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Parent–offspring regression has often been used for the estimation of breeding value and narrow-sense heritability in experimental populations, particularly for diploid species with regular disomic inheritance. With polysomic inheritance, estimates of heritability based on parent–offspring regression are expected to be systematically biased, particularly when intra- and inter-generation ploidy polymorphisms occur as a result of unusual megasporogenesis. Measuring the discrepancy between true and estimated heritability has important theoretical and practical implications for the genetic improvement of plantain and bananas. In this regard, formulas were developed to describe the relationships between parental and filial generations with different ploidy states and this information was used to estimate heritability for several traits of plantains and bananas. This approach may be extended to other polysomic species with similar meiotic behaviour and ploidy polymorphism.

Association mapping through linkage disequilibrium (LD) analysis is a powerful tool for the dissection of complex agronomic traits and for the identifi cation of alleles that can contribute to the enhancement of a target trait. With the developments of high throughput genotyping techniques and advanced statistical approaches as well as the assembling and characterization of multiple association mapping panels, maize has become the model crop for association analysis. In this paper, we summarize progress in maize association mapping and the impacts of genetic diversity, rate of LD decay, population size, and population structure. We also review the use of candidate genes and gene-based markers in maize association mapping studies that has generated particularly promising results. In addition, we examine recent developments in genome-wide genotyping techniques that promise to improve the power of association mapping and signifi cantly refi ne our understanding of the genetic architecture of complex quantitative traits. The new challenges and opportunities associated with genome-wide analysis studies are discussed. In conclusion, we review the current and future impacts of association mapping on maize improvement along with the potential benefi ts for poor people in developing countries who are dependent on this crop for their food security and livelihoods.

Selective genotyping of individuals from the two tails of the phenotypic distribution of a population provides a cost efficient alternative to analysis of the entire population for genetic mapping. Past applications of this approach have been confounded by the small size of entire and tail populations, and insufficient marker density, which result in a high probability of false positives in the detection of quantitative trait loci (QTL). We studied the effect of these factors on the power of QTL detection by simulation of mapping experiments using population sizes of up to 3,000 individuals and tail population sizes of various proportions, and marker densities up to one marker per centiMorgan using complex genetic models including QTL linkage and epistasis. The results indicate that QTL mapping based on selective genotyping is more powerful than simple interval mapping but less powerful than inclusive composite interval mapping. Selective genotyping can be used, along with pooled DNA analysis, to replace genotyping the entire population, for mapping QTL with relatively small effects, as well as linked and interacting QTL. Using diverse germplasm including all available genetics and breeding materials, it is theoretically possible to develop an “all-in-one plate” approach where one 384-well plate could be designed to map almost all agronomic traits of importance in a crop species. Selective genotyping can also be used for genomewide association mapping where it can be integrated with selective phenotyping approaches. We also propose a breeding-to-genetics approach, which starts with identification of extreme phenotypes from segregating populations generated from multiple parental lines and is followed by rapid discovery of individual genes and combinations of gene effects together with simultaneous manipulation in breeding programs.

The growing demands for food, feed, and bioenergy worldwide will require a 2% per annum increase in global maize (Zea mays L.) production. Maize is one of the most important staple food crops across the developing world as well as being an important feed crop for global livestock production and the emerging biofuel industry. Maize genotypes can range from 0.5 to 5 m standing height at fl owering, mature in 60 to 330 d from planting, produce 1 to 4 ears per plant, 10 to 1800 kernels per ear and yield from 0.5 to 23.5 Mg of grain per hectare. Even greater genetic diversity is present in related species yet surprisingly little of the maizerelated biodiversity is present in the current elite breeding pools. Improved methods and tools for germplasm conservation, characterization, and data sharing, as well as for population improvement, gene pool enhancement, and genomics-aided breeding are urgently needed if increases in maize productivity, particularly in the developing world, are to keep pace with predicted increases in demand. Progress in the private sector, particularly with the development of temperate maize cultivars, is far beyond that of the public sector, particularly regarding tropical maize cultivar development. This article provides an overview of progress at the International Maize and Wheat Improvement Center (CIMMYT) with national partners across the developing world. Particular emphasis is given to issues related to the continued development of elite maize breeding material as global public goods, especially regarding the introgression of new variations from genetic resources and the legal and phytosanitary issues related to international exchange of maize germplasm. Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT), Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico. Received 7 June 2009. *Corresponding author (r.ortiz@cgiar.org).

Phytoene synthase (PSY), which is encoded by the phytoene synthase 1 (PSY1) gene, is the first rate-limiting enzyme in the plant carotenoid biosynthetic pathway. In order to examine the genetic diversity and evolution pattern of PSY1 within the Andropogoneae, sequences of 76 accessions from 5 species (maize, teosinte, tripsacum, coix, and sorghum) of the Andropogoneae were tested, along with 4 accessions of rice (Oryza sativa L.) included as outliers. Both the number and the order of exons and introns were relatively conserved across the species tested. Three domains were identified in the coding sequence, including signal peptide (SP), PSY, and highly conserved squalene synthase (SQS) domain. Although no positive selection signal was detected at an overall coding level among all species tested, the SP domain and the region upstream of the SQS–PSY domain appear to have undergone rapid evolution, as evidenced by a high d N/d S ratio (>1.0). At the nucleotide level, positive selection and balancing selection were detected only among the yellow maize germplasm and the white maize germplasm, respectively. The phylogenetic tree based on full-length sequences of PSY1-like regions supported the monophyletic theory of the Andropogoneae and the closest relationship between Zea and Tripsacum among the Andropogoneae. Coix, which was theorized to have a closer relationship with maize due to similarities in morphology and chromosome number, has been shown in this study to have diverged relatively early from the other Andropogoneae, including maize.

Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin. Temperate and tropical/subtropical germplasm clearly clustered into two separate groups. The temperate germplasm could be further divided into six groups consistent with known heterotic patterns. The greatest genetic divergence was observed between temperate and tropical/subtropical lines, followed by the divergence between yellow and white kernel lines, whereas the least divergence was observed between dent and flint lines. Long-term selection for hybrid performance has contributed to significant allele differentiation between heterotic groups at 20% of the SNP loci. There appeared to be substantial levels of genetic variation between different breeding pools as revealed by missing and unique alleles. Two SNPs developed from the same candidate gene were associated with the divergence between two opposite Chinese heterotic groups. Associated allele frequency change at two SNPs and their allele missing in Brazilian germplasm indicated a linkage disequilibrium block of 142 kb. These results confirm the power of SNP markers for diversity analysis and provide a feasible approach to unique allele discovery and use in maize breeding programs.

Maize is an important crop for food, feed, forage, and fuel across tropical and temperate areas of the world. Diversity studies at genetic, molecular, and functional levels have revealed that, tropical maize germplasm, landraces, and wild relatives harbor a significantly wider range of genetic variation. Among all types of markers, SNP markers are increasingly the marker-of-choice for all genomics applications in maize breeding. Genetic mapping has been developed through conventional linkage mapping and more recently through linkage disequilibrium-based association analyses. Maize genome sequencing, initially focused on gene-rich regions, now aims for the availability of complete genome sequence. Conventional insertion mutation-based cloning has been complemented recently by EST- and map-based cloning. Transgenics and nutritional genomics are rapidly advancing fields targeting important agronomic traits including pest resistance and grain quality. Substantial advances have been made in methodologies for genomics-assisted breeding, enhancing progress in yield as well as abiotic and biotic stress resistances. Various genomic databases and informatics tools have been developed, among which MaizeGDB is the most developed and widely used by the maize research community. In the future, more emphasis should be given to the development of tools and strategic germplasm resources for more effective molecular breeding of tropical maize products.

Ascochyta blight (AB) caused by Ascochyta rabiei, is globally the most important foliar disease that limits the productivity of chickpea (Cicer arietinum L.). An intraspecific linkage map of cultivated chickpea was constructed using an F2 population derived from a cross between an AB susceptible parent ICC 4991 (Pb 7) and an AB resistant parent ICCV 04516. The resultant map consisted of 82 simple sequence repeat (SSR) markers and 2 expressed sequence tag (EST) markers covering 10 linkage groups, spanning a distance of 724.4 cM with an average marker density of 1 marker per 8.6 cM. Three quantitative trait loci (QTLs) were identified that contributed to resistance to an Indian isolate of AB, based on the seedling and adult plant reaction. QTL1 was mapped to LG3 linked to marker TR58 and explained 18.6% of the phenotypic variance (R2) for AB resistance at the adult plant stage. QTL2 and QTL3 were both mapped to LG4 close to four SSR markers and accounted for 7.7% and 9.3%, respectively, of the total phenotypic variance for AB resistance at seedling stage. The SSR markers which flanked the AB QTLs were validated in a half-sib population derived from the same resistant parent ICCV 04516. Markers TA146 and TR20, linked to QTL2 were shown to be significantly associated with AB resistance at the seedling stage in this half-sib population. The markers linked to these QTLs can be utilized in marker-assisted breeding for AB resistance in chickpea.

Leaf collection from the field, labeling and tracking back to the source plants after genotyp- ing are rate limiting steps in leaf DNA-based genotyping. In this study, an optimized genotyping method using endosperm DNA sampled from single maize seeds was developed, which can be used to replace leaf DNA-based genotyping for both genetic studies and breeding applications. A similar approach is likely to be suitable for all plants with relatively large seeds. Part of the endosperm was excised from imbibed maize seeds and DNA extracted in 96-tube plates using individuals from eight F2 populations and seven inbreds. The quality of the resultant DNA was functionally comparable to DNA extracted from leaf tissue. Extraction from 30 mg of endosperm yields 3-10 lg DNA, which is sufficient for analysis of 200-400 agarose-gel PCR-based markers, with the potential for several million chip-based SNP marker analyses. By comparing endosperm DNA and leaf DNA for individuals from an F2 population, geno- typing errors caused by pericarp contamination and hetero-fertilization were found to average 3.8 and 0.6%, respectively. Endosperm sampling did not affect germination rates under controlled conditions, although under normal field conditions the germina- tion rate, seedling establishment, and growth vigor were significantly lower than that of non-sampled controls for some genotypes. However, careful field management can compensate for these effects. Seed DNA-based genotyping lowered costs by 24.6% compared to leaf DNA-based genotyping due to reduced field plantings and labor costs. A substantial advantage of this approach is that it can be used to select desirable genotypes before planting. As such it provides an opportunity for dramatic improvements in the efficiency and selective gain of breeding systems based on optimum combinations of marker- assisted selection and phenotypic selection within and between generations.

The volume of publications on the development and to a lesser extent the application of molecular markers in plant breeding has increased dramatically during the last decade. However, most of the publications result from investments from donors with a strategic science quality or biotech advocacy mandate leading to insufficient emphasis on applied value in plant breeding. Converting promising publications into practical applications requires the resolution of many logistical and genetical constraints that are rarely addressed in journal publications. This results in a high proportion of published markers failing at one or more of the translation steps from research arena to application domain. The rate of success is likely to increase due to developments in gene-based marker development, more efficient quantitative trait locus (QTL) mapping procedures, and lower cost genotyping systems. However, some fundamental issues remain to be resolved, particularly regarding complex traits, before marker-assisted selection realizes its full potential in public sector breeding programs. These include the development of high throughput precision phenotyping systems for QTL mapping, improved understanding of genotype by environment interaction and epistasis, and development of publicly available computational tools tailored to the needs of molecular breeding programs.

