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PubMed2005

How can we use genomics to improve cereals with rice as a reference genome?

Rice serves as a model crop for cereal genomics. The availability of complete genome sequences, together with various genomic resources available for both rice and Arabidopsis, have revolutionized our understanding of the genetic make-up of crop plants. Both macrocolinearity revealed by comparative mapping and microcolinearity revealed by sequence comparisons among the grasses indicate that sequencing and functional analysis of the rice genome will have a significant impact on other cereals in terms of both genomic studies and crop improvement. The availability of mutants, introgression libraries, and advanced transformation techniques make functional genomics in rice and other cereals more manageable than ever before. A wide array of genetic markers, including anchor markers for comparative mapping, SSRs and SNPs are widely used in genetic mapping, germplasm evaluation and marker assisted selection. An integrated database that combines genome information for rice and other cereals is key to the effective utilization of all genomics resources for cereal improvement. To maximize the potential of genomics for plant breeding, experiments must be further miniaturized and costs must be reduced. Many techniques, including targeted gene disruption or allele substitution, insertional mutagenesis, RNA interference and homologous recombination, need to be refined before they can be widely used in functional genomic analysis and plant breeding.

Chromosome Mapping↗
PubMed1999

General evaluation of risk associated with the use of pesticides and other chemical substances on animal breeding and plant production farms.

A general characteristic of chemical risk on plant production farms in Poland is presented. The paper describes risk associated with the natural occurrence of chemical substances (such as ammonium and hydrogen sulfide) in the process of animal breeding and risk connected with the use of artificial fertilizers and pesticides. Pesticides are briefly described taking into consideration toxicity classes and the toxic effect of individual compounds. Exposure to pesticides is presented for individual methods and related activities. Finally, the author discusses pesticide risk on fruit-growing farms and in greenhouses.

Agriculture↗
PubMed2004

Seed-specific expression of a bacterial phosphoenolpyruvate carboxylase in Vicia narbonensis increases protein content and improves carbon economy.

An ambitious aim in plant breeding and biotechnology is to increase the protein content of crop seeds used for food and feed. Using an approach to manipulate assimilate partitioning, we succeeded in elevating the protein content in legume seeds up to 50%. Transgenic bean plants were generated which express a Corynebacterium glutamicum phosphoenolpyruvate carboxylase (PEPC) in a seed-specific manner. The bacterial enzyme was not feedback inhibited by malate. Transgenic seeds showed a higher [14C]-CO2 uptake and about a threefold increased incorporation of labelled carbon into proteins. Changed metabolite profiles of maturing cotyledons indicated a shift of metabolic fluxes from sugars/starch into organic acids and free amino acids. These changes were consistent with an increased carbon flow through the anaplerotic pathway catalysed by PEPC. Consequently, transgenic seeds accumulated up to 20% more protein per gram seed dry weight. Additionally, seed dry weight was higher by 20%-30%. We conclude that PEPC in seeds is a promising target for molecular plant breeding.

Journal Article↗
PubMed1992

RAPD and other PCR-based analyses of plant genomes using DNA extracted from small leaf disks.

A nondestructive, early DNA diagnostic system to implement marker-assisted selection in plant breeding programs has been developed. The main components of the system are a rapid and simple DNA microextraction method and fast DNA polymorphism analyses based on site-specific or arbitrary DNA amplification. A small disk (5 mm diameter) is collected from one cotyledon or the first leaf of a young seedling using a common paper punch. Disruption of plant tissues is done by enzymatic digestion of cell walls. This ensures protection from sample-to-sample contamination and uniform DNA yield. DNA isolated from the resulting protoplasts is sufficient to perform a minimum of five and a maximum of 20 PCR reactions/sample. Total DNA, nuclear DNA, and RNA can be analyzed selectively. The system has been tested successfully with eight major crops. Amplification products generated with DNA prepared with this quick procedure are equivalent to those obtained from CsCl-purified DNA. Up to 120 plants can be treated in 2 days and the procedure lends itself to automation. Potential applications in plant breeding will be discussed.

