commercial blend of fertilizer or oyster shells were applied compared to the farmer practice of not applying any fertilizer. Yield and financial returns were greater when a commercial fertilizer blend was applied compared with oyster shells. Severity of early leaf spot [caused by Passalora arachidicola (Hori) U. Braun] and late leaf spot [caused by Nothopassalora personata (Berk. & M.A. Curtis) U. Braun, C. Nakash., Videira & Crous], scarring and penetration of pods by arthropods, and the number of arthropods at harvest were higher for the farmer practice than for either fertility treatment; no difference was noted when comparing across fertility treatments. Less aflatoxin was observed for both improved practices in the field compared with the farmer practice. Drying peanut on tarps resulted in less aflatoxin compared to drying peanut on the ground regardless of treatments in the field. Aflatoxin concentration after storage was similar when comparing post-harvest treatments of drying on soil surface and storing in poly bags vs. drying on tarps and storing in hermetically-sealed bags. These results demonstrate that substantial financial gain can be realized when management in the field is increased compared with the traditional farmer practice. While aflatoxin concentrations differed between the farmer practice and the improved practices at harvest and after drying, these differences did not translate into differences after storage.

Aflatoxin in peanut (Arachis hypogaea L.) and other crops can negatively affect human health, especially in countries where regulatory agencies do not have limits on aflatoxin entering the food supply chain. While considerable research has been conducted addressing aflatoxin contamination in peanut at individual steps in the supply chain, studies that quantify aflatoxin contamination following combinations of interventions to crop management, drying, and storage are limited. Research was conducted during 2016 and 2017 in two villages in southern Ghana to follow aflatoxin contamination along the supply chain and to compare improved practices with traditional farmer practices used by smallholders. The farmer practice of only a single weeding was compared with improved practices during the growing season up to harvest that included applying local soaps to suppress aphids (Aphis gossypii Golver) that transmit peanut rosette virus disease (Umbravirus: Tombusviridaee), one additional weeding, and calcium applied at pegging. The improved practice for drying included placing pods removed from plants onto tarps compared with the traditional practice of drying on the ground. Storing peanut for four months in hermetically-sealed bags was the improved practice compared with storing in traditional poly bags. All improved practices individually resulted in lower aflatoxin contamination as compared to the farmer practices. While aflatoxin levels were very low (

New technologies combined with improved genetics and farmer access are important components required to improve productivity and efficiencies of cropping systems. The ability of the public and private sector to provide these components to farmers often vary considerably and can be challenging because of limited resource allocation and investment in institutions designed to provide these services. Partnerships among national programs where resources are limited and external entities can provide an effective platform to deliver improved cultivars and production and pest management practices that increase crop yield and economic viability of resource-poor farmers. In this note, we describe a partnership between the Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI) in Ghana, the International Center for Research in the Semi-Arid Tropics (ICRISAT), the US Agency for International Development Peanut Collaborative Research Support Program (USAID Peanut CRSP), the Feed the Future Innovation Lab on Peanut Productivity and Mycotoxin Control (PMIL), and North Carolina State University (NCSU) that resulted in the release of two ICRISAT-derived lines as cultivars to farmers in Ghana. The cultivars Otuhia (Arachis hypogaea L.) and Yenyawoso (Arachis hypogaea L.) were released by CSIR-CRI in 2012 following evaluations of breeding lines beginning in 1999. This case study provides insight into the research focus and timeline that occurred with this partnership during the research and development process. A portion of the data obtained to support release of these cultivars is provided.

