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.     

遗传标记在石榴种质资源研究中的应用

石榴属石榴科石榴属植物,具有较高的营养价值、药用价值和观赏价值。笔者从形态、细胞、生化和DNA分子等不同层面对遗传标记在石榴种质资源研究中的应用进行阐述,并对遗传标记方法的优缺点及存在的问题进行分析和探讨,最后提出了一些建议。遗传标记的应用,特别是分子标记的发展,将为石榴遗传多样性研究、亲缘关系分析、分类研究、品种鉴定、遗传图谱构建以及功能基因定位等相关研究开辟新的途径。     

Genetic resources and breeding of Capsicum spp.

Five species of Capsicum have been domesticated in the American tropics, but breeding programs have concentrated on the non-pungent cultivars of C. annuum. Studies of the consequences of human selection during and after domestication support theoretical calculations that there will be significant amounts of genetic diversity within as well as between species. Breeders have only recently begun to exploit this diversity. Multiple resistances are available to several pests and diseases, but have to be transferred from one agronomic or market type of pepper to another. Problems in selecting simultaneously for multigenic resistances and polygenic quality characters may be eased by the development of molecular markers and a molecular linkage map for Capsicum. Ploidy changes (both tetraploidy and haploidy) are relatively easy to induce in Capsicum species. Doubled haploids have proved particularly valuable in the analysis of the genetically complex basis of some resistances to pests and diseases. Barriers to interspecific gene transfer are similar to those found in other genera of Solanaceae: unilateral incompatibility, post-fertilisation abortion, and nucleo-cytoplasmic interactions leading to male sterility or other abnormalities. Information on the occurrence and effects of these barriers should be available if or when breeders need to turn to interspecific hybridisation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Cultivar identification and genetic fingerprinting of temperate fruit tree species using DNA markers

In recent years we have witnessed critical advances in the applications of molecular markers for genetic fingerprinting in cultivated plants. Their advantages have been widely recognised but they are even more important in woody perennials due to some particularities of these species such as their long generation time, their large individual size and their vegetative propagation. In this review, the information so far published in molecular fingerprinting of temperate fruit tree species using DNA markers is analysed with the goal of obtaining a common ground that will allow an easier and faster genetic identification that, at the same time, has to be reproducible among laboratories. This revised version was published online in July 2006 with corrections to the Cover Date.     

Mapping of Re,a gene conferring the red leaf trait in ornamental kale (Brassica oleracea L. var. acephala)

Variegated leaf colour is an important agronomic trait that affects the market value of ornamental kale (Brassica oleracea L. var. acephala). The red leaf phenotype in kale is due to anthocyanin accumulation. To investigate the pattern of inheritance of this trait, we constructed an F₂ population by crossing ‘Y005‐15’, a double haploid with red leaves, with a white‐leaved double haploid, ‘Y011‐13‐38’, followed by self‐pollination. An F₂ population consisting of 4284 individuals was used to study the inheritance of this trait, which showed that the character was controlled by a dominate gene. All of the 1050 white leaf trait plants in the F₂ were used for mapping and developing markers linked to Re gene. Results showed that Re was mapped to a locus on linkage group C09 of Brassica oleracea, and the locus was mapped between six SSR markers (C9Z1, C9Z16‐1, C9Z90, C9Z94, C9Z96 and C9Z99), with a genetic distance of 6.7, 1.0, 0.3, 2.0, 2.1 and 0.4 cM from Re gene, respectively. These results may facilitate marker‐assisted selection of the red leaf trait in kale breeding as well as map‐based cloning of the red leaf trait gene.     

