High density molecular linkage maps, comprised of more than 1000 markers with an average spacing between markers of approximately 1.2 cM (ca. 900 kb), have been constructed for the tomato and potato genomes. As the two maps are based on a common set of probes, it was possible to determine, with a high degree of precision, the breakpoints corresponding to 5 chromosomal inversions that differentiate the tomato and potato genomes. All of the inversions appear to have resulted from single breakpoints at or near the centromeres of the affected chromosomes, the result being the inversion of entire chromosome arms. While the crossing over rate among chromosomes appears to be uniformly distributed with respect to chromosome size, there is tremendous heterogeneity of crossing over within chromosomes. Regions of the map corresponding to centromeres and centromeric heterochromatin, and in some instances telomeres, experience up to 10-fold less recombination than other areas of the genome. Overall, 28% of the mapped loci reside in areas of putatively suppressed recombination. This includes loci corresponding to both random, single copy genomic clones and transcribed genes (detected with cDNA probes). The extreme heterogeneity of crossing over within chromosomes has both practical and evolutionary implications. Currently tomato and potato are among the most thoroughly mapped eukaryotic species and the availability of high density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies in these two important and well studied crop species.

https://www.genetics.org/content/genetics/132/4/1141.full.pdf

High density molecular linkage maps of the tomato and potato genomes.

INTRODUCTION. Internal Organization of the Plant Body. Summary of Types of Cells and Tissues. General References. DEVELOPMENT OF THE SEED PLANT. The Embryo. From embryo to the Adult Plant. Apical Meristems and Their Derivatives. Differentiation, Specialization, and Morphogenesis. References. THE CELL. Cytoplasm. Nucleus. Plastids. Mitochondria. Microbodies. Vacuoles. Paramural Bodies. Ribosomes. Dictyosomes. Endoplasmic Reticulum. Lipid Globules. Microtubules. Ergastic Substances. References. CELL WALL. Macromolecular Components and Their Organization in the Wall. Cell Wall Layers. Intercellular Spaces. Pits, Primary Pit--Fields, and Plasmodesmata. Origin of Cell Wall During Cell Division. Growth of Cell Wall. References. PARENCHYMA AND COLLENCHYMA. Parenchyma. Collenchyma. References. SCLERENCHYMA. Sclereids. Fibers. Development of Sclereids and Fibers. References. EPIDERMIS. Composition. Developmental Aspects. Cell Wall. Stomata. Trichomes. References. XYLEM: GENERAL STRUCTURE AND CELL TYPES. Gross Structure of Secondary Xylem. Cell Types in the Secondary Xylem. Primary Xylem. Differentiation of Tracheary Elements. References. XYLEM: VARIATION IN WOOD STRUCTURE. Conifer Wood. Dicotyledon Wood. Some Factors in Development of Secondary Xylem. Identification of Wood. References. VASCULAR CAMBIUM. Organization of Cambium. Developmental Changes in the Initial Layer. Patterns and Causal Relations in Cambial Activity. References. PHLOEM. Cell Types. Primary Phloem. Secondary Phloem. References. PERIDERM. Structure of Periderm and Related Tissues. Development of Periderm. Outer Aspect of Bark in Relation to Structure. Lenticels. References. SECRETORY STRUCTURES. External Secretory Structures. Internal Secretory Structures. References. THE ROOT: PRIMARY STATE OF GROWTH. Types of Roots. Primary Structure. Development. References. THE ROOT: SECONDARY STATE OF GROWTH AND ADVENTITIOUS ROOTS. Common Types of Secondary Growth. Variations in Secondary Growths. Physiologic Aspects of Secondary Growth in Roots. Adventitious Roots. References. THE STEM: PRIMARY STATE OF GROWTH. External Morphology. Primary Structure. Development. References. THE STEM: SECONDARY GROWTH AND STRUCTURAL TYPES. Secondary Growth. Types of Stems. References. THE LEAF: BASIC STRUCTURE AND DEVELOPMENT. Morphology. Histology of Angiosperm Leaf. Development. Abscission. References. THE LEAF: VARIATIONS IN STRUCTURE. Leaf Structure and Environment. Dicotyledon Leaves. Monocotyledon Leaves. Gymnosperm Leaves. References. THE FLOWER: STRUCTURE AND DEVELOPMENT. Concept. Structure. Development. References. THE FLOWER: REPRODUCTIVE CYCLE. Microsporogenesis. Pollen. Male Gametophyte. Megasporogenesis. Female Gametophyte. Fertilization. References. THE FRUIT. Concept and Classification. The Fruit Wall. Fruit Types. Fruit Growths. Fruit Abscission. References. THE SEED. Concept and Morphology. Seed Development. Seed Coat. Nutrient Storage Tissues. References. EMBRYO AND SEEDLING. Mature Embryo. Development of Embryo. Classification of Embryos. Seedling. References. Glossary. Index.