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.

Groundnut is one of the most important oilseed crops in the world. Bacterial wilt, caused byRalstonia solanacearumE. F. Smith, is one of the major biotic constraints to groundnut production particularly in South-East Asia and East Africa. Several sources of resistance to bacterial wilt have been identified through field screening of groundnut germplasm. The aim of the present study was to quantify the genetic diversity among selected bacterial wilt-resistant lines, in comparison with the levels of variation observable within the cultivatedA. hypogaeagene pool. Thirty-two SSR markers were used to assess the degree of molecular polymorphism between 46 selected genotypes revealing 107 alleles, of which 101 (99.4%) were polymorphic with gene diversity scores ranging from 0.103 to 0.669, averaging 0.386. Cluster and multidimensional scaling analysis revealed two distinct groups within the germplasm broadly corresponding to the two subspecies (hypogaeaandfastigiata) ofA. hypogaea. However, accessions of varietiesperuvianaandaequatorianagrouped together with the varieties from subsp.hypogaea, rather than grouping with the other varieties of subsp.fastigiata.Analysis of molecular variance (AMOVA) revealed that 15% of the total observed variation was accounted for by disease response groups. This analysis will be useful in the selection of parental genotypes for mapping populations and breeding programmes attempting to broaden the genetic base of future groundnut cultivars. In particular, this opens up significant opportunities for the development of intraspecific mapping populations that will be highly relevant to modern groundnut breeding programmes.

Breeders face many complex choices in the design of effi cient crossing and selection strategies aimed at combining desired alleles into a single target genotype. Both population genetic theory and a breeding simulation tool were used to study the effects of different strategies on population size and number of marker assays required to recover a target genotype in wheat (Triticum aestivum L.). Enriching the frequency of desirable alleles in the F 2 of single-cross and in the F 1 of backcross and topcross populations greatly reduced the minimum required population size, but the gain from another enrichment selection is minor. General equations were developed to determine appropriate crossing strategies, and sequential culling was proposed to minimize total marker screening costs. For a topcross of three adapted lines from an existing breeding program, simulation of changes in allele frequencies at nine target genes (seven unlinked) showed that population size was minimized with a three-stage selection strategy in the F 1 generation of the topcross (TCF 1 ), the F 2 generation of the topcross (TCF 2 ), and doubled haploid lines (DHs). Enrichment of allelic frequencies in TCF 2 reduced the total number of lines screened from >3500 to 0.97 after selection, while the tin reduced-tillering allele was only at 0.77 in the fi nal selected population due to its strong repulsion-phase linkage to the grain quality gene Glu-A3 in this cross and the incomplete linkage of the tin marker. Therefore, the presence of the tin gene needs to be further confi rmed by other methods.

The main elements of the international wheat improvement program of the Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT), also known as the International Maize and Wheat Improvement Center, have been shuttle breeding at two contrasting locations in Mexico, wide adaptation, durable rust and Septoria resistances, international multisite testing, and the appropriate use of genetic variation to enhance yield gains of subsequently produced lines. Such an approach yielded successes known collectively as the Green Revolution. However, at the beginning of the 21st century, this “cultivar assembly line” approach needs fine tuning to address crop needs under increasingly adopted resource conserving practices, as well as those related to nutritional requirements of the end-users. International wheat improvement will therefore focus on the targeting of traits in respective mega-environments, and the use of participatory methods, especially in marginal environments. The main features of this wheat improvement strategy include the introduction of new and novel sources of genetic variation through wild species, landraces, and, potentially, the use of transgenes for intractable traits. This variation will be combined using international shuttle breeding, and increased breeding efficiency will be achieved through marker-aided methods, more targeted use of crop physiology, plant genetics, biostatistics, and bioinformatics. Likewise, CIMMYT will increase its focus on the needs of end-users by emphasizing regional efforts in participatory research and client-oriented plant breeding.

Cultivated groundnut (Arachis hypogaea L.) is an agronomically and economically important oilseed crop grown extensively throughout the semi-arid tropics of Asia, Africa and Latin America. Rust (Puccinia arachidis) and late leaf spot (LLS, Phaseoisariopsis personata) are among the major diseases causing significant yield loss in groundnut. The development of varieties with high levels of resistance has been constrained by adaptation of disease isolates to resistance sources and incomplete resistance in resistant sources. Despite the wide range of morphological diversity observed in the cultivated groundnut gene pool, molecular marker analyses have thus far been unable to detect a parallel level of genetic diversity. However, the recent development of simple sequence repeat (SSR) markers presents new opportunities for molecular diversity analysis of cultivate groundnut. The current study was conducted to identify diverse disease resistant germplasm for the development of mapping populations and for their introduction into breeding programs. Twenty-three SSRs were screened across 22 groundnut genotypes with differing levels of resistance to rust and LLS. Overall, 135 alleles across 23 loci were observed in the 22 genotypes screened. Twelve of the 23 SSRs (52%) showed a high level of polymorphism, with PIC values ≥0.5. This is the first report detecting such high levels of genetic polymorphism in cultivated groundnut. Multi-dimensional scaling and cluster analyses revealed three well-separated groups of genotypes. Locus by locus AMOVA and Kruskal-Wallis one-way ANOVA identified candidate SSR loci that may be valuable for mapping rust and LLS resistance. The molecular diversity analysis presented here provides valuable information for groundnut breeders designing strategies for incorporating and pyramiding rust and late leaf spot resistances and for molecular biologists wishing to create recombinant inbred line populations to map these traits.