Characterization of a new prominent satellite DNA of Cucumis metuliferus and differential distribution of satellite DNA in cultivated and wild species of Cucumis and in related genera of Cucurbitaceae

A new species-specific, tandemly arranged satellite (pMetSat) DNA was characterized by Southern hybridization, cloning and sequencing for Cucumis metuliferus, a cultivated species that originated in Africa. The 346 bp repeats share short stretches of remarkable sequence similarity with satellite DNA of other cultivated Cucumis species, in particular types I-IV of C. sativus (cucumber) and the 352 bp satellite of C. melo (melon), although no cross-hybridization occurs applying stringent conditions. Minor arrays of the respective repeat types were also detected in other less cultivated or wild Cucumis species by PCR amplification or long exposure of Southern blots. For the Cucumis species, the pattern of satellite distribution appears to reflect the taxonomic classification. This suggests that in ancestral species a set of differential but related repeats was already present. During speciation and cultivation, specific members of this set underwent amplifications and modifications. Differential distribution of small arrays of the Cucumis satellites within the genomes of other Cucurbitaceae (tribus Benincaseae, Trichosantheae, Sicyeae) is shown. This revised version was published online in July 2006 with corrections to the Cover Date.     

Challenges and opportunities for conservation of forest genetic resources

Increased use of forest resources and a shrinking forestland base threaten the sustainability of forest genetic resources and highlight the importance of conservation and sustainable management of these resources. As forest trees are normally the keystone species of forest ecosystems, their continued existence is essential for many floral and faunal associations of these ecosystems. Major concepts, challenges and opportunities for conservation of forest genetic resources are briefly discussed in this paper. The major challenges include population decline and population structure changes due to forest removal and conversion of forest land to other uses,forest fragmentation, forestry practices, climate change, disease conditions,introduced pests, atmospheric pollution, and introgressive hybridization. Developing scientifically sound conservation strategies, maintaining minimum viable population sizes, and deployment of genetically engineered organisms represent other important challenges in conservation. The usefulness of various biochemical and molecular genetic markers, adaptive traits, and genetic diversity measures for developing conservation strategies for in situ and ex situ genetic resource conservation are also discussed. Major opportunities for conservation of forest genetic resources include: use of molecular genetic markers and adaptive traits for developing conservation strategies; in situ conservation through natural reserves,protected areas, and sustainable forest management practices; ex situ conservation through germplasm banks, common garden archives, seed banks, DNA banks, and tissue culture and cryopreservation; incorporation of disease, pest, and stress tolerance traits through genetic transformation;plantation forestry; and ecological restoration of rare or declining tree species and populations. Forest genetic resource conservation and resource use should be considered complementary rather than contradictory to each other. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic maps of RAPD, AFLP and ISSR markers in Ananas bracteatus and A. comosus using the pseudo-testcross strategy

Genetic maps of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLP) and inter simple sequence repeats (ISSR) markers in pineapple (2n = 2x = 50) are reported for the first time. On the basis of a segregating population of 46 F1 individuals from a cross Ananas comosus x A. bracteatus, genetic maps of these two species were constructed using the two‐way pseudo‐testcross approach. The A. bracteatus map consists of 335 markers (60 RAPDs, 264 AFLPs and 11 ISSRs) assembled into 50 linkage groups, 26 of them with at least four markers. The A. comosus map consists of 157 markers (33 RAPDs, 115 AFLPs, eight ISSRs and the ‘piping’ trait locus) organized into 30 linkage groups, 18 of them with at least four markers. These maps cover, respectively, 57.2% of the A. bracteatus genome estimated as 3693 cM long, and 31.6% of the A. comosus genome calculated as 4146 cM. A rough estimate of 120 and 127 kbp/ cM on average was found for the relationship between physical and genetic distance for A. bracteatus and A. comosus, respectively.     

Recent Progresses in the Studies of Genetic Engineering for Cold Resistance in Plants

Low temperature is one of abiotic stresses limiting the geographical location suitable for growing corps and periodically account for significant losses in plant productivity, so it's important for agriculture to improve the cold resistance of corps. Many plants can acquire increased frost tolerance after a period of exposure to low, non-freezing temperature through a complex adaptive process called cold acclimation. In the past ten years, with the great advance in the researches of molecular mechanism of cold acclimation, the studies of genetic engineering for cold resistance in plants have also been carried out extensively. Currently, there are two kinds of genes used in plant cold-resistant genetic engineering, Which are protective genes and regulating genes. Many studies indicate both kinds of genes have good prospect for improving the cold resistance of plants. However, there are also many problems in this field to be solved immediately.     

