Genome-wide InDel marker system for application in rice breeding and mapping studies

In order to widen the genetic basis for local rice breeding programs, a set of 506 PCR-based novel insertion/deletion (InDel) markers were designed. The markers have size differences larger than 30 base-pairs and were generated by published genome sequences of rice (Oryza sativa L.) indica and japonica subspecies. Among the 506 InDel markers, 133 markers are polymorphic between the selected parents Taiken 2 and Taichung Sen 10, which are elite Taiwanese japonica and indica varieties, respectively. The InDel to amplicon size ratios, based on the japonica template, were in the range of 8.8–45.6 %, with an average of 21.6 %. As a result, the PCR product can be efficiently separated and easily scored by running 30 min of non-submerging electrophoresis on 2–3 % agarose gels. Commonly observed non-parental bands originated from heteroduplex are considered beneficial in distinguishing homo- and hetero-zygotes. A linkage map constructed solely on these markers arranged in 12 linkage groups and extended over 1,413.9 cM with an average distance of 9.8 cM between markers, based on a segregating population of 286 F₂ individuals derived from a cross between Taiken 2 and Taichung Sen 10. The result indicated that InDel markers with moderate size differences were abundant and uniformly distributed across the whole genome of rice. Due to their simplicity in design and robustness in genotyping, these InDel markers have been routinely used in our quantitative trait loci mapping studies and marker-assisted selection programs for rice. We suggest that InDel markers with moderate size differences could be a valuable alternative in addition to the widely used SSR and SNP markers for rice breeding, and particularly suitable for field laboratories at breeding stations and/or laboratories with limited resources.     

AFLP fingerprinting in Medicago spp.: Its development and application in linkage mapping

Cultivated alfalfa (Medicago sativa L., 2n= 4x= 32) is one of the most important forage crops in temperate climates. The genus Medicago includes diploid species that are a valuable source of wild germplasm for studying the reproductive system of alfalfa and its abnormalities. A linkage map of an apomeiotic mutant of Medicago falcata (L.) Arcang. (2n= 2x= 16) that spanned 368.6 cM and included 29 amplified fragment length polymorphism (AFLP), 35 random amplified polymorphic DNA (RAPD) and three restriction fragment length polymorphism (RFLP) loci was constructed using a one-way pseudo-testcross mapping strategy. The success of such a strategy depends on the presence of sufficiently high levels of heterozygosity in the individual plant which is being mapped and on the informativeness of the marker system that is used. In general: (1) highly informative and reproducible RAPD and AFLP fingerprints were generated and several genome-specific primers selected; (2) of 67 marker loci mapped, 51 were arranged in 11 main linkage groups and eight additional couples of linked marker loci were detected; (3) mapping of an F₁ population theoretically allowed a better estimation of linkage distances since it avoided segregation distortion (x² analyses revealed segregation distortion in only 5.2% of marker loci); (4) the high frequency of unlinked marker loci obtained suggests that, in this alfalfa genotype, DNA markers are distributed throughout the genome. This type of genetic map should find application and prove useful in marker-assisted selection and map-based breeding programmes in meiotic mutants of alfalfa for which there is a lack of suitable genetic markers.     

The New Zealand apple genome mapping project

Summary This project was initiated three years ago to support the New Zealand apple breeding programme at HortResearch and is funded by both the New Zealand Foundation for Research, Science and Technology and the New Zealand Apple and Pear Marketing Board. Our initial goal is to construct a linkage map comprising RFLP, RAPD and isoenzyme markers as well as characters of importance to our breeders and this will enable the breeders to use marker assisted selection to identify the most promising seedlings within progeny populations at an early age. Characters of interest in the shorter term include resistances to scab, powdery mildew, woolly apple aphid and silver leaf, and in the longer term more complex traits such as early and late fruit maturity, fruit quality characters, low temperature tolerance and rootstock influences such as dwarfing and precocity are under consideration. We are currently developing long-term plans for isolation of apple genes in association with other molecular biologists in Hort Research. We have used a cDNA library from apple flesh as a prolific source of RFLP probes and detect their hybridization to Southern blots using a chemiluminescent method. We have screened our mapping line of seedlings for more than 160 markers so far (1/3 RFLP, 2/3 RAPD). Detection of in situ hybridization of key RFLP probes to metaphase chromosome preparations for the purpose of associating marker linkage groups with physical chromosomes is by a digoxygenin or biotin linked immunoassay. The project has collaborative links to apple genome mapping projects in America and Europe.     

The European Prunus mapping project Progress in the almond linkage map

Summary Six European research groups are collaborating to develop genetic markers and linkage maps for use inPrunus breeding programmes. A basic map with 200 RFLPs and 50 more markers including isozymes and RAPDs will be constructed using two highly segregating populations: an interspecific peach × almond F₂ and a cherry F₂. Then, the parents of eleven almond, cherry, peach or plum breeding progenies segregating for target characters will be screened for polymorphisms at the marker loci, and a set of reduced maps, one per progeny, will be constructed with markers spaced 20–30 cM and covering the whole genome. Cosegregation analysis of markers and characters of interest will allow us to find linkages between markers and major genes or quantitative trait loci responsible for the expression of these traits. A map with 72 markers, 7 isozymes and 65 RFLPs, has been developed at the IRTA-Cabrils laboratory using an intraspecific almond progeny, ‘Ferragnes’ × ‘Mono’. Probes for the analysis of RFLPs were obtained from almond genomic and cDNA libraries. The level of polymorphism for RFLPs and the distribution of markers in the chromosomes of almond are discussed.     