Groundnut (Arachis hypogaea L.) is an important cash crop in the lowland areas of Ethiopia. However, prevalence of Aspergillus invasions and subsequent aflatoxin contamination compromises the quality of groundnut kernels. This study was conducted to evaluate the effect of farm yard manure (FYM) and seed treatments against Aspergillus species pod colonization and aflatoxin accumulation under field conditions. The inhibitory efficacy of Trichoderma species as biocontrol agents was also assessed. A total of 20 treatment combinations including pre-planting applications of FYM at 0, 2.5, 5, and 7.5 tons/ha and seed treatments with carbendazim at 2 g/kg and mancozeb at 3 g kg-1, and Trichoderma harzianum and Trichoderma viride each at 5 g/kg as well as untreated seed as control were used. Treatments were laid out in a randomized complete block design (RCBD) in three replications. The experiment was conducted in two consecutive seasons (2014 and 2015) at Babile Haramaya University sub-Research Station. The highest pod and seed yields (1901.5 and 1281.5 kg/ha, respectively) were recovered from plots treated with T. harzianum at 5 g/kg seed. A. flavus was abundantly recorded in control plots, which could be responsible for the high aflatoxin B1 (5704.4 µg/kg) and B2 (2219.0 µg/kg) contamination. However, plots treated with T. harzianum at 5 g/kg seed and FYM at 5 tons/ha + T. harzianum at 5 g/kg were free from aflatoxin. Integrations of T. harzianum as biocontrol seed treatment and soil amendment with FYM were effective in the pre-harvest management of Aspergillus spp. and aflatoxins contamination. Key words: Aflatoxin, Aspergillus, carbendazim, farm yard manure, groundnut, mancozeb, Trichoderma species.

An indirect, passive, wooden dryer, with a galvanized steel panel (4.5 m2) and four wire mesh shelves (2.62 m2 each), was constructed in Kumasi, Ghana. The dryer was evaluated for its capacity in drying of freshly-harvested in-shell peanuts on a single layer (8.5 Kg), and then up-scaled to four layers (4x18 Kg). Equal amounts of peanuts, dried simultaneously on a concrete floor under the open sun, served as comparisons. The moisture content of solar dried peanuts decreased from 35.85-5.25% and 32.00 %-4.25% in the single-layer and four-layer drying, respectively, in 4 days. Faster drying rates were observed when peanuts had relatively higher moisture contents with R2 values ranging from 0.72-0.95. The average daily solar radiation ranged from 360-592.99 W/m2 and daily energies generated were from 42.24-69.16 MJ. The drying efficiency ranged from 1.50-6.47% in the single-layer drying and 23.07-24.93% in the four-layer drying whereas the thermal efficiency was 3.15-21.60% in the single-layer drying and 3.08-24.93% in the four-layer drying. Peanuts from the solar dryer had lower free fatty acid and peroxide values but higher germination percentage compared to open sundried peanuts. The study suggests that solar drying can be used effectively for improving peanut safety and preserving peanut quality in Ghana.

This study was conducted to assess major Aspergillus species and aflatoxins associated with groundnut seeds and cake in Eastern Ethiopia and evaluate growers’ management practices. A total of 160 groundnut seed samples from farmers’ stores and 50 groundnut cake samples from cafe and restaurants were collected. Fungal isolation was done from groundnut seed samples. Aspergillus flavus was the dominant species followed by Aspergillus parasiticus. Aflatoxin analyses of groundnut seed samples were performed using ultra performance liquid chromatography; 22.5% and 41.3% of samples were positive, with total aflatoxin concentrations of 786 and 3135 ng g−1 from 2013/2014 and 2014/2015 samples, respectively. The level of specific aflatoxin concentration varied between 0.1 and 2526 ng g−1 for B2 and B1, respectively. Among contaminated samples of groundnut cake, 68% exhibited aflatoxin concentration below 20 ng g−1, while as high as 158 ng g−1 aflatoxin B1 was recorded. The study confirms high contamination ...

A consumer survey was conducted to identify the factors that influence food choices in Malawi. Consumer segments were also identified and characterized based on the determined food choice motives and the consumers' demographic and socioeconomic data. Using a Food Choice Questionnaire (FCQ) it was determined that mood, health, price and preparation convenience, sensory appeal, and familiarity were the main factors influencing food choices of Malawian consumers. However, other factors are also influencing food choices in Malawi that were not revealed by the FCQ. Unlike in most affluent societies, the sensory appeal of food was not the most dominant food choice motive in Malawi. In general, the factor structure and factor ranking were different from those found in developing countries as hypothesized. Four consumer clusters emerged, comprising 33%, 30%, 24%, and 13% of the sample and the consumers' demographic and socioeconomic profiles had a significant effect (p