Chickpea is one of the most important grain legume crops in the world. Large collections of genetic resources are maintained in the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and International Center for Agricultural Research in the Dry Areas (ICARDA) genebanks. Association mapping using neutral markers has been suggested as a means to identify useful alleles in the vast reservoirs of genetic diversity existing in the germplasm collections that could be associated with the phenotypes among the population individuals. ICRISAT in collaboration with ICARDA developed a global composite collection of 3000 accessions that will be profiled using 50 polymorphic simple sequence repeat (SSR) markers. The data generated through this collaborative effort will be used to define the genetic structure of the global composite collection and to select a reference sample of 300 accessions representing the maximum diversity for the isolation of allelic variants of candidate gene associated with beneficial traits. It is then expected that molecular biologists and plant breeders will have opportunities to use diverse lines in functional and comparative genomics, in mapping and cloning gene(s), and in applied plant breeding to diversify the genetic base of the breeding populations which should lead to the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.

Conservation of crop germplasm diversity involves the establishment of in situ and ex situ genebanks. The major activities for ex situ genebanks include assembling, conserving, characterizing and providing easy access to germplasm for scientists. More than six million accessions are currently assembled in over 1300 genebanks worldwide. ICRISAT is one of the 15 CGIAR centres, with headquarters at Patancheru, India, and conserves genetic resources of sorghum, pearl millet, chickpea, pigeonpea, groundnut, and six small millets. The ICRISAT genebank holds 114,870 accessions from 130 countries, including both archival materials from various organizations throughout the world, and from fresh collections resulting from 213 missions in 62 countries. The ICRISAT genebank supplies annually over 40,000 germplasm samples to scientists worldwide. Sixty-six varieties selected from the basic germplasm have been released for cultivation in 44 countries, and ICRISAT has restored/repatriated crop germplasm to eight countries. The research focus is on germplasm diversity assessment, developing core and mini-core collections, and using a molecular characterization approach to both enhance the utilization of germplasm in research and improve the efficiency of germplasm management. Following these approaches, we have been able to identify a significant number of accessions with traits potentially relevant for crop improvement.

The importance of root systems in acquiring water has long been recognized as crucial to cope with drought conditions. This investigation was conducted to: (i) evaluate the variability on root length density (RLD) of chickpea in the vegetative growth stage; (ii) estimate the effect of RLD on seed yield under terminal drought conditions; and (iii) set up a procedure to facilitate the screening of chickpea genotypes with largeRLD. Twelvediversechickpea genotypes weregrown in tall PVC cylinders with two different soil water treatments in 2000 and 2001, and in field under water deficit conditions during 2000/2001 and 2001/2002. In field trials, the mean RLD at 35 days after sowing showed a significant positive correlation with seed yield in both years. Similarly, the RLD in the 15‐30 cm soil depth had significant positive effects to the seed yield in both years. The importance of the root trait was particularly relevant in 2001/2002, a more severe drought year, when the RLD in deeper soil layer, 30‐60 cm depth, showed a significant positive relationship with seed yield. Also, the RLD at deeper soil layer, 30‐60 cm depth, was higher in 2001/2002 than in 2000/2001, in particular in tolerant genotypes. The PVC cylinder trials were set up to facilitate the screening of chickpea genotypes with large RLD. RLD of plants grown in cylinders with 70% field capacity was correlated with RLD in the field trials (r = 0.731; p = 0.01). This work highlights the importance of roots in coping with terminal drought in chickpea. The cylinder system offers a much easier procedure to screen chickpea genotypes with large RLD. # 2005 Elsevier B.V. All rights reserved.

Cultural, morphological and pathogenic variation in Indian isolates of Ascochyta rabiei, the causal agent of blight of chickpea, was investigated. Fungal isolates representative of seven agroclimatic regions in north western plain zones (NWPZ) of India showed variation in colony colour as mouse gray with green hue, light mouse gray with slate gray centre and gray with dark brown centre, when grown on chickpea dextrose agar (CDA). Conidiomatal color of the isolates varied from brown to slate gray and black. The number of conidiomata and conidia formed on CDA ranged from 49.7 to 90.7 and , respectively. The size of conidiomata and conidia of A. rabiei isolates varied from , and from , respectively. Fourteen A. rabiei isolates from the seven agroclimatic regions of NWPZ were evaluated for their virulence on 180 chickpea genotypes in controlled environment. Cluster analysis based on the disease rating on a 1-9 scale indicated higher similarity coefficient (> 0.65) between isolates from different agroecological regions, while few isolates from the same region had less similarity. The 14 isolates were grouped into eight pathotypes at > 0.5 similarity coefficient. Sixteen genotypes were identified as probable differentials to distinguish A. rabiei isolates.

Chickpea, a lesser-studied grain legume, is being investigated due to its taxonomic proximity with the model legume genome Medicago truncatula and its ability to endure and grow in relatively low soil water contents making it a model legume crop for the study of agronomic response to drought stress. Public databases currently contain very few sequences from chickpea associated with expression in root tissues. However, root traits are likely to be one of the most important components of drought tolerance in chickpea. Thus, we have generated a set of over 2800 chickpea expressed sequence tags (ESTs) from a library constructed after subtractive suppressive hybridization (SSH) of root tissue from two closely related chickpea genotypes possessing different sources of drought avoidance and tolerance (ICC4958 and Annigeri respectively). This database provides researchers in legume genomics with a major new resource for data mining associated with root traits and drought tolerance. This report describes the development and utilization of the database and provides the tools we have developed to facilitate the bioinformatics pipeline used for analysis of the ESTs in this database. We also discuss applications that have already been achieved using this resource.

Trichoderma species offer considerable potential for controlling aflatoxin contamination in groundnut and other crops. Initial classification of 48 Trichoderma isolates, derived from four different groundnut cultivation sites in India was based on alignment of 28S rDNA sequences to GenBank sequences of ex-type strains. This was found to be substantially more reliable than our routine morphological characterization, but did not provide a comprehensive diagnostic solution, as unique single nucleotide polymorphism (SNP) haplotypes could not be identified for all species. However, all the Trichoderma isolates could be readily distinguished by amplified fragment length polymorphism (AFLP) analysis, based on six primer pair combinations, which generated 234 polymorphic bands. In addition, individual AFLP bands were identified which differentiate closely related species. Similarly, AFLP bands were identified that correlated with different types of antagonism to Aspergillus flavus. The implications of these results for the development of simple polymerase chain reaction (PCR)-based diagnostic assays for antagonistic isolates of Trichoderma is discussed.