作物产量性状QTL定位的研究现状及应用前景

作物的许多农艺性状和经济性状是数量性状。研究作物数量性状遗传对农作物育种具有十分重要的意义。本文综述了数量性状基因座QTL（quantitative trait locus）定位的原理和常用方法及分子标记在水稻、小麦、玉米、棉花、大豆、番茄、大麦和油菜等重要作物产量性状基因定位中的研究现状,并对目前产量性状QTL定位存在的问题和发展前景进行了探讨     

New approach to the study of erosion in cultivated lands

A spectacular activity of erosion, in situations that are considered to be hardly erosive if at all, particularly in cultivated lands, has led the author to put the advances in computer science and electronics to use in finding better approaches to this phenomenon and, on the basis of acquired results, to propose a modeling test.3 system designed and laboratory — tested by the author, with installations set up under authentic conditions on cultivated soils sensitive to erosion (loess) with the scientific collaboration of the INRA. The experience was started in May 1989 at Erlon (north side of the Parisian Basin) on a 28 hectare drainage basin of low slope (2 to 6%). The first goal was to generate quantified data of erosion synchronously, instantaneously, and then to correlate the main parameters occuring in this process; with the results obtained, i.e. solid and liquid flow rates, and finally to analyze them physically and chemically to draw up a quantitative and qualitative balance (ex: nitrates polluting ground waters). In this procedure geomorphologic and pedologic data, soil uses (cultivation techniques and vegetation), surface states are evidently considered. We aim at obtaining accurate knowledge of degradation of cultivated soils in order to propose their more reasonable and vigilant management.     

The application of TDR in laboratory column experiments

An automated TDR system was used together with an automated tensiometer system in laboratory column experiments for the measurement of unsaturated hydraulic properties of soils. The laboratory experiments were a stationary flux (sprinkling infiltrometer) carried out with different fluxes, and a transient (evaporation) method. Simultaneous measurements of water content and pressure head give the water retention characteristic and enable the application of the instantaneous profile analysis for calculating the hydraulic conductivity. This direct analysis is compared with the traditional analysis methods normally used for the laboratory experiments. The application of automated measurement techniques and the use of TDR increases the speed of the measurements, generates more data points and requires less assumptions in the data analysis. Moreover, TDR measurements give insight in the flow process, including effects of hysteresis and heterogeneity within a sample. Performing the sprinkling infiltrometer and evaporation experiments on the same sample enables the determination of the unsaturated hydraulic conductivity at pressure heads ranging from −0.01 m to −6 m.     

转基因番茄育种和产业化研究进展

综述了番茄转基因技术在培育抗病虫害、抗除草剂、抗逆、延迟成熟、品质改良番茄品种和番茄雄性不育系育种方面的应用,以及我国转基因番茄的快繁和产业化研究进展。     

基因芯片在药用植物研究中的应用

基因芯片作为一个高通量筛选工具能同时解析多个基因/基因组的表达。通过检测药物对生物体基因表达谱的影响,基因芯片可用于筛选新药物靶标、评价药物活性和毒理。药用植物有效成分的化学结构复杂多样,他们能同时调控多个靶点,因而在药物研发中越来越受到重视。基因芯片技术在药用植物有效成分的筛选、药理、毒理机制的研究方面的应用必将极大地推进了中药现代化进程。     

Economic evaluation of the environmental effects of erosion

Erosion of the soil is an important aspect of the environment, more so in the Third World where major environmental problems may stem mainly from low land productivity and are directly related to poverty, poor nutrition and paucity of employment opportunities. However, the allocation of resources for preventing and combating erosion does not usually receive its due priority. This is because of the insidious nature of the wide-ranging baneful consequences of erosion. Explicit ex-ante evaluation of investment options is obligatory in reaching rational land-use decisions, including optimal soil conservation and watershed management practices. Various tools of economic evaluation have been considered; benefit-cost analysis in a systems context could provide an appropriate approach. Methodological principles are postulated whereby it appears possible to rank options commensurably as well as to get around the difficulty of quantifying the intagible effects of erosion in terms of market value which, otherwise, can only be imputed at the risk of inaccurate measurements, heuristic trade-offs, subjective value judgements and socio-economically untenable assumptions. Attempts at improving the methodology and making case studies would be warranted for convincing the decision maker to consider anti-erosion and allied measures among gainful economic activities, especially for improving the earth's environment from a social standpoint.     

