利用SSR标记分析野生小豆及其近缘野生植物的遗传多样性

利用28对SSR引物对96份野生小豆资源、小豆近缘野生植物及栽培小豆品种进行遗传多样性分析,共检测到255个等位变异,平均每对SSR引物9.10个,多态信息含量的变异范围从0.374到0.865,平均为0.722。野生小豆材料和近缘植物Vigna minima遗传变异丰富。来自不同地域的野生小豆材料具有大量特异等位变异,基于非加权成组配对算术平均法的聚类分析可将不同地理来源的野生小豆单独分群,且与主坐标分析的结果相一致。4份栽培小豆材料与日本野生小豆遗传距离较近,表明目前国内小豆育种中较多使用了含有日本血缘的小豆材料,以及国内野生小豆资源的搜集和利用工作落后于日本。本研究对国内野生小豆资源的搜集和保存具有指导意义,并可以为这些资源的评价、利用和优异基因的发掘提供参考。     

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.     

On-farm Conservation Strategy to Ensure Crop Genetic Diversity in Changing Agro-ecosystems in the Republic of Korea

With the recognition of certain limitations of ex situ methods for conservation of plant genetic resources the Convention on Biological Diversity (CBD) at the ‘Earth Summit’ in 1992 highlighted the importance of traditional knowledge of indigenous and local communities that are relevant for the conservation and sustainable use of biological diversity and gave considerable attention to on‐farm and other forms of in situ conservation. Unlike semi‐static nature of ex situ conservation the in situ or on‐farm conservation (OFC) is a dynamic evolutionary process. In developing countries like Republic of Korea, where there is a continuum between the use of traditional and modern cultivars, integration of OFC with already existing gene‐bank activities in the country will be an effective approach for conservation and sustainable use of the country's crop genetic resources. However, very little efforts have been made so far in developing strategies for OFC, therefore, in this paper we describe the importance of OFC and strategies for its development in Republic of Korea. Surveys over the last 20 years have shown that the landraces of major crops have been almost replaced by newly bred varieties in the country. But some vegetatively propagated or minor crop species are still being maintained in the farmers’ fields. We have identified crop landraces, which can be classified into four different categories from the OFC point of view. These are vegetatively propagated landraces, sexually reproduced landraces, landraces with improved varieties and landraces cultivated for the reasons of personal preference. The related issues on OFC including implementation methods from the point of national cooperative system in designated specific condition are also discussed to ensure the genetic diversity in the fast changing agro‐ecosystem of the country.     

Construction of a crop—wild hybrid population for broadening genetic diversity in cultivated sunflower and first evaluation of its combining ability: the concept of neodomestication

The genetic base of sunflower elite lines is very narrow, due to many years of selection and breeding. To broaden the genetic diversity of the cultivated sunflower, in 1995 73 wild sunflower populations were crossed with 3 cultivated lines (Testers), and 219 hybrid offspring’s were evaluated in the field. GCA and SCA effects were computed suggesting for all traits a genetic potential for improvement through selection. Study of the hybrids revealed that the wild accessions bear different genetic abilities to combine with the testers for traits of morphological architecture, phenology and yield (seed weight and seed oil). The variance due to GCA and SCA showed that gene action was additive for days to flowering, branching and plant height. Genotypes derived from the same geographic origin may have either good or poor general combing ability. The correlation between GCA and per se genotype performance was positive for all traits except for seed oil content. This was the first attempt to evaluate wild-cultivated hybrids in sunflower on a large scale and will be the starting point for the management of hybrid Helianthus annuus populations for breeding. GCA and SCA estimations will facilitate the definition of strategies to manage and exploit the natural diversity for this crop.     

Cisgenesis and genome editing: combining concepts and efforts for a smarter use of genetic resources in crop breeding

Plant genetic resources (PGR) represent valuable sources of genetic variability for crop breeding. The development of novel biotechnologies is necessary for increasing the efficiency of their use in pre‐breeding and breeding work. The genome sequencing of hundreds of genotypes and the mining of allele diversity in major crops and populations of landraces and wild relatives allow the isolation of genes underlying characters of interest and their precise modification or transfer into targeted varieties. The technological developments and applications of new plant breeding techniques (NPBT) that maximize the similarity with gene transfer by crossing (cisgenesis/intragenesis) or the accuracy of biotechnological approaches (genome editing) are reviewed. Their potentialities and current limitations as well as the possible advantages of using them separately or combined for the exploitation of PGR in crop breeding are also discussed. Above‐mentioned NPBT tackle some objections to the application of biotechnologies in agriculture and are under review worldwide to assess the possible exclusion from the current regulation systems for genetically modified plants.     

