Databases for Managing Genetic Resources Collections and Mapping Populations of Forage and Related Species

Effective management of plant material used in crop improvement and underpinning research is greatly facilitated by a properly designed data structure accessible by all those working with the material. At IGER we have developed the Aberystwyth Genetic Resources Information System, AGRIS, for managing genetic resources acquired through collecting trips, seed exchange, breeding and transgenic programmes. Recently this has been complemented by MaPIS, a Mapping Populations Information System, which links with AGRIS and allows for storage and documentation of information about plant mapping populations, including pedigrees, status and physical locations of accessions and individual genotypes. IGER also maintains the European Central Crop Databases for Lolium species and Trifolium repens, and the UK National Inventory of all plant genetic resources conserved ex situ in the UK; by November 2004, the UKNI had contributed over 220000 accessions to the 900000 in the Europe-wide database EURISCO

Evolution of plant senescence

BACKGROUND: Senescence is integral to the flowering plant life-cycle. Senescence-like processes occur also in non-angiosperm land plants, algae and photosynthetic prokaryotes. Increasing numbers of genes have been assigned functions in the regulation and execution of angiosperm senescence. At the same time there has been a large expansion in the number and taxonomic spread of plant sequences in the genome databases. The present paper uses these resources to make a study of the evolutionary origins of angiosperm senescence based on a survey of the distribution, across plant and microbial taxa, and expression of senescence-related genes. RESULTS: Phylogeny analyses were carried out on protein sequences corresponding to genes with demonstrated functions in angiosperm senescence. They include proteins involved in chlorophyll catabolism and its control, homeoprotein transcription factors, metabolite transporters, enzymes and regulators of carotenoid metabolism and of anthocyanin biosynthesis. Evolutionary timelines for the origins and functions of particular genes were inferred from the taxonomic distribution of sequences homologous to those of angiosperm senescence-related proteins. Turnover of the light energy transduction apparatus is the most ancient element in the senescence syndrome. By contrast, the association of phenylpropanoid metabolism with senescence, and integration of senescence with development and adaptation mediated by transcription factors, are relatively recent innovations of land plants. An extended range of senescence-related genes of Arabidopsis was profiled for coexpression patterns and developmental relationships and revealed a clear carotenoid metabolism grouping, coordinated expression of genes for anthocyanin and flavonoid enzymes and regulators and a cluster pattern of genes for chlorophyll catabolism consistent with functional and evolutionary features of the pathway. CONCLUSION: The expression and phylogenetic characteristics of senescence-related genes allow a framework to be constructed of decisive events in the evolution of the senescence syndrome of modern land-plants. Combining phylogenetic, comparative sequence, gene expression and morphogenetic information leads to the conclusion that biochemical, cellular, integrative and adaptive systems were progressively added to the ancient primary core process of senescence as the evolving plant encountered new environmental and developmental contexts

Discriminating Stay-Green Grasses Using Hyperspectral Imaging and Chemometrics

Screening of plant collections for traits can be expensive, in terms of the number of plants to be screened, the duration of the plant lifecycle and the required observations. This study describes the application of a non-invasive method, hyperspectral imaging, combined with multivariate analysis, to distinguish between homozygous wild-type (YY) Lolium multiflorum and Lolium multiflorum F2 back cross plants heterozygous for y, a recessive Festuca pratensis stay-green gene (Thomas et al., 1997)

High temperature effects on seedling emergence and embryo protein synthesis of sorghum