Anatomy of Seed Plants

mRNA stability in mammalian cells.

Phytochromes are a family of plant photoreceptors that mediate physiological and developmental responses to changes in red and far-red light conditions. In Arabidopsis, there are genes for at least five phytochrome proteins. These photoreceptors control such responses as germination, stem elongation, flowering, gene expression, and chloroplast and leaf development. However, it is not known which red light responses are controlled by which phytochrome species, or whether the different phytochromes have overlapping functions. We report here that previously described hy3 mutants have mutations in the gene coding for phytochrome B (PhyB). These are the first mutations shown to lie in a plant photoreceptor gene. A number of tissues are abnormally elongated in the hy3(phyB) mutants, including hypocotyls, stems, petioles, and root hairs. In addition, the mutants flower earlier than the wild type, and they accumulate less chlorophyll. PhyB thus controls Arabidopsis development at numerous stages and in multiple tissues.

/pdf/mutations-in-the-gene-for-the-red-far-red-light-receptor-492d0b0n6n.pdf

Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout arabidopsis development

Phytochrome is a plant regulatory photoreceptor that mediates red light effects on a wide variety of physiological and molecular responses. DNA blot analysis indicates that the Arabidopsis thaliana genome contains four to five phytochrome-related gene sequences. We have isolated and sequenced cDNA clones corresponding to three of these genes and have deduced the amino acid sequence of the full-length polypeptide encoded in each case. One of these proteins (phyA) shows 65-80% amino acid sequence identity with the major, etiolated-tissue phytochrome apoproteins described previously in other plant species. The other two polypeptides (phyB and phyC) are unique in that they have low sequence identity (approximately 50%) with each other, with phyA, and with all previously described phytochromes. The phyA, phyB, and phyC proteins are of similar molecular mass, have related hydropathic profiles, and contain a conserved chromophore attachment region. However, the sequence comparison data indicate that the three phy genes diverged early in plant evolution, well before the divergence of the two major groups of angiosperms, the monocots and dicots. The steady-state level of the phyA transcript is high in dark-grown A. thaliana seedlings and is down-regulated by light. In contrast, the phyB and phyC transcripts are present at lower levels and are not strongly light-regulated. These findings indicate that the red/far light-responsive phytochrome photoreceptor system in A. thaliana, and perhaps in all higher plants, consists of a family of chromoproteins that are heterogeneous in structure and regulation.

/pdf/novel-phytochrome-sequences-in-arabidopsis-thaliana-1w8da8ma5w.pdf

Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family

Translatable phytochrome mRNA represents ≈5 × 10-3% of the total poly(A)-RNA present in etiolated Avena seedlings, as determined by incorporation of radioactivity into the immunoprecipitable apoprotein in a cell-free translation system. Irradiation of such seedlings with 5-s red light induces a decline in this mRNA that is detectable within 15-30 min, shows a 50% reduction within 50-60 min, and results in a >95% reduction within 2 hr. The effect of the red light pulse is reversed by an immediately subsequent far-red pulse to the level of the far-red-light control, indicating that phytochrome exerts autoregulatory control over its own translatable mRNA level. This result necessitates revision of existing concepts of how phytochrome concentrations are modulated in vivo. Red-light dose-response curves show that the response is sensitive to very low light levels. Conversion of <1% of the total cellular phytochrome to the biologically active far-red-absorbing form is sufficient to induce ≈60% of the maximal response, and 20% far-red-absorbing form saturates the response. The observed change in translatable phytochrome mRNA level is one of the most rapid phytochrome-induced alterations in any cellular mRNA yet recorded. Thus, autoregulation of phytochrome mRNA provides an attractive opportunity to examine the early sequence of events in phytochrome control of gene expression.

