Showing papers on "Molecular breeding published in 2008"

Molecular Plant Breeding as the Foundation for 21st Century Crop Improvement

Abstract: The fundamental discoveries of Darwin and Mendel established the scientific basis for plant breeding and genetics at the turn of the 20th century. Similarly, the recent integration of advances in biotechnology, genomic research, and molecular marker applications with conventional plant breeding

Marker-Assisted Selection in Plant Breeding: From Publications to Practice

Abstract: 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.

Breeding for Yield Potential and Stress Adaptation in Cereals

Abstract: The need to accelerate breeding for increased yield potential and better adaptation to drought and other abiotic stresses is an issue of increasing urgency. As the population continues to grow rapidly, the pressure on resources (mainly untouched land and water) is also increasing, and potential climate change poses further challenges. We discuss ways to improve the efficiency of crop breeding through a better physiological understanding by both conventional and molecular methods. Thus the review highlights the physiological basis of crop yield and its response to stresses, with special emphasis on drought. This is not just because physiology forms the basis of proper phenotyping, one of the pillars of breeding, but because a full understanding of physiology is also needed, for example, to design the traits targeted by molecular breeding approaches such as marker-assisted selection (MAS) or plant transformation or the way these traits are evaluated. Most of the information in this review deals with cereals...

Some Prospective Strategies for Improving Crop Salt Tolerance

Abstract: Soil salinity is a major environmental constraint to crop productivity worldwide. The “biological” approach to this problem focuses on the management, exploitation, or development of plants able to thrive on salt‐affected soils. This chapter reviews strategies by which plants can be enabled to grow on saline soils. The first strategy is to prime seeds before planting by treating them with inorganic or organic chemicals and/or with high or low temperatures. The second strategy involves exogenous application of organic chemicals, such as glycine betaine, proline, or plant growth regulators, or inorganic chemicals to plants under salinity stress. Considerable improvements in growth and yield have been reported in a number of crops using these approaches. The third strategy is to employ selection and breeding. Major efforts have been made to develop salt‐tolerant lines or cultivars of crops using conventional plant breeding. However, the complexity of the tolerance mechanisms, lack of selection criteria, and variation in responses of plants at different developmental stages have resulted in only limited success. The emphases for developing salt‐tolerant lines/cultivars are now on marker‐assisted breeding and genetic transformation. The development of salt‐tolerant transgenic plants is still at an early stage but may become increasingly more effective as better knowledge of the complex mechanisms involved in plant salt tolerance is acquired. Furthermore, the rapid expansion in knowledge on genomics and proteomics will undoubtedly accelerate the transgenic and molecular breeding approaches However, to date, there are few conclusive reports indicating successful performance of transgenic cultivars under natural stressful environments.

Improving salinity tolerance in crop plants: a biotechnological view

Abstract: Salinity limits the production capabilities of agricultural soils in large areas of the world. Both breeding and screening germplasm for salt tolerance encounter the following limitations: (a) different phenotypic responses of plants at different growth stages, (b) different physiological mechanisms, (c) complicated genotype × environment interactions, and (d) variability of the salt-affected field in its chemical and physical soil composition. Plant molecular and physiological traits provide the bases for efficient germplasm screening procedures through traditional breeding, molecular breeding, and transgenic approaches. However, the quantitative nature of salinity stress tolerance and the problems associated with developing appropriate and replicable testing environments make it difficult to distinguish salt-tolerant lines from sensitive lines. In order to develop more efficient screening procedures for germplasm evaluation and improvement of salt tolerance, implementation of a rapid and reliable screening procedure is essential. Field selection for salinity tolerance is a laborious task; therefore, plant breeders are seeking reliable ways to assess the salt tolerance of plant germplasm. Salt tolerance in several plant species may operate at the cellular level, and glycophytes are believed to have special cellular mechanisms for salt tolerance. Ion exclusion, ion sequestration, osmotic adjustment, macromolecule protection, and membrane transport system adaptation to saline environments are important strategies that may confer salt tolerance to plants. Cell and tissue culture techniques have been used to obtain salt tolerant plants employing two in vitro culture approaches. The first approach is selection of mutant cell lines from cultured cells and plant regeneration from such cells (somaclones). In vitro screening of plant germplasm for salt tolerance is the second approach, and a successful employment of this method in durum wheat is presented here. Doubled haploid lines derived from pollen culture of F1 hybrids of salt-tolerant parents are promising tools to further improve salt tolerance of plant cultivars. Enhancement of resistance against both hyper-osmotic stress and ion toxicity may also be achieved via molecular breeding of salt-tolerant plants using either molecular markers or genetic engineering.