High soil temperatures (>45°C) inhibit the field emergence of sorghum [Sorghum bicolor (L.) Moench] in the semiarid tropics. The objective of this study is to demonstrate that the measurement of embryo protein synthesis (EPS) is convenient an d rapid technique for the assessment of sorghum emergence at high soil temperatures. Two experiments were conducted, one using four landrace accessions and another using 14 commercially available lines. Seedling emergence was measured in a large water bath containing a series of soil-filled clay pots. The temperature of the soil in the pots could be regulated (35–50°C) using infrared lamps. Protein synthesis was measured by incubating embryo-containing half-seeds with 14C-labeled amino acids at different temperatures (35–40°C); the resulting labeled proteins were extracted for counting. The relative rankings of the landraces with respect to EPS and emergence demonstrated that the EPS technique clearly distinguished between lines that were able or unable to emerge at 50°C. However, with the commercially available lines, despite the agreement between the ranking of EPS and emergence, two lines diverged from this relationship, which is attributed to the greater complexity of the overall emergence process

Introgression Mapping in The Grasses

Key points Lolium perenne/Festuca pratensis hybrids and their derivatives provide an ideal system for intergeneric introgression. The Lolium perenne/Festuca pratensis system is being exploited to elucidate genome organisation in the grasses, determination of the genetic control of target traits and the isolation of markers for MAS in breeding programmes. The potential of the system as an aid to contig the Lolium and Festuca genomes and for gene isolation is discussed

Genetic analysis of the naked trait in panicles of hexaploid oat

The aim of this study was to estimate the number of genes that control the naked (hull-less) trait and the mode of expression of this characteristic in panicles of hexaploid white oat. Parents and the segregating population (in the F2 and F3 generations) were evaluated in regard to the presence and distribution of naked grains in panicles of individual oat plants. For each plant, a drawing of the main panicle was developed. From the drawings obtained in the progenies of the F2 population, six distinct phenotypic classes were produced. The expected phenotypic proportion of 3:9:4 (naked:segregating:hulled) was that which best fit by the Chi-square test. In the F3 generation, the results showed agreement with the hypothesis observed in the F2 generation. The naked trait in oat is passed on by two genes and the greatest expression of this trait occurs in the upper third of the panicles. Expression of this trait in oats is not complete, even in homozygous genotypes

Gene expression modules in primary breast cancers as risk factors for organotropic patterns of first metastatic spread: a case control study

Background Metastases from primary breast cancers can involve single or multiple organs at metastatic disease diagnosis. Molecular risk factors for particular patterns of metastastic spread in a clinical population are limited. Methods A case-control design including 1357 primary breast cancers was used to study three distinct clinical patterns of metastasis, which occur within the first six months of metastatic disease: bone and visceral metasynchronous spread, bone-only, and visceral-only metastasis. Whole-genome expression profiles were obtained using whole genome (WG)-DASL assays from formalin-fixed paraffin-embedded (FFPE) samples. A systematic protocol was developed for handling FFPE samples together with stringent data quality controls to identify robust expression profiling data. A panel of published and novel gene sets were tested for association with these specific patterns of metastatic spread and odds ratios (ORs) were calculated. Results Metasynchronous metastasis to bone and viscera was found in all intrinsic breast cancer subtypes, while immunohistochemically (IHC)-defined receptor status and specific IntClust subgroups were risk factors for visceral-only or bone-only first metastases. Among gene modules, those related to proliferation increased the risk of metasynchronous metastasis (OR (95% CI) = 2.3 (1.1–4.8)) and visceral-only first metastasis (OR (95% CI) = 2.5 (1.2–5.1)) but not bone-only metastasis (OR (95% CI) = 0.97 (0.56–1.7)). A 21-gene module (BV) was identified in estrogen-receptor-positive breast cancers with metasynchronous metastasis to bone and viscera (area under the curve = 0.77), and its expression increased the risk of bone and visceral metasynchronous spread in this population. BV was further orthogonally validated with NanoString nCounter in primary breast cancers, and was reproducible in their matched lymph nodes metastases and an external cohort. Conclusion This case-control study of WG-DASL global expression profiles from FFPE tumour samples, after careful quality control and RNA selection, revealed that gene modules in the primary tumour have differing risks for clinical patterns of metasynchronous first metastases. Moreover, a novel gene module was identified as a putative risk factor for metasynchronous bone and visceral first metastatic spread, with potential implications for disease monitoring and treatment planning