Autoregulatory control of translatable phytochrome mRNA levels

The present invention is directed to promoter fragments isolated from maize and particularly to a 4.7 kbp upstream promoter region designated ZRP2 of a ZRP2 genomic DNA clone, specific fragments thereof designated ZRP2(2.0) and ZRF2(1.0) and functional equivalents thereto. The promoter has particular utility in driving root preferential expression of heterologous genes that impart increased agronomic, horticultural and/or pesticidal characteristics to a given plant. This invention is also directed to DNA molecules including said promoters and transformed plant tissue including a DNA molecule comprising a promoter of the invention operably linked to a heterologous gene or genes and the seeds thereof.

https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1304&context=patents

Root preferential promoter

ZRP4, a 1.4-kb mRNA that preferentially accumulates in roots of young Zea mays L. plants, was identified by isolation of the corresponding cDNA clone. Genomic Southern analysis indicates that the zrp4 gene is represented once in the corn genome. The deduced ZRP4 polypeptide of 39,558 D is rich in leucine, serine, and alanine. Comparison of the deduced ZRP4 polypeptide sequence to polypeptide sequences of previously cloned plant and animal genes indicates that ZRP4 may be an O-methyltransferase. The ZRP4 mRNA preferentially accumulates in young roots and can be detected only at low levels in leaf, stem, and other shoot organs. ZRP4 mRNA accumulation is developmentally regulated within the root, with very low levels of accumulation in the meristematic region, higher levels in the regions of cell elongation, highest levels in the region of cell maturation, and low levels in the mature regions of the root. ZRP4 mRNA is predominantly located in the endodermis, with lower levels in the exodermis. An intriguing possibility is that the ZRP4 mRNA may code for an O-methyltransferase involved in suberin biosynthesis.

An mRNA putatively coding for an O-methyltransferase accumulates preferentially in maize roots and is located predominantly in the region of the endodermis.

Phytochrome A (phyA) mRNA abundance decreased rapidly in total RNA samples isolated from 4-day-old etiolated oat seedlings following a red light pulse. Putative in vivo phyA mRNA degradation products were detectable both before and after red light treatment. Cordycepin-treated coleoptiles were unable to accumulate the chlorophyll a/b-binding protein mRNA in response to red light, indicating that cordycepin effectively inhibited mRNA synthesis. In cordycepin-treated coleoptiles, phyA mRNA rapidly decreased in abundance, consistent with the hypothesis that phyA mRNA is inherently unstable, rather than being destabilized after red light treatment of etiolated oat seedlings.

Red Light-Independent Instability of Oat Phytochrome mRNA in Vivo.

Pure phytochrome RNA sequence synthesized in an SP6-derived in vitro transcription system has been used as a standard to quantitate phytochrome mRNA abundance in Avena seedlings using a filter hybridization assay. In 4-day-old etiolated Avena seedlings phytochrome mRNA represents ∼0.1% of the total poly(A)(+) RNA. Irradiation of such seedlings with a saturating red-light pulse or continuous white light induces a decline in this mRNA that is detectable within 30 min and results in a 50% reduction by ∼60 min and >90% reduction within 5 h. The effect of the red-light pulse is reversed, approximately to the level of the far-red control, by an immediately subsequent far-red pulse. In seedlings maintained in extended darkness after the red-light pulse, the initial rapid decline in phytochrome mRNA level is followed by a slower reaccumulation such that 50-60% of the initial abundance is reached by 48 h. White-light grown seedlings transferred to darkness exhibit a similar accumulation of phytochrome mRNA that is accelerated by removal of residual Pfr with a far-red light pulse at the start of the dark period. The data establish that previously reported phytochrome-regulated changes in translatable phytochrome mRNA levels result from changes in the physical abundance of this mRNA rather than from altered translatability.

James T. Colbert

Papers

Autoregulatory control of translatable phytochrome mRNA levels

Root preferential promoter

An mRNA putatively coding for an O-methyltransferase accumulates preferentially in maize roots and is located predominantly in the region of the endodermis.

Red Light-Independent Instability of Oat Phytochrome mRNA in Vivo.

Phytochrome regulation of phytochrome mRNA abundance