Base Sequence↗
PubMedDate not supplied

[Differentiation, identification and development of database of T. aestivum L. varieties of Ukrainian selection on the basis of sequence-tagged analysis of microsatellite repeats].

Determination of the variety genotype is very important for the development of theory and practice of plant breeding and for right protection of a variety originator. In this reason attention is focused on the molecular markers generated by polymerase chain reaction. On the basis of STMS-analysis principles of identification and development of database, which reflect molecular-genetics peculiarities of some varieties of the Plant Breeding and Genetics Institute and other Ukrainian breeding organizations, are formulated. Allelic state at microsatellite loci and their distribution were investigated. Wheat varieties were ranged according to genetic distances, data on pedigree and cluster distribution of varieties obtained using computer programs were compared.

Cluster Analysis↗
PubMedDate not supplied

[Protein markers of traits of plants in breeding spring wheat for grain productivity and quality].

A comparative study of the composition of gliadin proteins contained in grains of different-quality wheat cultivars Rollo and Drott and four forms of hybrids F9 and F10, obtained by crossing these cultivars, has been performed. The traits of grain productivity of ears, quality of flour, dough, and gluten were analyzed. Groups of genetically linked gliadin components, controlled by chromosomes 1 and 6 of homoeologous groups, have been identified as protein markers of selectively valuable traits of plants.

Biomarkers↗
PubMed1996

[A PCR marker-based selection for resistance to bacterial blight in rice].

Molecular marker-based selection in plant breeding requires not only suitable molecular markers closely linked to the known genes, but a simple, economic and reliable analyzing technique. We report here a useful PCR marker for genetic diagnostics in breeding for resistance to rice bacterial blight. Xa21 is a newly found gene of rice which confers resistance to bacterial blight caused by Xanthomonas oryzae pv. oryzae. We produced two F2 populations between one resistant line IRBB21 containing Xa21 and two susceptible varieties, respectively. One PCR marker, PB78, detected polymorphism between the susceptible varieties and the resistant line. Cosegregation between Xa21 and PB78 was studied in the two F2 populations. The results showed that Xa21 was closely linked to the molecular marker, the crossing over value was 2.48%. Marker-based selection revealed that 100% of the plants with homozygous resistant genotype of PB78 showed resistance to bacterial blight. The available approaches detecting molecular markers in plant breeding are also discussed.

Base Sequence↗
PubMed2001

Molecular cytogenetics of introgressive hybridization in plants.

Introgressive hybridization (introgression) is genetic modification of one species by another through hybridization and repeated backcrossing. Introgression is important in the evolution of flowering plants. It is also important in plant breeding where a desirable trait can be transferred from wild to crop species. One of the most recent advances in molecular techniques for studying hybridization and introgression is in situ hybridization of genomic probes to cytological preparations (GISH, genomic in situ hybridization). The present paper describes a successful GISH protocol for detection of intergenomic introgression in breeding materials and in allopolyploid species. In addition, the paper introduces a new possibility of using dispersed repeats to detect introgression and to gain insights into its molecular basis. The approach is referred to as dFISH for dispersed fluorescence in situ hybridization, and the best candidate for this type of probes is probably a retroelement. Southern hybridization data are also presented to support the effectiveness of GISH and dFISH for introgression mapping.

Biological Evolution↗
PubMed2004

A priori choice of hybrid parents in plants.

Plant breeding deals with high-yielding genotypes. However, how best to choose parents of these genotypes remains an unsolved question. Here, we focus on a priori choice based on parental distances by means of agronomic and molecular data. Despite numerous theoretical and empirical studies, a priori choice continues to be a controversial procedure. Both success and failure are commonly reported. We looked at these ambiguous results in order to investigate their possible causes. A total of 139 articles on genetic divergence were sampled to examine aspects such as type and number of markers utilized. We suggest that the mean number of 160, 281 and 25 for RAPD and RFLP markers, and SSR loci, respectively, which we found in these papers, should be increased for accurate analysis. A second sample composed of 54 articles was used to evaluate the divergence-heterosis association. Most of them (28) detected positive divergence-heterosis association, whereas 26 revealed negative or inconclusive results. We examined several causes that influence a priori choice positively and negatively.