Precision of genetic relationship estimates based on molecular markers

Genetic progress through selection is directly related to the amount of variability present in the population and the quality of genes contributed by the parents. Genetic relationships between lines were studied using DNA marker-based estimates of genetic similarity. A statistical methodology using the width of a confidence interval was developed to determine the number of probes to be surveyed and the precision in the estimation of genetic distance between pairs of cultivars. Precision was affected by type of genetic distance used, the number of cultivars, and amount of genetic diversity present in the studied group. The width of a (1-α)% confidence interval decreased as the number of RFLP fragments increased. Oat and wheat diversity studies were used to illustrate the methodology. This revised version was published online in July 2006 with corrections to the Cover Date.     

Mapping of powdery mildew and leaf rust resistance genes on the wheat-rye translocated chromosome T1BL·1RS using molecular and biochemical markers

Powdery mildew and leaf rust resistance genes on the 1RS arm of the T1BL·1RS translocated chromosome were mapped in relation to the Sec‐1 locus and AFLP and restriction fragment length polymorphism markers, respectively, employing segregating F₃ populations. Integration of molecular markers indicated that Pm17 lies between the Lr26 and Sec‐1 loci, with both resistance genes allocated distally to the Sec‐1 locus in the satellite of the 1RS arm.     

Inheritance of the resistance to Leptosphaeria maculans of Brassica nigra and B. juncea in near-isogenic lines of B. napus

The inheritance of resistance to Leptosphaeria maculans was studied in near-isogenic lines derived from asymmetric somatic hybrids between Brassica napus+Brassica nigra and Brassica napus+Brassica juncea, respectively. The hybrids had been backcrossed to B. napus for seven generations before the genetic segregation of the blackleg resistance was determined. The results of the inheritance studies suggested that one single dominant allele controls the resistance in the Brassica napojuncea line, whereas two independent dominant loci were found in the Brassica naponigra line. Total leaf DNA from the near-isogenic lines was isolated and 89 loci were detected by hybridization to 66 restriction fragment length polymorphism (RFLP) markers previously mapped in the B. nigra genome. Out of the 89 loci, eight loci were detected in the B. naponigra line and six were found in the B. napojuncea line. RFLP markers co-segregating with blackleg resistance in adult leaves were also found. Two markers associated with linkage group 5 and 8, respectively, of the B genome were found in the B. naponigra line and one marker was associated with linkage group 2 in the B. napojuncea line.     

Molecular markers and their applications in wheat breeding

In recent years, considerable emphasis has been placed on the development of molecular markers to be used for a variety of objectives. This review attempts to give an account of different molecular markers—restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), sequence-tagged sites (STS), DNA amplification fingerprinting (DAF), amplified fragment length polymorphisms (AFLPs) and microsatellites (STMS)—currently available for genome mapping and for tagging different traits in wheat. Other markers, including microsatellite-primed polymerase chain reaction (MP-PCR), expressed sequence tags (ESTs) and single nucleotide polymorphisms (SNPs) are also discussed. Recent information on synteny in cereal genomes, marker-assisted selection, marker validation and their relevance to cereal breeding in general and wheat breeding in particular are also examined.     

Biotechnology in trees: Towards improved paper pulping by lignin engineering

Lignin is a heterogenous phenolic polymer that plays crucial roles in the development and physiology of vascular plants. However, it needs to be removed from cellulose by toxic and energy-requiring processes for the production of high-quality paper. Therefore, a major biotechnological challenge is to obtain transgenic trees with modified lignin to improve the quality of wood for paper making. Here, we review the results obtained by alterating the expression of genes of the monolignol biosynthesis pathway in trees and the effect of these modifications on the lignin polymer and on pulping. The data reported show that lignin engineering is a promising strategy to improve wood quality for the pulp and paper industry. This revised version was published online in July 2006 with corrections to the Cover Date.     

Kazusa Marker DataBase: a database for genomics,genetics, and molecular breeding in plants

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.     