Peanuts are a valuable source of nutrients, but peanut consumption patterns, consumption frequencies, and the factors influencing peanut consumption in Malawi are not known. This study surveyed consumers to fill this knowledge gap and to assess Malawian consumers&rsquo, readiness to try new food products. Out of the 489 respondents surveyed, all but three consumed peanuts (in any form). The majority (70.4%) consumed peanuts at least three times in a week. Chi-square test showed that demographic and socioeconomic variables had significant effects (p &lt, 0.05) on peanut product preferences, the frequency of peanut consumption, and readiness to try new foods. For instance, women mostly preferred peanut flour compared to men, and peanut butter was the most preferred form for younger consumers. Logistic regression analysis showed that consumers with high school education or below were 2.35 times more likely to eat peanuts more often than consumers with post high school education. Among the participants that were ready to try new foods (54%), men and those with post high school education were 1.90 and 2.74 times more likely to try new foods than their respective counterparts. In general, the diversity of peanut products on the Malawian market is limited, and socioeconomic restrictions override consumer preferences. Therefore, future peanut-based food products innovations should explore ways to overcome such restrictions.

More than 400 million people in the developing world depend on dryland agriculture for their livelihoods. Dryland agriculture involves a complex combination of productive components: staple crops, vegetables, livestock, trees and fish interacting principally with rangeland, cultivated areas and watercourses. Managing risk and enhancing productivity through diversification and sustainable intensification is critical to securing and improving rural livelihoods. The main biophysical constraints are natural resource limitations and degradation, particularly water scarcity and encroaching desertification. Social and economic limitations, such as poor access to markets and inputs, weak governance and lack of information about alternative production technologies also limit the options available to farmers. Past efforts to address these constraints by focusing on individual components have either not been successful or are now facing a declining rate of impact, indicating the need for new integrated approaches to research for development of dryland systems. This article outlines the characteristics of such an approach, integrating agro-ecosystem and livelihoods approaches and presents a range of empirical examples of its application in dryland contexts. The authors draw attention to new insights about the design of research required to accelerate impact by integrating across disciplines and scales.

Groundnut (Arachis hypogaea L.) is an important food and cash crop grown mainly in semi-arid tropics (SAT) regions of the world where drought is the major constraint on productivity. With the aim of understanding the genetic basis and identification of quantitative trait loci (QTL) for drought tolerance, two new recombinant inbred line (RIL) mapping populations, namely ICGS 76 × CSMG 84-1 (RIL-2) and ICGS 44 × ICGS 76 (RIL-3), were used. After screening of 3,215 simple sequence repeat (SSR) markers on the parental genotypes of these populations, two new genetic maps were developed with 119 (RIL-2) and 82 (RIL-3) SSR loci. Together with these maps and the reference map with 191 SSR loci based on TAG 24 × ICGV 86031 (RIL-1), a consensus map was constructed with 293 SSR loci distributed over 20 linkage groups, spanning 2,840.8 cM. As all these three populations segregate for drought-tolerance-related traits, a comprehensive QTL analysis identified 153 main effect QTL (M-QTL) and 25 epistatic QTL (E-QTL) for drought-tolerance-related traits. Localization of these QTL on the consensus map provided 16 genomic regions that contained 125 QTL. A few key genomic regions were selected on the basis of the QTL identified in each region, and their expected role in drought adaptation is also discussed. Given that no major QTL for drought adaptation were identified, novel breeding approaches such as marker-assisted recurrent selection (MARS) and genomic selection (GS) approaches are likely to be the preferred approaches for introgression of a larger number of QTL in order to breed drought-tolerant groundnut genotypes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9660-0) contains supplementary material, which is available to authorized users.

A chickpea simple sequence repeat (SSR) marker reference kit has been developed based on the genotyping of the global chickpea composite collection (3,000 accessions) with 35 SSR markers. The kit consists of three pools of chickpea accessions along with supporting documentation on the SSR markers, polymerase chain reaction and detection conditions, and the expected allele sizes for each of the 35 SSR loci. These markers were selected based on quality criteria, genome coverage and locus-specific information content. Other important SSR selection criteria were quality of amplification products, locus complexity, polymorphism information content and well-dispersed location on a chickpea genetic map. The developed SSR kit has a wide range of applications, especially for genetic diversity studies in chickpea. Using the markers and reference accessions in the kit, scientists in other laboratories will be able to compare the genotypic data that they obtain for their germplasm with that obtained using the global composite collection.