Breeding↗
PubMed2002

Engineering pathogen resistance in crop plants.

As the world population continues to increase, food supplies must also grow to meet nutritional requirements. One means of ensuring the stability and plentitude of the food supply is to mitigate crop loss caused by plant pathogens. Strategies for combating disease include traditional technologies such as plant breeding and chemical applications; current technologies such as generating transgenic plants that express components of known defense signaling pathways; and the adaptation of newer technologies such as RNA silencing of pathogen and plant transcripts. Breeding has been used to pyramid resistance (R) genes into many different plants including rice. Chemical strategies include application of salicylic acid (SA) analogs to stimulate systemic acquired resistance (SAR) responses. Genetic screens in Arabidopsis have identified genes controlling SAR and these genes have been manipulated and used to engineer crop plants. The diseases caused by plant viruses are being thwarted through the initiation of endogenous RNA silencing mechanisms. Many of these strategies show great promise, some limitations, and exciting opportunities to develop many new tools for combating plant pests.

Crops, Agricultural↗
PubMed2005

Wheat genetic diversity trends during domestication and breeding.

It has been claimed that plant breeding reduces genetic diversity in elite germplasm which could seriously jeopardize the continued ability to improve crops. The main objective of this study was to examine the loss of genetic diversity in spring bread wheat during (1) its domestication, (2) the change from traditional landrace cultivars (LCs) to modern breeding varieties, and (3) 50 years of international breeding. We studied 253 CIMMYT or CIMMYT-related modern wheat cultivars, LCs, and Triticum tauschii accessions, the D-genome donor of wheat, with 90 simple sequence repeat (SSR) markers dispersed across the wheat genome. A loss of genetic diversity was observed from T. tauschii to the LCs, and from the LCs to the elite breeding germplasm. Wheat's genetic diversity was narrowed from 1950 to 1989, but was enhanced from 1990 to 1997. Our results indicate that breeders averted the narrowing of the wheat germplasm base and subsequently increased the genetic diversity through the introgression of novel materials. The LCs and T. tauschii contain numerous unique alleles that were absent in modern spring bread wheat cultivars. Consequently, both the LCs and T. tauschii represent useful sources for broadening the genetic base of elite wheat breeding germplasm.

Breeding↗
PubMed1993

Plant genetics: out with the old, in with the new?

Plant breeding represents an evolving technology based largely on genetic principles. Approximately one-half of the increased yields of major crop plants can be attributed to the genetic improvement of the crop. Although the breeding technology and undergirding science are sound, additional information on the biochemical pathways underlying agronomic and quality traits and their genetic control would allow new genetic technologies to be used more fully. Current developments in molecular biology, plant cell and tissue culture, genetic engineering, and use of molecular genetics will facilitate the selection of complex traits. Genetic improvement of plants in the future will be based on an integration of modern plant-breeding methods and the new genetic technologies. Thus, the new genetic approaches do not represent a replacement technology but will add to the arsenal of tools available for improving crops.

Agriculture↗
PubMedDate not supplied

Artificial mutagenesis as an aid in overcoming genetic vulnerability of crop plants.

Artificially induced genetic variation is being used effectively to supplement or complement sources of natural origin for practical plant breeding. Thus, creating genetic variation uill become increasingly important as crop genetic resources become more difficult to obtain via plant exploration. The aritificial induction of useful genetic variation offers important elements that can be used for overcoming genetic vulnerability: (1) new, previously unknown alleles can be induced in crop plant species to broaden the base of variation; (2) useful genetic variation can be induced in modern cultivars helping to shorten breeding time or to extend production "life"; (3) characteristics of existing genetic resource stocks can be improved to make them more useful in breeding; and (4) recombination in crosses may be enhanced. The performance of induced mutant crop cultivars and the successful uses of induced genetic variation in cross breeding indicate that artificial mutagenesis will play an increasingly greater role in plant breeding.