This is the first report of targeted development of B genome microsatellite markers in Musa. A total of 44 sequences with microsatellites were isolated from an enriched library of Musa balbisiana cv. 'Tani' (BB genome). Of these, 25 were polymorphic when screened on 14 diverse diploid and triploid Musa accessions. The number of alleles detected by each marker ranged between one and seven. All 25 microsatellite markers generated amplification products in all species and genome complements. These new microsatellite markers fill an important gap for diversity assessment and linkage mapping studies in plantain (AAB) and cooking banana (ABB)

Crop biotechnology seems to be in its infancy in Africa, some national researchers are well trained in this area but lack of funding from their national governments does not allow them take advantage of their knowledge and professional skills. Among the agro-biotechnology tools, tissue culture ranks first in the micro-propagated and tree crops. DNA marker-aided breeding for a range of traits (particularly to overcome diseases and pests or low input environments) should become the second most important application of agro-biotechnology in the mid-term. Molecular markers are being used worldwide to tag specific chromosome segments bearing the desired gene(s) to be transferred (or incorporated) into breeding lines (or populations). In this way, indirect selection with co-dominant molecular markers tightly linked to the gene(s) controlling the characteristic(s) of interest improves response to selection, because heritability for co-dominant markers equals to 1. Molecular markers are therefore descriptors that offer reproducible results for characterizing genotypes. Similarly, applied plant genomics also improves the understanding of crop gene pools, which are being enlarged by including transgenes and “native” gene pools. Furthermore, finding new genes adds value to traditional agricultural products. There are many on-going applications of DNA markers in research-for-development and crop improvement for crops grown by African farmers. Marker-assisted selection and –aided introgression are being employed by private and public plant breeders mostly to locate and select genes for controlling important quality and disease or pest resistant traits. Key Words: Genomics, crops, biotechnology, breeding, Africa. African Journal of Biotechnology Vol.3(10) 2004: 489-496

Deep and prolific root systems have been associated with enhanced avoidance of terminal drought stress in chickpea. This research evaluated the root traits of 257 recombinant inbred lines (RILs) derived from a cross between a breeding line with a large root system (ICC 4958) and an agronomically preferred variety (Annigeri) to assess the potential for identifying QTL for desirable root traits and to investigate the relationship between root traits, plant growth and seed yield under terminal drought stress. The root traits of field-grown chickpea RILs were measured using the monolith method during the 2001-2002 cropping season, while their shoot biomass and seed yield were evaluated during both 2000-2001 and 2001-2002 seasons. Significant genetic variation was observed amongst the RIL population for root length density, root dry weight and shoot dry weight at 35 days after sowing and for shoot biomass and seed yield at maturity. A linear relationship was observed between root dry weight and shoot dry weight at 35 days after sowing. The overall distribution of root length density and root dry weight among the RILs indicated that these traits are likely to be under polygenic control. The heritability of root dry weight was 0.27 and root length density was 0.23, compared to 0.49 for shoot dry weight at the same stage. The RILs exhibited a range of combinations of root size and seed yield, with a few RILs showing large root systems and high seed yield. However, there was no general correlation between seed yield and root size. High shoot biomass and harvest index contributed to high seed yield of the RILs. The implications for the molecular breeding of drought-avoidance root traits in chickpea are discussed.

Transgenic resistance to insects has been demonstrated in plants expressing insecticidal genes such as δ -endotoxins from Bacillus thuringiensis (Bt), protease inhibitors, enzymes, secondary plant metabolites, and plant lectins. While transgenic plants with introduced Bt genes have been deployed in several crops on a global scale, the alternative genes have received considerably less attention. The protease inhibitor and lectin genes largely affect insect growth and development and, in most instances, do not result in insect mortality. The effective concentrations of these proteins are much greater than the Bt toxin proteins. Therefore, the potential of some of the alternative genes can only be realized by deploying them in combination with conventional host plant resistance and Bt genes. Genes conferring resistance to insects can also be deployed as multilines or synthetic varieties. Initial indications from deployment of transgenics with insect resistance in diverse cropping systems in USA, Canada, Arge...

Recombinant DNA technology offers opportunities for widening the available gene pool for crop improvement. Genetic engineering also allows the introduction of several desirable genes in a single event, and can reduce the time to introgress novel genes into elite backgrounds. Genes conferring resistance to insects have been inserted into crop plants such as cotton, maize, potato, tobacco, rice, broccoli, lettuce, walnut, apple, alfalfa, and soybean. Genetically transformed crops with Bacillus thuringiensis (Bt) genes have been deployed for cultivation primarily in the USA, China, Argentina, Canada, Mexico, South Africa, and Australia. The potential of insect-resistant transgenic plants with Bt genes can be enhanced when deployed in combination with alternate protective genes such as protease inhibitors, enzymes, and plant lectins, or in combination with insect-resistant cultivars derived through conventional breeding. While several transgenic crops with insecticidal genes have been introduced in t...