In recent years, Pongamia has been considered as important renewable source of biodiesel, however not much molecular information is available in this species. Molecular characterization of this legume tree will enhance our understanding in improving the optimal yields of oil through breeding and enable us to meet the future demands for biodiesel. To assess the molecular genetic diversity in 46 Pongamia pinnata accessions collected from six different states of India, amplified fragment length polymorphism (AFLP) marker system was employed. Five AFLP primer combinations produced 520 discernible fragments, of which 502 (96.5%) were polymorphic. AFLP primer informativeness was estimated evaluating four parameters namely polymorphism information content (PIC), effective multiplex ratio (EMR), marker index (MI) and resolving power (RP). In total, 51 unique fragments were detected of which 19 unique fragments were observed with primer combination E-ACG / M-CTA. Although neighbour joining (NJ) method did not group accessions strictly according to their region of collection, a good level of genetic diversity was observed in examined germplasm. However, accessions collected from Karnataka showed comparatively higher diversity than accessions from other states. The diverse accessions identified in this study may be useful in Pongamia pinnata improvement to meet the future demands of biodiesel.

With an objective to expand the repertoire of molecular markers in pigeonpea (Cajanus cajan), 36 microsatellite or simple sequence repeat (SSR) loci were isolated from a SSR-enriched genomic library. Primer pairs were designed for 23 SSR loci, of which 16 yielded amplicons of expected size. Thirteen SSR markers were polymorphic amongst 32 cultivated and eight wild pigeonpea genotypes representing six Cajanus species. These markers amplified a total of 72 alleles ranging from two to eight alleles with an average of 5.5 alleles per locus. The polymorphic information content for these markers ranged from 0.05 to 0.55 with an average of 0.32 per marker. Phenetic analysis clearly distinguished all wild species genotypes from each other and from the cultivated pigeonpea genotypes. These markers should be useful for genome mapping, trait mapping, diversity studies and assessment of gene flow between populations in pigeonpea.

In order to maximize polymorphism in the mapping populations for mapping loci for Fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea, a set of 32 pigeonpea lines were screened for polymorphism with 30 microsatellite or simple sequence repeat markers. A total of 23 marker loci showed polymorphism with 2–4 alleles and the polymorphism information content for these markers ranged from 0.12 to 0.65 with an average of 0.43 per marker. High number of polymorphic markers, higher genetic dissimilarity coefficient and contrasting phenotypic data taken into consideration and five parental combinations were identified and crosses initiated for developing five genetically diverse mapping populations. Of these crosses, one cross segregates for FW resistance, two for SMD resistance and the remaining two crosses segregate for resistance to both FW and SMD. Development of mapping populations is in progress for mapping loci for resistance to FW and SMD in pigeonpea.

A set of 22 pearl millet inbred lines including the parents of eleven mapping populations, was screened with 627 markers including 100 pearl millet genomic SSRs (gSSRs), 60 pearl millet EST-SSRs (eSSRs), 410 intron sequence haplotypes (ISHs), and 57 exon sequence haplotypes (ESHs). In all, 267 (59%) of the markers were informative for at least one of the 11 mapping populations, which segregate for traits like drought and salinity tolerance; host plant resistance to downy mildew, rust and blast; fertility restoration and sterility and maintenance of cytoplasmic male sterility etc. An average of 116 polymorphic markers was identified per mapping population. The average PIC values and number of profiles (P) per polymorphic marker were: gSSRs (PIC = 0.62, P = 6.1), ISHs (PIC = 0.39, P = 2.6), eSSRs (PIC = 0.36, P = 3.1) and ESHs (PIC = 0.35, P = 3.1). A high correlation (r > 0.97, P

There are only a few reports of successful crosses between cultivated peanut (Arachis hypogaea L., section Arachis) and wild species from sections other than section Arachis. Many of the wild Arachis species harbor important traits necessary for the improvement of peanut. For example, Arachis kretschmeri Krapov., W.C. Gregory & C.E. Simpson (section Procumbentes) can grow under water-logged conditions and has been identified as one of the few wild species of Arachis with resistance to late leaf spot (LLS) and peanut rosette disease. Peanut rosette, caused by a combination of viruses, is an economically important disease only in Africa, while LLS, caused by Cercosporidium personatum, is an important fungal disease in Asia and the Americas as well as Africa. Interspecific hybrids between A. hypogaea and A. kretschmeri were produced by applying growth regulators to pollinated pistils and hybrid plants were obtained by germinating embryos in vitro. A total of seven hybrids were produced and confirmed by Simple Sequence Repeat (SSR) analysis. All hybrids were fertile, although initially slow growing. F1 hybrids were backcrossed to A. hypogaea and all plants in the F1BC1 generation were single-seeded with a prominent beak, characteristic of A. kretschmeri, but many of the F1BC2 pods were double-seeded resembling A. hypogaea. F1BC2 plants were moderately resistant to LLS. When a large number of seeds are obtained, the progeny will be screened for resistance to both LLS and rosette disease. Thus crosses with species outside the section Arachis may not only confer disease resistance but will also broaden the genetic base of cultivated peanut.