The methodological approach to soil erosion and important land resources evaluation of the European community

Problems of land resources are acute in the Mediterranean region. Good quality land is scarce, and often threatened by development; soil erosion is encouraged not only by physical conditions but also by agricultural intensification. Faced with these problems, the European Commission has been carrying out a project to assess and map soil erosion risk and land quality, as a basis for policy formulation, within the context of the CORINE Programme. This paper outlines the methods which have been developed, indicates the results which will be achieved, and presents a brief critique of the approach. It is concluded that, whilst problems of data availability have meant that the methods are inevitably no more than a first approximation, the project represents the first genuine attempt to provide consistent information on soil erosion risk and land quality for policy applications at the European level. As such it both helps to highlight future research needs and forms a basis for better informed policy on land resources conservation.     

Disease pattern and grade distribution of coast erosion in Liaodong bay

To identify distribution and development of coast erosion in Liaodong bay, erosion situations of typical coastal zone are studied on the basis of field investigation data. The results show that according to erosion landform features, coast erosion in Liaodong bay can be divided into five patterns: washing and abrasion type, wave collapse type, block avalanche type, karst depression type, interface slip type; according to degree of corrosion and siltation, coast erosion in Liaodong bay can be divided into five grades: serious erosion, intensive erosion, erosion, micro-erosion, stability. Sandy coast is eroded mainly in wave collapse type, rocky coast is eroded mainly in block avalanche type and karst depression type, and silty mud coast is eroded mainly in washing and abrasion type. Investigation on disease pattern and grade distribution of coast erosion is helpful to prevention of coastal zone in Liaodong bay.     

Progress in mapping agronomic genes in apple (The European Apple Genome Mapping Project)

Summary The progress of the European Apple Genome Mapping Project is described. Populations segregating for a range of agronomic genes have been established in six European countries. The need for robust methods of analysis has been identified, especially with regard to the development of molecular markers. Isozyme systems, RAPDs, RFLPs and amplified genes are being used to construct a reference genetic linkage map. Standardisation and precise definition of both genotypic and phenotypic measurements has been recognised as being essential for future exploitation of genetic markers in apple breeding. Phenotypic measurements are being replicated in different geographical locations over several years. Statistical and genetic analyses are aimed at defining components of genetic variation which account for ‘genes’, as defined by apple breeders. A relational database is being constructed which will combine disparate sources of data relating to the genetics of apple. Comparative mapping has been identified as an efficient means of expanding genetic knowledge within and between Rosaceae genomes.     

Wide mapping of a T-DNA insertion site in oilseed rape using bulk segregant analysis and comparative mapping

Doubled haploid oilseed rape lines segregating for a transgene inducing herbicide resistance (bar gene) were investigated for the wide mapping of the T-DNA insertion site. Bulk segregant analysis using presence/absence and intensity polymorphisms between the bulks, as well as comparative mapping with a linkage group deriving from another cross, led to the identification of 11 random amplified polymorphic DNA (RAPD) markers tightly or loosely linked to the bar gene. Ten RAPD loci out of 11 were located on the same side of the bar locus, strongly suggesting that the T-DNA integrated in a telomeric or subtelomeric position. The eleventh RAPD marker exhibited a strong segregation distortion, which could be the result of a heteroduplex formation. Comparison of the linkage groups obtained from the two crosses showed different recombination rates between markers, possibly reflecting differences in parental genetic backgrounds. Consequences and potential applications in transgene dispersal safety assessment studies are discussed.     

The application of in vitro tiller induction in Lolium multiflorum

Summary Eight Lolium multiflorum genotypes were micropropagated for over one year. Using Murashige & Skoog's basal medium, various growth regulators (6-benzylaminopurine, indole acetic acid, adenine sulphate) were tested for their effect on micropropagation. Plantlet handling methods, culture conditions and culture procedures were also compared. Differences were observed in rates of micropropagation between plant genotypes. Under the best conditions for micropropagation, an average of approximately 50 tillers were produced in a 5–6 week period, compared with an estimated 8–15 tillers from soil-grown plants over the same period. Tillers must reach a certain developmental stage before they will grow independently, therefore the number of surviving propagules at subculture under micropropagation and in soil is about half the number of tillers produced. A proposed system for the micropropagation of Lolium multiflorum is described.     

The low down on association mapping in hexaploid wheat (Triticum aestivum L.)

The past few decades have witnessed hundreds of family-based linkage studies mapping for numerous traits but only a limited number of QTLs were actually cloned, tagged, or used for marker-assisted selection. Although providing valuable information, this conventional approach cannot be scaled up to underpin the incredible amount of phenotypic variation in the form of 266, 589 hexaploid wheat accessions maintained in public germplasm collections. Association mapping has recently emerged as an alternative and more powerful mapping approach where a natural population is surveyed to determine marker-trait associations using linkage disequilibrium (LD). After its first application for milling quality in 2006, association mapping studies in hexaploid wheat are being extended to tag yield traits, protein quality, and tolerance to biotic and abiotic stresses. Advances in genotyping technology and statistical approaches greatly accelerated the shift from conventional linkage-based mapping to LD-based association mapping. Association mapping stands out because of simultaneous utilization of a large number of ex situ-conserved natural variation due to historical recombination events accumulated over centuries.