Recombinant DNA technology has significantly augmented the conventional crop improvement, and has a great promise to assist plant breeders to meet the increased food demand predicted for the 21st century. Dramatic progress has been made over the past two decades in manipulating genes from diverse and exotic sources, and inserting them into microorganisms and crop plants to confer resistance to insect pests and diseases, tolerance to herbicides, drought, soil salinity and aluminum toxicity; improved post-harvest quality; enhanced nutrient uptake and nutritional quality; increased photosynthetic rate, sugar, and starch production; increased effectiveness of biocontrol agents; improved understanding of gene action and metabolic pathways; and production of drugs and vaccines in crop plants. Despite the diverse and widespread beneficial applications of biotechnology products, there remains a critical need to present these benefits to the general public in a real and understandable way that stimulates an unbiased and responsible public debate. The development, testing and release of agricultural products generated through biotechnology-based processes should be continuously optimized based on the most recent experiences. This will require a dynamic and streamlined regulatory structure, clearly supportive of the benefits of biotechnology, but highly sensitive to the well being of humans and environment.

Genetic diversity amongst 76 plantain landraces has been studied using RAPD analysis at two levels of intensity and compared with groupings based on phenotypic indices and morphotype. There was a good correlation (R2=0.78) between estimates of genetic diversity based on 76 RAPD bands and 164 RAPD bands. However, there was a poor correlation between RAPD-based estimates of genetic diversity and a phenotypic index based on agronomic characters. There was also a poor correlation between RAPD analyses and morphotype group (based on bunch type and stature). These results suggest that the traditional designations of plantain landraces based on morphotype do not provide a true reflection of overall genetic divergence. Similarly, classification systems using phenotypic indices based on agronomic characters may not provide accurate taxonomic differentiation. The level of genetic divergence within morphogroups based on bunch type suggests that True Horn plantains are derived from False Horn plantains which in turn are derived from French plantains. Genetic divergence was found to be generally quite low within the plantain landrace genepool, which is consistent with the proposed evolution of this germplasm through somatic mutation of a relatively small number of introductions. However, putative synonyms/duplicates have been shown to be genetically distinct. In contrast, a group of 12 landraces have been identified that are highly distinct from one another (showing 20–35% dissimilarity). Fertile members of this group may be useful for generating genetically diverse 2x and 4x breeding populations that can be used in breeding secondary triploid hybrid plantain varieties.

Traditional approaches to the breeding of Musa crops are highly demanding in terms of both time and space. However, the application of molecular genetic analysis may dramatically improve breeding efficiency. The objectives of the present study were to compare pedigree and DNA marker methods of estimating genetic relationships across and within generations among diploid, triploid and tetraploid accessions of plantain and banana. Pedigree-based estimates of parent-offspring relationships were substantially different from those obtained from molecular data. The marker-based contribution of triploid maternal accessions to their diploid offspring was greater than expected from published models of meiosis in Musa. Conversely, the maternal contribution to tetraploid offspring was less than expected. Pedigree-based similarity was smallest for clones with no common parent and greatest for full-sibs. There was no association between marker-based similarity and pedigree relationships. While DNA markers may provide a more accurate description of genetic relatedness, this study suggests that pedigree-based analysis may prove useful for the selection of prospective parental combinations in Musa breeding.

Pedigree and DNA marker-based methods were used to predict the performance of triploid progeny from tetraploid-diploid crosses, based on parental heterozygosity, genetic relatedness, and expected contribution to their progeny. There was no significant correlation between parental and progeny performance. Prediction of progeny bunch weight was best when based on genealogical distance and equal parental contribution. Predicted fruit size was most accurate when DNA marker data were used and the assumption of an unequal parental contribution was made. Consideration of parental heterozygosity produced larger residuals for all traits. No statistically significant differences were found between the mean residuals obtained under the assumption of an equal vs an unequal contribution of the 4x and 2x genotypes to their 3x progeny, regardless of the method used to estimate genetic relationships.

Progress in the breeding of plantain and banana has been restricted by the complex genetic structure and behaviour of cultivated polyploid Musa. Genetic improvement has been hindered due to the large amount of space required for growth and maintenance of plant populations, in addition to the long growth cycle and the low levels of fertility and seed viability characteristic of cultivated genotypes. Molecular marker assisted breeding has the potential to dramatically enhance the pace and efficiency of genetic improvement in Musa. This study was conducted to compare different PCR-based marker systems (RAPD, VNTR and AFLP) for the analysis of breeding populations generated from two diverse Musa breeding schemes. All three assays detected a high level of polymorphism between parental genotypes and within progeny populations. As expected, AFLP assays had by far the highest multiplex ratio while VNTR analysis detected the highest levels of polymorphism. AFLP analysis of a full-sib tetraploid hybrid population confirmed previous reports based on VNTR analysis, of a high frequency of recombination during 2n (3x) gamete formation by a triploid plantain landrace. In addition, both VNTR and RAPD analyses of a full-sib triploid hybrid population suggested a high frequency of homoeologous recombination during n (2x) gamete formation by tetraploid hybrids. In general, there was a poor correlation between estimates of genetic similarity based on different types of marker. The implications of these findings for the molecular breeding of Musa crops are discussed.

The physical sites of 18S-5.8S-25S and 5S rRNA genes and telomeric sequences in theMusaL. genome were localized by fluorescentin situhybridization on mitotic chromosomes of selected lines. A single major intercalary site of the 18S-5.8S-25S rDNA was observed on the short arm of the nucleolar organizing chromosome in each genome. AA and BB genome diploids had a single pair of sites, triploids had three sites while a tetraploid hybrid had four sites. The probe is useful for quick determination of ploidy, even using interphase nuclei from slowly growing tissue culture material. Variation in the intensity of signals was observed among heterogeneousMusalines indicating variation in the number of copies of the 18S-5.8S-25S rRNA genes. Eight subterminal sites of 5S rDNA were observed in Calcutta 4 (AA) while Butohan 2 (BB) had six sites; some were weaker in both genotypes. Triploid lines showed six to nine major sites of 5S rDNA of widely varying intensity and near the limit of detection. The diploid hybrids had five to nine sites of 5S rDNA while the tetraploid hybrid had 11 sites. The telomeric sequence was detected as pairs of dots at the ends of all the chromosomes analysed but no intercalary sequences were seen. The molecular cytogenetic studies ofMusausing repetitive and single copy DNA probes should yield insight into the genome and its evolution and provide data forMusabreeders, as well as generating genetic markers inMusa.