Eucalyptus applied genomics: from gene sequences to breeding tools.

Abstract: Contents Summary 911 I. Introduction 912 II. Eucalyptus biology and domestication 913 III. Eucalyptus breeding and clonal forestry 913 IV. Marker-assisted management of genetic variation in breeding populations 914 V. Genetic mapping and quantitative trait locus (QTL) analysis 915 VI. Gene discovery and genetical genomics 916 VII. Association mapping 918 VIII. Molecular breeding 920 IX. From gene sequences to breeding tools 922 X. Future developments and challenges 924 Acknowledgements 926 References 926 Summary Eucalyptus is the most widely planted hardwood crop in the tropical and subtropical world because of its superior growth, broad adaptability and multipurpose wood properties. Plantation forestry of Eucalyptus supplies high-quality woody biomass for several industrial applications while reducing the pressure on tropical forests and associated biodiversity. This review links current eucalypt breeding practices with existing and emerging genomic tools. A brief discussion provides a background to modern eucalypt breeding together with some current applications of molecular markers in support of operational breeding. Quantitative trait locus (QTL) mapping and genetical genomics are reviewed and an in-depth perspective is provided on the power of association genetics to dissect quantitative variation in this highly diverse organism. Finally, some challenges and opportunities to integrate genomic information into directional selective breeding are discussed in light of the upcoming draft of the Eucalyptus grandis genome. Given the extraordinary genetic variation that exists in the genus Eucalyptus, the ingenuity of most breeders, and the powerful genomic tools that have become available, the prospects of applied genomics in Eucalyptus forest production are encouraging.

SuperSAGE: the drought stress-responsive transcriptome of chickpea roots

Abstract: Drought is the major constraint to increase yield in chickpea (Cicer arietinum). Improving drought tolerance is therefore of outmost importance for breeding. However, the complexity of the trait allowed only marginal progress. A solution to the current stagnation is expected from innovative molecular tools such as transcriptome analyses providing insight into stress-related gene activity, which combined with molecular markers and expression (e)QTL mapping, may accelerate knowledge-based breeding. SuperSAGE, an improved version of the serial analysis of gene expression (SAGE) technique, generating genome-wide, high-quality transcription profiles from any eukaryote, has been employed in the present study. The method produces 26 bp long fragments (26 bp tags) from defined positions in cDNAs, providing sufficient sequence information to unambiguously characterize the mRNAs. Further, SuperSAGE tags may be immediately used to produce microarrays and probes for real-time-PCR, thereby overcoming the lack of genomic tools in non-model organisms. We applied SuperSAGE to the analysis of gene expression in chickpea roots in response to drought. To this end, we sequenced 80,238 26 bp tags representing 17,493 unique transcripts (UniTags) from drought-stressed and non-stressed control roots. A total of 7,532 (43%) UniTags were more than 2.7-fold differentially expressed, and 880 (5.0%) were regulated more than 8-fold upon stress. Their large size enabled the unambiguous annotation of 3,858 (22%) UniTags to genes or proteins in public data bases and thus to stress-response processes. We designed a microarray carrying 3,000 of these 26 bp tags. The chip data confirmed 79% of the tag-based results, whereas RT-PCR confirmed the SuperSAGE data in all cases. This study represents the most comprehensive analysis of the drought-response transcriptome of chickpea available to date. It demonstrates that – inter alias – signal transduction, transcription regulation, osmolyte accumulation, and ROS scavenging undergo strong transcriptional remodelling in chickpea roots already 6 h after drought stress. Certain transcript isoforms characterizing these processes are potential targets for breeding for drought tolerance. We demonstrate that these can be easily accessed by micro-arrays and RT-PCR assays readily produced downstream of SuperSAGE. Our study proves that SuperSAGE owns potential for molecular breeding also in non-model crops.