黄麻应用核心种质的DNA分子身份证构建

构建并研究黄麻应用核心种质是促进黄麻遗传育种和挖掘优异基因的必要途径。在300份黄麻种质资源的农艺性状观察统计基础上,构建了黄麻应用核心种质,包含61份品种(系),可划分为高产、优质、抗病等16种应用类型。为准确鉴定这61份应用核心种质,以46对核心引物为基础,筛选出12对荧光核心引物,采用荧光标记毛细管电泳分析这12对引物的多态性,共检测出140个多态性位点。将毛细管电泳得到的分子量数据以数字+英文字母方式编码,选取了12对荧光核心引物的组合,构建出该应用核心种质的字符串DNA分子身份证,进而构建了相应的条形码和二维码DNA分子身份证,可迅速被电子设备识别。这些结果可促进黄麻种质资源的高效利用及快速分子鉴定。     

棉花单核苷酸多态性标记研究进展

单核苷酸多态性标记已在农作物研究中得到广泛应用并取得重大进展。为了便利棉花SNP(Single nucleotide polymorphism)标记的研究和应用,介绍了利用基因芯片、简化基因组测序、重测序等在棉花中开发SNP标记的方法 ,综述了SNP标记在棉花遗传图谱构建、数量位点的定位和分子标记辅助育种、基因组测序以及系统进化等研究中的应用。并对异源四倍体棉花中SNP标记开发时,同源序列位点和部分同源序列位点上的SNP标记辨别问题进行了系统探讨,对其快捷的开发、检测方式和在数量基因定位中的应用前景进行了展望。     

Genetic and molecular characterization of resistance to Heterodera glycines race isolates 1, 3, and 5 in Peking

Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, has caused severe damage to soybean [Glycine max (L.) Merr.] worldwide since its discovery in 1954. ‘Peking’ is one of the most important sources in breeding SCN resistant soybean cultivars because it is resistant to Races 1, 3, and 5. Genetic information on SCN Races 1, 3, and 5 from Peking is essential to efficiently develop resistant soybean cultivars. Resistance to Race 3 in Peking was found to be controlled by three genes, but little is known on the inheritance of resistance to Races 1 and 5, and whether alleles conditioning resistance to Races 1 and 5 belong to the same linkage group and are allelic to genes giving resistance to Race 3. To determine the genetic bases of resistance to SCN Races 1, 3, and 5, Peking was crossed to the susceptible line ‘Essex’ to generate F₁ hybrids. The F₂ population and F _2:3 families were advanced from the F₁ and evaluated for resistance to SCN Race isolates 1, 3, and 5. Resistance to H. glycines Race isolates 1, 3, and 5 in Peking was found to be conditioned by three genes, one dominant and two recessive (Rhg, rhg, rhg). Peking may share similar sets of resistance loci between Races 1 and 3, but not between Races 3 and 5, or between Races 1 and 5. This revised version was published online in July 2006 with corrections to the Cover Date.     

Occurrence of microsatellites in spinach sequences from computer databases and development of polymorphic SSR markers

Microsatellites are valuable tools as molecular markers in plant breeding. To establish genetic linkage maps or for population studies, information about the occurrence and usability of microsatellite markers in different species is necessary. Sequences of spinach Spinacia oleracea from computer databases were therefore searched for the presence of microsatellites. Sixty simple sequence repeats were found in 237 spinach sequences with a total of 349.4 kb DNA. After removing duplicated sequences, 50 different microsatellites with various motifs remained. Differences between nuclear and chloroplast DNA were not in the number of microsatellites but in their type and length. Chloroplast sequences from spinach contain only short strings of A and AT repeats, whereas nuclear sequences show a wider variety of motifs. Flanking primers for polymerase chain reaction (PCR) analysis were designed for 13 of these microsatellites and tested with two different varieties of spinach. Twelve primer pairs gave amplification products and seven of these showed polymorphisms in the variety ‘Wiremona’ but only one in the variety ‘Monatol’. These markers may be used for linkage analysis or population studies in spinach.