The triploid genome of plantain (Musa spp., AA group) has been considered intractable to genetic improvement because of the producttion of putatively homogeneous 2n (= 3x ) gametes. Plantain breeding schemes have been based on the hybridization of 2n megaspores from the triploid plantain and haploid microspores from a wild diploid banana. The resultant full-sib populations of tetraploid hybrids exhibited extreme variation in phenotypic characteristics. This study was conducted to analyze the genetic constitution of tetraploid hybrids in order to characterize the nature of the gametes from which they were derived. Parental genotypes were screened with 31 primer pairs specific to different Musa microsatellite loci. Primers which detected polymorphisms between the parental genotypes were used to screen a population of 14 full-sib tetraploid hybrids A subset of primers was also used to screen a population generated by self-pollination of the parental diploid banana. During analysis of the tetraploid hybrid population, 75% of the alleles donated by the maternal genotype (Obino l'Ewai) were observed to segregate. These data demonstrate the occurrence of recombination during the formation of 2n megaspores in triploid plantain. Analysis of the paternal diploid banana accession (Calcutta 4) and its selfed progeny suggests that this accession is highly heterozygous. These data demonstrate the importance of genetic characterization to Musa breeding, and also indicate that microsatellite markers are well suited for marker-assisted selection systems in Musa.

Genome size variation occurs within and across generations in Musa spp., which reduces the predictive accuracy of parental performance on progeny value for yield and other traits with complex inheritance. Parental selection through progeny testing of prospective parents is required to achieve further genetic gains. This was carried out in this study, using a factorial mating design involving five 4x females and five 2x males. Genetic differences among offspring families were essentially due to differences in additive effects of the parents. Thus, little recombinative heterosis can be expected upon 4x-2x cross-breeding, and breeding strategies should target the development of 4x and 2x cultivars by accumulation of favorable alleles through recurrent selection within each ploidy pool. Offspring yield was positively correlated with parental GCAs but not with mid-parent values. Hybrid performance was also associated but not significantly correlated with genetic similarity indices based on both pedigree and molecular data. This study further suggests that current genetic models may not be adequate for populations with intergeneration genome size polymorphism.

The genomic constitutions of some Musa L. lines (bananas, plantains and artificial hybrids) were identified using molecular cytogenetic techniques. Double target in situ DNA:DNA hybridization to chromosome spreads using as probes, total genomic DNA isolated from diploid Musa lines of known AA (labelled with biotin-11-dUTP) and BB (labelled with digoxigenin-11-dUTP) genome constitution was carried out. The use of 60% acetic acid combined with heating over a flame gave high quality chromosome spreads free of cytoplasm for in situ hybridization. Total genomic A DNA labelled broad centromeric regions of all 22 chromosomes of the diploid line, Calcutta 4 ( M. acuminata Colla. ssp. burmanniccoides ; A genome) with some chromosomes showing stronger hybridization. Labelled DNA from the B genome hybridized strongly to the centromeric regions of all 22 chromosomes of Butohan 2 ( M. balbisiana Colla; B genome). The two satellited chromosomes of genome B labelled strongly with genomic A DNA. In situ hybridization of labelled A and B genomic DNA to metaphase chromosomes of triploid AAB and ABB cultivars discriminated between A and B genome chromosomes. The plantains Agbagba, Obino l'Ewai and Mbi Egome showed 22 genome A and 11 genome B chromosomes while the cooking bananas Bluggoe and Fougamou showed 11 genome A and 22 genome B chromosomes. Hybridization of labelled A and B genomic DNA to chromosomes of the hybrids showed that TMP2x 2829-62 has all 22 genome A chromosomes while TMPx 4698-1 has 33 genome A and 11 genome B chromosomes. In situ hybridization of labelled total genomic DNA to chromosomes has immense potential for identification of chromosome origin and can be used to characterize cultivars and hybrids produced in Musa breeding.

Following a brief introduction on the phylogeny, taxonomy, production, uses, diseases, pests, environmental stress and variation in genomes of grain legumes, this review focuses on the available genetic resources of key legume crops (tropical and temperate legumes, and model species related to grain legumes); management and utilization of legume genetic resources; impact of genetic resources in conventional legume breeding (germplasm distribution, domesticated germplasm and breeding gains, wild germplasm, conventional manipulation of genetic resources); enhanced molecular strategies for manipulating novel genetic variation for legume breeding (interspecific hybridization, linkage mapping and QTL detection, linkage disequilibrium and association mapping, dissection and manipulation of legume physiology); advanced applications in legume molecular breeding (comparative genomics and allele mining, functional genomics and gene discovery, new technologies for marker-assisted selection, and molecular breeding in legumes

The use of transgenic crops is steadily increasing around the world, led by soybean (based on total area) and maize (in terms of total number of countries). Transgenic maize is grown in at least 17 countries across four continents: Africa, America, Asia and Europe. The comprehensive global spread of transgenic maize has significant implications for organizations involved in germplasm conservation and genetic enhancement; particularly as some countries require a GMO-free declaration when receiving shipments of maize germplasm. This article describes the protocol used by the International Maize and Wheat Improvement Center (CIMMYT) for monitoring unintentional transgene flow in maize genebank and breeding plots. The protocol is based on polymerase chain reaction (PCR) markers for detecting specific recombinant DNA sequences in bulked samples collected from sentinel plots. To date, no unintentional transgene flow has been detected in CIMMYT fields of maize genebank accessions or breeding materials.

A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets.