Cowpea, a multifunctional legume.

Abstract: Cowpea [Vigna unguiculata (L.) Walp.] is an important warm-season legume grown primarily in the semi-arid tropics. The majority of cowpea is grown by subsistence farmers in west and central sub-Saharan Africa, where its grain and stover are highly valued for food and forage. Despite its economic and social importance in developing parts of the world, cowpea has received relatively little attention from a research standpoint. To a large extent it is an underexploited crop where relatively large genetic gains can likely be made with only modest investments in both applied plant breeding and molecular genetics. A major goal of many cowpea breeding and improvement programs is combining resistance to numerous pests and diseases and other desirable traits, such as those governing maturity, photoperiod sensitivity, plant type, and seed quality. New opportunities for improving cowpea exist by leveraging the emerging genomic tools and knowledge gained through research on other major legume crops and model species. The use of marker-assisted selection and other molecular breeding systems for tracking single gene traits and quantitatively inherited characteristics will likely increase the overall efficiency and effectiveness of cowpea improvement programs in the foreseeable future and provide new opportunities for development of cowpea as a food staple and economic resource.

DArT markers: diversity analyses and mapping in Sorghum bicolor

Abstract: The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obtain sufficient return on investment to justify the routine use of marker-assisted breeding for many traits and particularly quantitative traits. Diversity Arrays Technology (DArT™) is a cost effective hybridisation-based marker technology that offers a high multiplexing level while being independent of sequence information. This technology offers sorghum breeding programs an alternative approach to whole-genome profiling. We report on the development, application, mapping and utility of DArT™ markers for sorghum germplasm. A genotyping array was developed representing approximately 12,000 genomic clones using Pst I+Ban II complexity with a subset of clones obtained through the suppression subtractive hybridisation (SSH) method. The genotyping array was used to analyse a diverse set of sorghum genotypes and screening a Recombinant Inbred Lines (RIL) mapping population. Over 500 markers detected variation among 90 accessions used in a diversity analysis. Cluster analysis discriminated well between all 90 genotypes. To confirm that the sorghum DArT markers behave in a Mendelian manner, we constructed a genetic linkage map for a cross between R931945-2-2 and IS 8525 integrating DArT and other marker types. In total, 596 markers could be placed on the integrated linkage map, which spanned 1431.6 cM. The genetic linkage map had an average marker density of 1/2.39 cM, with an average DArT marker density of 1/3.9 cM. We have successfully developed DArT markers for Sorghum bicolor and have demonstrated that DArT provides high quality markers that can be used for diversity analyses and to construct medium-density genetic linkage maps. The high number of DArT markers generated in a single assay not only provides a precise estimate of genetic relationships among genotypes, but also their even distribution over the genome offers real advantages for a range of molecular breeding and genomics applications.

An Introduction to Plant Breeding

Abstract: 1 Introduction 2 Modes of reproduction and types of cultivar 3 Breeding objectives 4 Breeding schemes 5 Genetics and plant breeding 6 Predictions 7 Selection8 Alternative techniques in plant breeding 9 Some Practical considerations Index

Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations

Abstract: Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information-coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools-provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to "bridge the application gap" between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs.

Transformation of Kalanchoe blossfeldiana with rol-genes is useful in molecular breeding towards compact growth.