Alleles↗
PubMed1999

The golden decade of molecular floral development (1990-1999): A cheerful obituary

Cloning of genes involved in the specification of floral meristem and organ identity and in the transition to flowering in some model plants such as Arabidopsis, Antirrhinum, and Petunia during the last decade represents an unprecedented step forward towards an understanding of floral development. Most of these genes belong to conserved and widespread gene families encoding transcription factors, such as the MADS-box genes, FLO-like, and AP2-like genes. Current work on the molecular genetic basis of floral development still focuses on a deeper understanding of the classical model systems, which are all higher eudicots. However, in order to apply the current knowledge about floral developmental genetics to plant breeding and evolutionary biology, flowering plant diversity is now also seriously taken into account. In the next decade, developmental control genes will be studied less and less individually, but rather as components of complex gene regulatory networks. The necessary technology is currently being developed. Learning to understand the origin and evolution of these gene networks will also help to clarify the origin and diversification of flowers, one of the most "abominable" and long-standing mysteries of botany. Copyright 1999 Wiley-Liss, Inc.

Journal Article↗
PubMed2005

Transgenic plants: an historical perspective.

The development of technologies that allow the introduction and functional expression of foreign genes in plant cells has extended in less than two decades to the production of transgenic plants with improved insect and disease resistance, seeds and fruits with enhanced nutritional qualities, and plants that are better adapted to adverse environmental conditions. Vaccines against serious human diseases and other important products have also been developed using transgenic plants. Many more agronomic and quality traits are currently being engineered in both academic and industrial laboratories, which are limited only by our poor knowledge of plant gene function. The emergence of new functional genomic strategies for the identification and characterization of genes promises to provide a wealth of information with an enormous potential to enhance traditional plant breeding and to genetically engineer plants for specific purposes. This chapter describes some of the highlights in the development of these technologies and some of the major achievements in production and commercialization of transgenic crops. We also discuss some of the biosafety issues related to release of this novel class of plants into the environment.

Biolistics↗
PubMed2024

Editing of SlWRKY29 by CRISPR-activation promotes somatic embryogenesis in Solanum lycopersicum cv. Micro-Tom.

At present, the development of plants with improved traits like superior quality, high yield, or stress resistance, are highly desirable in agriculture. Accelerated crop improvement, however, must capitalize on revolutionary new plant breeding technologies, like genetically modified and gene-edited crops, to heighten food crop traits. Genome editing still faces ineffective methods for the transformation and regeneration of different plant species and must surpass the genotype dependency of the transformation process. Tomato is considered an alternative plant model system to rice and Arabidopsis, and a model organism for fleshy-fruited plants. Furthermore, tomato cultivars like Micro-Tom are excellent models for tomato research due to its short life cycle, small size, and capacity to grow at high density. Therefore, we developed an indirect somatic embryo protocol from cotyledonary tomato explants and used this to generate epigenetically edited tomato plants for the SlWRKY29 gene via CRISPR-activation (CRISPRa). We found that epigenetic reprogramming for SlWRKY29 establishes a transcriptionally permissive chromatin state, as determined by an enrichment of the H3K4me3 mark. A whole transcriptome analysis of CRISPRa-edited pro-embryogenic masses and mature somatic embryos allowed us to characterize the mechanism driving somatic embryo induction in the edited tomato cv. Micro-Tom. Furthermore, we show that enhanced embryo induction and maturation are influenced by the transcriptional effector employed during CRISPRa, as well as by the medium composition and in vitro environmental conditions such as osmotic components, plant growth regulators, and light intensity.

Solanum lycopersicum↗
PubMed2005

Peditree: pedigree database analysis and visualization for breeding and science.

At the Wageningen Laboratory of Plant Breeding, a software package has been developed to query a simple structured database with variety pedigree data. The package, called Peditree, creates a tree-shaped representation of pedigree information and has several visualization and lookup options. Estimates of inbreeding coefficient within a pedigree or coefficients of coancestry among pedigrees can be obtained. Furthermore trait data--if available--can be linked, displayed within the pedigree tree, and used to highlight pedigree entries that comply with set criteria.

Animals↗