Wheat, being an important source of calories across the Americas, Europe, North Africa and Asia, is the most widely grown food crop in the world. Wheat yields have undergone a spectacular rise over the last half century, contributing to the Green Revolution in Asia. However, productivity increases appear to have reached a plateau in recent years and many consider that new advances in genomics will be essential to delivery the rates of productivity increases necessary to prevent hunger. New molecular tools will enhance on-going wheat breeding, offering the plant breeder considerable advantages in time, cost, and response to selection. Perhaps most importantly, it is believed that genomics tools will also facilitate much more efficient utilization of new sources of genetic variation for important agronomic traits from wild species. This chapter provides an overview of the botany and conventional breeding of wheat including a summary of past successes, the current primary breeding targets, and the major constraints to achieving those goals. We then focus on genomic advances in bread wheat and durum wheat during the past decade and the implications of these advances for increasing resilience, stability and productivity in tropical, sub-tropical and semi-arid production systems across the world. This includes the use of genomics to improve the search for, and the characterization of, new beneficial genetic variation and the identification of molecular markers to facilitate the efficient manipulation of that variation in breeding programs. Finally, we provide a list of the currently available trait markers and a perspective on likely future trends and challenges in wheat molecular breeding.

Tropical maize is a major staple crop providing food and feed across the developing world. Genomics of maize is very well advanced but heavily focused on temperate germplasm. Tropical maize germplasm is substantially more diverse than temperate maize with a wide range of landraces and types of varieties. Thus, diversity analysis at genetic, molecular, and functional levels is important for underpinning translational genomics from temperate to tropical maize. Virtually all types of markers have been used for molecular linkage mapping in maize over the past decade. However, single nucleotide polymorphic markers are now very well developed in maize and are becoming the marker of choice for most applications. Both linkage and association-based mapping has been used for identifying markertrait associations. Maize genome sequencing is now well advanced but focused on gene-rich regions due to its high density of repetitive elements. Functional genomics activities have made use of insertional mutation-based cloning as well as expressed sequence tags and map-based cloning. A wide range of genomic databases and tools have been developed, of which MaizeGDB features a wealth of data and resources facilitating the scientific study of maize. Genomics-assisted breeding is at an advanced stage in temperate, especially in private sector breeding programs, and applications in tropical maize are also common. Marker-assisted selection has been used in maize for yield, grain quality, abiotic and biotic stresses. Using these approaches, commercial maize breeding programs have reported twice the rate of genetic gain compared with phenotypic selection. However, reports in the literature from public breeding programs are inconsistent and generally less promising. Applied maize genomics in the tropics should in the future focus on tropical maize fingerprinting, haplotype establishment, allele mining, gene discovery, understanding genotype-byenvironment interactions, and development of decision support tools and networks for developing countries to facilitate effective applications of genomics in maize breeding.

Molecular markers and genetic maps are available for most important food crops. Marker-trait associations have been established for a diverse array of traits in these crops, and research on marker/quantitative trait loci (QTL) validation and refinement is increasingly common. Researchers are now routinely using candidate gene-based mapping and genome-wide linkage disequilibrium and association analysis in addition to classical QTL mapping to identify markers broadly applicable to breeding programs. Marker-assisted selection (MAS) is practiced for enhancing various host plant resistances, several quality traits, and a number of abiotic stress tolerances in many well-researched crops. Markers are also increasingly used to transfer yield or quality- enhancing QTL alleles from wild relatives to elite cultivars. Large-scale MAS-based breeding programs for crops such as rice, maize, wheat, barley, pearl millet, and common bean have already been initiated worldwide. Advances in "omics" technologies are now assisting researchers to address complex biological issues of significant agricultural importance: modeling genotype-by-environment interaction; fine-mapping, cloning, and pyramiding of QTL; gene expression analysis and gene function elucidation; dissecting the genetic structure of germplasm collections to mine novel alleles and develop genetically structured trait-based core collections; and understanding the molecular basis of heterosis. The challenge now is to translate and integrate this knowledge into appropriate tools and methodologies for plant breeding programs. The role of computational tools in achieving this is becoming increasingly important. It is expected that harnessing the outputs of genomics research will be an important component in successfully addressing the challenge of doubling world food production by 2050.

Bacterial wilt (BW) caused by Ralstonia solanacearum is an important constraint to peanut (Arachis hypogaea L.) production in several Asian and African countries, and planting BW-resistant cultivars is the most feasible method for controlling the disease. Although several BW-resistant peanut germplasm accessions have been identified, the genetic diversity among these has not been properly investigated, which has impeded efficient utilization. In this study, the genetic relationships of 31 peanut genotypes with various levels of resistance to BW were assessed based on SSR and AFLP analyses. Twenty-nine of 78 SSR primers and 32 of 126 AFLP primer combinations employed in this study were polymorphic amongst the peanut genotypes tested. The SSR primers amplified 91 polymorphic loci in total with an average of 3.14 alleles per primer, and the AFLP primers amplified 72 polymorphic loci in total with an average of 2.25 alleles per primer. Four SSR primers (14H06, 7G02, 3A8, 16C6) and one AFLP primer (P1M62) were found to be most efficient in detecting diversity. The genetic distance between pairs of genotypes ranged from 0.12 to 0.94 with an average of 0.53 in the SSR data and from 0.06 to 0.57 with an average of 0.25 in the AFLP data. The SSR-based estimates of the genetic distance were generally larger than that based on the AFLP data. The genotypes belonging to subsp. fastigiata possessed wider diversity than that of subsp. hypogaea. The clustering of genotypes based on the SSR and AFLP data were similar but the SSR clustering was more consistent with morphological classification of A. hypogaea. Optimum diverse genotypes of both subsp. hypogaea and subsp. fastigiata can be recommended based on this analysis for developing mapping populations and breeding for high yielding and resistant cultivars.

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.