Contact: fax: +91 40 30713074/30713075. E-mail address: r.k.varshney@cgiar.org; International audience; The transcription factor, DREB2A, is one of the promising candidate genes involved in dehydration tolerance in crop plants. In order to isolate DREB2A homologues across cereals (rice, barley and sorghum) and legumes (common bean and chickpea), specific or degenerate primers were used. Gene/phylogenetic trees were constructed using a non-redundant set of 19 DREB1A and 27 DREB2A amino acid sequences and were combined with taxonomic/species tree to prepare reconciled phylogenetic trees. In total, 86 degenerate primers were designed for different clades and 295 degenerate primer combinations were used to amplify DREB homologues in targeted crop species. Successful amplification of DREB2A was obtained in case of sorghum. In parallel, gene-specific primers were used to amplify DREB2A homologues in rice, barley, common bean and chickpea. Seven to eight diverse genotypes from targeted species were used for sequence analysis at DREB2A locus identified/isolated. A maximum of eight SNPs were found in the common bean DREB2A, indicating two distinct haplotypes, three SNPs with five haplotypes were observed in barley whereas a single SNP was observed in rice, sorghum and chickpea. Parsimony based phylogenetic tree revealed distinct clustering of cereals and legumes. Furthermore, alignment of corresponding amino acid sequences showed conservation of AP2 domain across the targeted species.

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.

Many of the world's most important food legumes are grown in arid and semi-arid regions of Africa and Asia, where crop productivity is hampered by biotic and abiotic stresses. Until recently, these crops have also suffered from a dearth of genomic and molecular-genetic resources and thus were 'orphans' of the genome revolution. However, the community of legume researchers has begun a concerted effort to change this situation. The driving force is a series of international collaborations that benefit from recent advances in genome sequencing and genotyping technologies. The focus of these activities is the development of genome-scale data sets that can be used in high-throughput approaches to facilitate genomics-assisted breeding in these legumes.

The International Maize and Wheat Improvement Center (CIMMYT) aims to genetically enhance both crops and generate public sector-provided products for the resource poor, e.g., drought tolerant wheat and insect resistant maize, and through international-national partnerships facilitate the acquisition of improved germplasm for non-mandate crops in the cropping systems where maize and wheat thrives; e.g., GM-papaya through a national food security undertaking in Bangladesh. The Center also engages in public awareness campaigns in projects such as Insect Resistance Maize for Africa (IRMA), which includes food, feed and environmental safety, monitoring of resistance and establishment of refugia, non-target effects and gene flow. Monitoring of genetic resources is a wide concern among the centers of the Consultative Group on International Agricultural Research (CGIAR), with an emphasis on the quality of gene banks. Decisions, policies and procedures about monitoring should be science-based, and this requires education, an area where CIMMYT and other CGIAR centers can play an important role. There will be a need to continue to evaluate the need for, and type of monitoring, as new (and unique) products are developed and released in the emergent economies of the world.

Salinity is an ever-increasing problem in agriculture worldwide, especially in South Asia (India, Pakistan) and Australia. Improved genotypes that are well adapted to saline conditions are needed to enhance and sustain production in these areas. A screening of 263 accessions of chickpea, including 211 accessions from ICRISAT's mini-core collection (10% of the core collection and 1% of the entire collection), showed a 6-fold range of variation for seed yield under salinity (1.9 L of 80 mM NaCl per 7.5 kg Vertisol), with several genotypes yielding 20% more than a previously released salinity tolerant cultivar. The range of variation in yields under salinity was similar in both kabuli and desi chickpeas, indicating that breeding for salinity tolerance can be undertaken in both groups. A strong relationship ( r 2 = 0.50) was found between the seed yield under salinity and the seed yield under a non-saline control treatment, indicating that the seed yield under salinity was explained in part by a yield potential component and in part by salinity tolerance per se . Seed yields under salinity were therefore computed to separate the yield potential component from the residuals that accounted for salinity tolerance per se . Among the genotypes evaluated, desi genotypes had higher salinity tolerance than kabuli genotypes. The residuals were highly correlated to the ratio of seed yield under salinity to that of the control, indicating that both parameters can be used to assess salinity tolerance. A similar ratio was calculated for shoot dry weight at 50 days after sowing. However, no significant correlation was found between the shoot dry weight ratio and the yield ratio, indicating that differences in salinity tolerance among genotypes could not be inferred from measurements in the vegetative stage. The major trait related to salinity tolerance was the ability to maintain a large number of filled pods, whereas seed size was similar in tolerant and sensitive genotypes. Salinity tolerance was not related to the shoot Na + or K + concentrations.