Abstract: Dwarf genotypes of the economically important flowering potted plant Kalanchoe blossfeldiana were developed by molecular breeding. Root inducing (Ri)-lines were regenerated by applying CPPU to the hairy roots, which were produced by inoculating leaf explants with a wild-type Agrobacterium rhizogenes strain ATCC15834. Amplification by polymerase chain reaction (PCR) and Southern blot analysis confirmed the presence of T-DNA in the Ri-lines. Six Ri-lines were characterised in a greenhouse trial revealing that several morphological traits changed with respect to ornamental value such as plant height, number of lateral shoots, leaf size, leaf number, flower size and number of flowers. The Ri-lines differed in their degree of Ri-phenotype, and the internodes of the Ri-lines were clearly shorter, giving a compact growth habit compared to control plants. Time to anthesis was the same in Ri-line 331 as in control plants and delayed by only 3 days in Ri-line 306 as compared to control plants. A compact plant without delayed flowering can be assumed to be valuable for further breeding.

Towards molecular breeding of reproductive traits in cereal crops

Abstract: The transition from vegetative to reproductive phase, flowering per se, floral organ development, panicle structure and morphology, meiosis, pollination and fertilization, cytoplasmic male sterility (CMS) and fertility restoration, and grain development are the main reproductive traits. Unlocking their genetic insights will enable plant breeders to manipulate these traits in cereal germplasm enhancement. Multiple genes or quantitative trait loci (QTLs) affecting flowering (phase transition, photoperiod and vernalization, flowering per se), panicle morphology and grain development have been cloned, and gene expression research has provided new information about the nature of complex genetic networks involved in the expression of these traits. Molecular biology is also facilitating the identification of diverse CMS sources in hybrid breeding. Few Rf (fertility restorer) genes have been cloned in maize, rice and sorghum. DNA markers are now used to assess the genetic purity of hybrids and their parental lines, and to pyramid Rf or tms (thermosensitive male sterility) genes in rice. Transgene(s) can be used to create de novo CMS trait in cereals. The understanding of reproductive biology facilitated by functional genomics will allow a better manipulation of genes by crop breeders and their potential use across species through genetic transformation.

Genomics of Eucalyptus, a Global Tree for Energy, Paper, and Wood

Abstract: Planted Eucalyptus forests occupy more than 18 million hectares globally and have become the most widely planted hardwood tree in the world, supplying high quality woody biomass for several industrial applications. This chapter attempts to link current eucalypt breeding practice and the genomic tools available or in development. A brief introduction is presented on the main features of modern eucalypt breeding and clonal forestry to provide a better understanding of the challenges and opportunities that lie ahead. Some current low technological input applications of molecular markers in support of operational breeding and clonal deployment are introduced. After reviewing the status of QTL mapping and gene discovery by EST sequencing, the prospects for physical mapping and association genetics in Eucalyptus are discussed. Challenges and opportunities for the application of genomic information to improve relevant traits are described within the framework of molecular breeding for trait improvement. Finally, with the expectation of a draft of a Eucalyptus grandis genome within the next three years, a discussion is included on the prospects of gene identification and subsequent applications in breeding.

Molecular breeding for wheat fusarium head blight resistance in China

Abstract: Wheat Fusarium head blight (FHB) may cause serious losses in grain yield and quality in China. More than 7 million hectares which approximately accounts for 25% of the total areas in China is infected by the disease. The cultivation of wheat varieties with resistance to Fusarium head blight is recognized as one of the most important components to diminish losses due to this disease. Chinese wheat breeders have commenced the research on FHB since 1950s. Wheat cultivars with improved FHB resistance were developed through conventional breeding. Some famous resistant varieties such as Sumai 3, Yangmai 158 and Ning 7840 were released from Jiangsu Academy of Agricultural Sciences, these varieties were widely applied in wheat production and breeding programs. Significant achievements concerning molecular mapping and marker assisted selection have been made in the past decade. The major QTL on chromosome 3BS was identified and located in the same region on chromosome 3BS in Sumai 3, Ning 894037, Wangshuibai, and Chinese Spring. Using SSR marker in this QTL region for assisted selection, some lines with the same resistance to FHB were obtained. New STS markers and SSCP markers were developed and will be tested for the efficiency of MAS. However, further achievements are still hindered by a number of constraints. More FHB resistance genetic resources from landrace in middle to lower reaches of Yangtze River are necessary to be used for improving FHB resistant. The genetic mechanism of the varieties contributing the resistance to improved cultivars is needed to be understood. Development of functional markers for FHB is discussed.