Plant breeding: past,present and future

Plant breeders can help farmers increase food production by breeding new cultivars better adapted to their chosen farming systems, but these must be capable of providing the necessary plant inputs for the required levels of crop production in 2050. Until 200 years ago the farmers themselves were the plant selectors. Plant domestications, extensive crop dispersions and farmers’ selections produced thousands of locally adapted landraces of cultivated plants. During the twentieth century these were largely replaced by relatively few high yielding cultivars and the natural habitats of many of their wild relatives became endangered. Hence in situ and ex situ conservation, and evaluation and use of plant genetic resources is vital for future plant breeding. The development of scientific breeding from the beginning of the twentieth century was based on understanding the mechanism of inheritance and the mating systems of crop plants. The types of genetically uniform, high yielding cultivars that have been bred from genetically heterogeneous landraces were determined by the mode of reproduction and mating system of the cultivated plant species: inbred line (wheat) and hybrid (rice) cultivars for inbreeding species, hybrid (maize) cultivars for outbreeding species, and clonal (potato) cultivars for vegetatively propagated species. When genetically heterogeneous crops are desired, mixtures of cultivars and synthetic cultivars can be produced. Future progress in crop improvement will come from three complementary approaches: use of hybridization and selection in further conventional breeding, base broadening and introgression; mutation breeding, cisgenesis and gene editing; and genetically modified crops.     

用于中国小豆种质资源遗传多样性分析SSR分子标记筛选及应用

以375份小豆核心种质为试验材料, 利用从小豆及其近缘种SSR引物中筛选出的13对引物进行遗传多样性分析。检测结果显示, 小豆种质资源具有丰富的遗传多样性, 共检测到133个等位变异, 每对SSR引物检测到等位变异4~19个, 平均10.23个, 国内各省多态信息含量(PIC)平均为0.561, 多态位点比例(P)平均为93.523%。聚类结果表明, 小豆资源遗传关系与生态分区间有明显的联系, 且东北地区资源与中南部资源遗传关系较近。湖北、安徽、陕西3省资源的PIC较高, 且基本位于主坐标三维图的中心区域, 推断湖北、安徽、陕西是中国栽培小豆的起源地或多样性中心。该结果有助于更好地对小豆种质资源进行收集、保护和利用。     

Genetic diversity and relationships in accessions from different cultivar groups and origins in the tree tomato (<Emphasis Type="Italic">Solanum betaceum</Emphasis> Cav.)

Tree tomato (Solanum betaceum) is an Andean small tree cultivated for its juicy fruits. Little information is available on the characterization of genetic resources and breeding of this neglected crop. We have studied the molecular diversity with AFLP markers using 11 combinations of primers of a collection of 25 S. betaceum accessions belonging to four cultivar groups, most of which had been previously morphologically characterized, as well as one accession of the wild relative S. cajanumense. A total of 197 AFLP fragments were scored, of which 84 (43 %) were polymorphic. When excluding S. cajanumense from the analysis, the number of polymorphic AFLP fragments was 78 (40 %). Unique AFLP fingerprints were obtained for every accession, but no AFLP fragments specific and universal to any of the four cultivar groups were found. The total genetic diversity (H _T ) of cultivated accessions was H _T  = 0.2904, while for cultivar groups it ranged from H _T  = 0.1846 in the orange group to H _T  = 0.2498 in the orange pointed group. Genetic differentiation among cultivar groups (G _ST ) was low (G _ST  = 0.2248), which was matched by low values of genetic distance among cultivar groups. The diversity of collections from Ecuador, which we hypothesize is a center of diversity for tree tomato, was similar to that from other origins (H _T  = 0.2884 and H _T  = 0.2645, respectively). Cluster and PCoA analyses clearly separated wild S. cajanumense from the cultivated species. However, materials of different cultivar groups and origins were intermingled in both analyses. The Mantel test correlation coefficient of the matrices of morphological and AFLP distances was low (−0.024) and non-significant. Overall, the results show that a wide diversity is present in each of the cultivar groups, indicate that Ecuador may be regarded as a center of accumulation of diversity for this crop, and confirm that AFLP and morphological characterization data are complementary. The results obtained are of value for the conservation of genetic resources and breeding of tree tomato, as an assessment of the genetic diversity and relationships among different cultivar groups and geographic origins is obtained.     