Pigeonpea is a major legume of the semi-arid tropics that has been neglected in terms of molecular breeding. The objectives of this study were to develop microsatellite markers and evaluate their potential for use in pigeonpea genetics and breeding. Two hundred and eight microsatellite loci were isolated by screening a non-enriched partial genomic library. Primers were designed for 39 microsatellite loci, 20 of which amplified polymerase chain reaction products of the expected size. Nineteen of the primer pairs were polymorphic amongst 15 cultivated and nine wild pigeonpea accessions providing evidence for cross-species transferability within the genus Cajanus. A total of 98 alleles were detected at the 19 polymorphic loci with an average of 4.9 alleles per locus. The observed heterozygosity ranged from 0.17 to 0.80 with a mean of 0.42 per locus. Less allelic variation (31 alleles) was observed within the cultivated species than across the wild species (92 alleles). The diversity analysis readily distinguished all wild relatives from each other and from the cultivated germplasm. Development of more microsatellites is recommended for future genomic studies in pigeonpea.

Recent advances in cereal genomics have made it possible to analyse the architecture of cereal genomes and their expressed components, leading to an increase in our knowledge of the genes that are linked to key agronomically important traits. These studies have used molecular genetic mapping of quantitative trait loci (QTL) of several complex traits that are important in breeding. The identification and molecular cloning of genes underlying QTLs offers the possibility to examine the naturally occurring allelic variation for respective complex traits. Novel alleles, identified by functional genomics or haplotype analysis, can enrich the genetic basis of cultivated crops to improve productivity. Advances made in cereal genomics research in recent years thus offer the opportunities to enhance the prediction of phenotypes from genotypes for cereal breeding.

Leaf and stripe rusts, caused by Puccinia triticina and P. striiformis, respectively, are globally important fungal diseases of wheat that cause significant annual yield losses. A gene that confers slow rusting resistance to leaf rust, designated as Lr46, has recently been located on wheat chromosome 1B. The objectives of our study were to establish the precise genomic location of gene Lr46 using molecular approaches and to determine if there was an association of this locus with adult plant resistance to stripe rust. A population of 146 F5 and F6 lines produced from the cross of susceptible ‘Avocet S’ with resistant ‘Pavon 76’ was developed and classified for leaf rust and stripe rust severity for three seasons. Using patterns of segregation for the two diseases, we estimated that at least two genes with additive effects conferred resistance to leaf rust and three to four genes conferred resistance to stripe rust. Bulked segregant analysis and linkage mapping using amplified fragment length polymorphisms with the ‘Avocet’ × ‘Pavon 76’ population, F3 progeny lines of a single chromosome recombinant line population from the cross ‘Lalbahadur’ × ‘Lalbahadur (Pavon 1B)’, and the International Triticeae Mapping Initiative population established the genomic location of Lr46 at the distal end of the long arm of wheat chromosome 1B. A gene that is closely linked to Lr46 and confers moderate levels of adult plant resistance to stripe rust is identified and designated as Yr29.

New light shed on the risk premium of stocks over long U.S. Treasury bonds indicates that most research has overstated the advantages of stocks over bonds. Over long periods, bonds have actually outperformed equities. Certain conditions are found to have likely produced these results.

Background The genus Arachis, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the Arachis species are diploids (2n = 2x = 20) and the tetraploid species (2n = 2x = 40) are found in sections Arachis, Extranervosae and Rhizomatosae. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of Arachis by using simple sequence repeat (SSR) markers developed from Arachis hypogaea genomic library and gene sequences from related genera of Arachis. Results The average transferability rate of 101 SSR markers tested to section Arachis and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, Arachis pusilla exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (A. duranensis) and the B-genome accession ICG 8206 (A. ipaënsis) were found most closely related to A. hypogaea. Conclusion A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of Arachis, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of A. monticola and A. hypogaea as well as on the most probable donor of A and B-genomes of cultivated groundnut.