Methods for sequence-directed molecular breeding

Abstract: The present invention provides breeding methods and compositions to enhance the germplasm of a plant by the use of direct nucleic acid sequence information. The methods describe the identification and accumulation of preferred nucleic acid sequences in the germplasm of a breeding population of plants.

Progress and Prospects of Breeding by Gene Design in Rice

Abstract: Progress in molecular markers,gene engineering and genomics are beneficial to direct selection and crop breeding by design.Breeding by design is a concept that aims to control all allelic variation for all genes of agronomic importance.This concept can be achieved through a combination of precise genetic mapping,high-resolution chromosome haplotyping and extensive phenotyping.Thanks to marker technology and software tools available today,and the fine-mapped/cloned genes in rice and their related GP data bank,this goal can now be achieved.Some related techniques concerning molecular breeding and breeding by gene-design,a highlight of breeding by gene-design and progress in functional research for key genes and their molecular utilization in rice breeding are presented in the paper.In addition,the prospects of rice gene-design breeding are discussed.

Marker-assisted selection for the development of improved barley and wheat lines

Abstract: Marker-assisted selection (MAS) is an efficient modern method for transferring alleles or specific chromosome segments including important agronomic traits into elite cultivars. This approach makes genotypic selection possible, whereby the selection process is more effective. The Research Institute of Plant Production Piesťany uses genetic markers linked to important traits in the following pre-breeding programmes: 1. development of winter barley lines resistant to BaYMV/BaMMV, 2. development of spring barley lines resistant to BYDV, 3. development of winter wheat lines resistant to leaf rust (gene pyramiding), 4. improvement of wheat quality by new combination(s) of known HMW-GS and/or by introduction of novel HMW-GS alleles. Several hundreds of genotypes are usually analysed for the presence or absence of linked molecular markers and selected for use in breeding programmes.

Perspectives on genome mapping and marker-assisted breeding of eucalypts

Abstract: In Eucalyptus and forest tree breeding in general, the generalised application of molecular markers for directional selection is still an unfulfilled promise. In highly heterogeneous eucalypts, while conventional quantitative trait loci (QTL) mapping has revealed useful markers that are currently exploited in within-family selection tactics, only a more direct linkage disequilibrium mapping approach will likely uncover population-wide applicable marker–trait associations. Due to the very low-range linkage disequilibrium seen in Eucalyptus , a whole-genome association approach does not seem immediately feasible. Association studies based on candidate genes have been started in Eucalyptus , but only small proportions of the variation have been accounted for by such genes to be exciting news to breeders. Selection of candidate genes for direct manipulation or association studies based on their presumed biochemical role is not an easy task even for well-defined phenotypes and/or known metabolic pathways. Going from phenotypes to genes by a forward genomics approach based on an integrative expression–QTL mapping route, should prove to be a powerful way to choose target genes for marker-assisted selection. In this context at least two possibilities have recently emerged. The first one is to use high-performance genotyping technologies that would allow sufficient throughput and low cost for association genetic analysis of thousands of genes at a time. The second one would be to have access to a whole genome sequence so that candidate genes in a fine mapping interval delimited by flanking markers could be mined, reannotated and then analysed in association mapping. A fully public draft of the E. grandis genome will be sequenced by the US Department of Energy within the next few years following a proposal submitted by the International Eucalyptus Genome Network (EUCAGEN). As this genome project advances and more powerful tools become accessible, the true challenge for understanding and manipulating the complex nature of important traits in Eucalyptus will depend to a large extent on our ability to accurately phenotype trees, analyse the overwhelming amount of genomic data and translate this into truly useful molecular tools for breeding. Keywords: Eucalyptus ; genomics; molecular breeding Southern Forests 2008, 70(2): 69–75