Amplified fragment length polymorphism (AFLP) was employed to assess the diversity in the elite germplasm collection of Jatropha curcas, which has gained tremendous significance as a biofuel plant in India and many other countries recently. Forty-eight accessions, collected from six different states of India, were used with seven AFLP primer combinations that generated a total of 770 fragments with an average of 110 fragments per primer combination. A total of 680 (88%) fragments showed polymorphism in the germplasm analyzed, of which 59 (8.7%) fragments were unique (accession specific) and 108 (15.9%) fragments were rare (present in less than 10% accessions). In order to assess the discriminatory power of seven primer combinations used, a variety of marker attributes like polymorphism information content (PIC), marker index (MI) and resolving power (RP) values were calculated. Although the PIC values ranged from 0.20 (E-ACA/M-CAA) to 0.34 (E-ACT/M-CTT) with an average of 0.26 per primer combination and the MI values were observed in the range of 17.60 (E-ACA/M-CAA) to 32.30 (E-ACT/M-CTT) with an average of 25.13 per primer combination, the RP was recognized the real attribute for AFLP to determine the discriminatory power of the primer combination. The RP values for different primer combinations varied from 23.11 (E-ACA/M-CAA) to 46.82 (E-ACT/M-CTT) with an average of 35.21. Genotyping data obtained for all 680 polymorphic fragments were used to group the accessions analyzed using the UPGMA-phenogram and principal component analysis (PCA). Majority of groups obtained in phenogram and PCA contained accessions as per geographical locations. In general, accessions coming from Andhra Pradesh were found diverse as these were scattered in different groups, whereas accessions coming from Chhattisgarh showed occurrence of higher number of unique/rare fragments. Molecular diversity estimated in the present study combined with the datasets on other morphological/agronomic traits will be very useful for selecting the appropriate accessions for plant improvement through conventional as well as molecular breeding approaches.

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 large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.

Simple sequence repeats (SSRs) or microsatellites are an important class of molecular markers for genome analysis and plant breeding applications. In this paper, the SSR distributions within ESTs from the legumes soybean (Glycine max, representing 135.86 Mb), medicago (Medicago truncatula, 121.1 Mb) and lotus (Lotus japonicus, 45.4 Mb) have been studied relative to the distributions in cereals such as sorghum (Sorghum bicolor, 98.9 Mb), rice (Oryza sativa, 143.9 Mb) and maize (Zea mays, 183.7 Mb). The relative abundance, density, composition and putative annotations of di-, tri-, tetra- and penta-nucleotide repeats have been compared and SSR containing ESTs (SSR-ESTs) have been clustered to give a non-redundant set of EST-SSRs, available in a database. Further, a subset of such candidate EST-SSRs from sorghum have been tested for their ability to detect polymorphism between Striga-susceptible, stay-green drought tolerant mapping population parent 'E 36-1' and its Striga-resistant, non-stay-green counterpart 'N13'. Primer sets for 64% of the EST-SSRs tested produced a clear and specific PCR product band and 34% of these detected scorable polymorphism between the N13 and E 36-1 parental lines. Over half of these markers have been genotyped on 94 RILs from the (N13 x E 36-1)-based mapping population, with 42 markers mapping onto the ten sorghum linkage groups. This establishes the value of this database as a resource of molecular markers for practical applications in cereal and legume genetics and breeding. The primer pairs for non-redundant EST-SSRs have been designed and are freely available through the database (http://intranet.icrisat.org/gt1/ssr/ssrdatabase.html).

A minimal requirement to initiate a comparative genomics study on plant responses to abiotic stresses is a dataset of orthologous sequences. The availability of a large amount of sequence information, including those derived from stress cDNA libraries allow for the identification of stress related genes and orthologs associated with the stress response. Orthologous sequences serve as tools to explore genes and their relationships across species. For this purpose, ESTs from stress cDNA libraries across 16 crop species including 6 important cereal crops and 10 dicots were systematically collated and subjected to bioinformatics analysis such as clustering, grouping of tentative orthologous sets, identification of protein motifs/patterns in the predicted protein sequence, and annotation with stress conditions, tissue/library source and putative function. All data are available to the scientific community at http://intranet.icrisat.org/gt1/tog/homepage.htm. We believe that the availability of annotated plant abiotic stress ortholog sets will be a valuable resource for researchers studying the biology of environmental stresses in plant systems, molecular evolution and genomics.

Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/gt-bt/lims/lims.asp.

While the rate of increase in the world’s population is decreasing, up to two hundred people are still being added to the planet every minute. Over 90% of the increase is in developing countries (Swaminathan, 1995). It is forecast that by the year 2050, the world’s population may increase to over 8 billion people. To feed this population, these people will require a staggering increase in food production. It has been estimated that the world will need to produce more than twice as much food during the next 50 years as was produced since the beginning of agriculture 10,000 years ago!

Background Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. Results The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection. Conclusion The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.

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.

Local lesion formation on plant leaves can result from physiological stress, wounding or disease. The lesions are often diagnostic for the factor which promoted lesion formation. For example, the lesion size, shape and pattern of spread on particular genotypes are used as identification criteria for many plant diseases. In this paper we will discuss a class of mutations of maize called disease lesion mimics. These mutations promote the production of discrete leaf lesions in the absence of obvious stress, wounding or disease on the plant. As found in authentic disease and stress responses, lesion mimic expression depends on the plant genotype and environmental conditions. We propose that the disease lesion mimic mutations of maize provide a simplified system for the study of plant response to disease and stress. Using the disease lesion mimics it is possible to study the plant response and lesion formation without the causative agent present.

A nomograph is presented which has proved to be useful in calculations related to the design of high-energy particle accelerators. Rest mass is given in the range from 0.0001 to 100 atomic mass units with the energy equivalent of this mass in electron volts. The final velocity and mass of the particle are given for a range of energies from 5000 to 1015 electron volts. The equation for particle velocity is given in the form ?/c = [1 - 1/(1 + E/E0)2]?, where E is the particle energy and E0 is the energy equivalent of its rest mass. The frequency required for operation of a proton synchrotron is determined to illustrate the use of the nomograph.

Background Chickpea (Cicer arietinum L.), an important grain legume crop of the world is seriously challenged by terminal drought and salinity stresses. However, very limited number of molecular markers and candidate genes are available for undertaking molecular breeding in chickpea to tackle these stresses. This study reports generation and analysis of comprehensive resource of drought- and salinity-responsive expressed sequence tags (ESTs) and gene-based markers. Results A total of 20,162 (18,435 high quality) drought- and salinity- responsive ESTs were generated from ten different root tissue cDNA libraries of chickpea. Sequence editing, clustering and assembly analysis resulted in 6,404 unigenes (1,590 contigs and 4,814 singletons). Functional annotation of unigenes based on BLASTX analysis showed that 46.3% (2,965) had significant similarity (≤1E-05) to sequences in the non-redundant UniProt database. BLASTN analysis of unique sequences with ESTs of four legume species (Medicago, Lotus, soybean and groundnut) and three model plant species (rice, Arabidopsis and poplar) provided insights on conserved genes across legumes as well as novel transcripts for chickpea. Of 2,965 (46.3%) significant unigenes, only 2,071 (32.3%) unigenes could be functionally categorised according to Gene Ontology (GO) descriptions. A total of 2,029 sequences containing 3,728 simple sequence repeats (SSRs) were identified and 177 new EST-SSR markers were developed. Experimental validation of a set of 77 SSR markers on 24 genotypes revealed 230 alleles with an average of 4.6 alleles per marker and average polymorphism information content (PIC) value of 0.43. Besides SSR markers, 21,405 high confidence single nucleotide polymorphisms (SNPs) in 742 contigs (with ≥ 5 ESTs) were also identified. Recognition sites for restriction enzymes were identified for 7,884 SNPs in 240 contigs. Hierarchical clustering of 105 selected contigs provided clues about stress- responsive candidate genes and their expression profile showed predominance in specific stress-challenged libraries. Conclusion Generated set of chickpea ESTs serves as a resource of high quality transcripts for gene discovery and development of functional markers associated with abiotic stress tolerance that will be helpful to facilitate chickpea breeding. Mapping of gene-based markers in chickpea will also add more anchoring points to align genomes of chickpea and other legume species.