Population genetic structure and genetic diversity of <Emphasis Type="Italic">Jatropha curcas</Emphasis> germplasm as investigated by 5′-anchored simple sequence repeat primers

Jatropha (Jatropha curcas L.) is widely distributed in the tropics with a promise for use as an oil crop for biodiesel. Understanding population genetic structure and diversity of J. curcas is important for germplasm collection and planning for breeding programs. Twelve 5′-anchored simple sequence repeat primers were selected and used for evaluation of population genetic structure and genetic diversity of J. curcas accessions collected from different regions within Thailand and introduced from other countries. A moderate level of genetic variation was found in all accessions studied. Cluster analysis did not reflect geographical distance in general as revealed by the Mantel test. An analysis of molecular variance showed that the majority (83.3%) of genetic diversity was within populations, indicating a high level of overlap and little population subdivision with respect to geographic area. An absence of subpopulation structure among neighboring regions may be caused by exchanging germplasm with vegetative propagation. This study provides a basis for breeders on selection of parental material to maximize genetic polymorphism in J. curcas breeding programs.     

Habitat and management affect genetic structure of Festuca pratensis but not Lolium multiflorum ecotype populations

Genetic diversity present in permanent grassland may be valuable for broadening gene pools in breeding programmes and for conservation of genetic resources. However, little is known about the amount of genetic diversity present at specific habitats and about site‐related factors affecting it. To identify valuable habitats, genetic diversity of 12 ecotype populations and four reference cultivars of both Festuca pratensis Huds. and Lolium multiflorum Lam. was analysed using Simple sequence repeat markers (SSR). Analysis of molecular variance revealed a larger within population variation for L. multiflorum (97.1%) than for F. pratensis (92.6%). F. pratensis ecotype populations were clearly separated from cultivars and formed three distinct subclusters according to the geographic regions they were sampled from. Differences between L. multiflorum ecotype populations and cultivars were small and no grouping of populations was observed. Thus, only F. pratensis ecotype populations were structured and habitat as well as management had a slight influence on genetic structure. This information may allow the design of individual strategies for targeted utilization of genetic resources in plant breeding programmes.     

Molecular evaluation of genetic variability in wild populations of mulberry (Morus serrata Roxb.)

Sixteen populations of the wild mulberry, Morus serrata Roxb., were analysed for their genetic diversity with the aim of using them in introgressive breeding programmes with cultivated relatives. Five genets from each population were collected from different natural populations of M. serrata present in Uttaranchal and Himachal Pradesh in India, and diversity of morpho‐anatomical traits and inter‐simple sequence repeat (ISSR) markers were studied. Significant amounts of genetic diversity were observed among these populations for morpho‐anatomical as well as DNA markers. The 17 ISSR primers generated a total of 95 DNA markers, 51 of which were polymorphic, revealing 67% polymorphism among the populations. The pair‐wise genetic distance, estimated from these DNA markers varied from 0.091 between Urgam‐3 and Kathpuria to 0.258 between Dakrakao‐1 and Dunda with an average genetic distance of 0.165. Clustering analysis grouped these 16 populations into three broad groups. The grouping showed a moderate correlation with the geographical distances. Based on the morphological traits and molecular genetic variability, plants of Urgam‐1, Bhowali farm, Nainitikar, Dunda or Korwa‐2 can be selected for breeding and conservation programmes.     

Legume genetic resources: management, diversity assessment, and utilization in crop improvement

Grain legumes contribute significantly to total world food production. Legumes are the primary source of dietary proteins in many developing countries, where protein hunger and malnutrition are widespread. Grain legumes germplasm constitute ~15% of the 7.4 M accessions preserved globally. Nearly, 78% of the CGIAR??s, 0.217 M accessions, have been characterized, compared to 34% of national genebank collections. Interestingly, limited data on grain quality are available as the primary focus has been on morpho-agronomic traits. Clearly, more resources should be targeted on biochemical evaluation to identify nutritionally rich and genetically diverse germplasm. The formation of core and mini core collections has provided crop breeders with a systematic yet manageable entry point into global germplasm resources. These subsets have been reported for most legumes and have proved useful in identifying new sources of variation. They may however not eliminate the need to evaluate entire collections, particularly for very rare traits. Molecular characterization and association mapping will further aid to insights into the structure of legume diversity and facilitate greater use of collections. The use of high resolution elevational climate models has greatly improved our capacity to characterize plant habitats and species?? adaptive responses to stresses. Evidence suggests that there has been increased use of wild relatives as well as new resources resulting from mutagenesis to enhance the genetic base of legume cultigens.     

Interspecific and intergeneric hybridization and chromosomal engineering of Brassicaceae crops

In Brassicaceae crop breeding programs, wild relatives have been evaluated as genetic resources to develop new cultivars with biotic and abiotic stress resistance. This has become necessary because of the diversification of ecotypes of diseases and pests, changing food preferences, advances in production technology, the use of new approaches such as in vitro breeding programs, and the need for economical production of F₁ seed. To produce potential new cultivars, interspecific and intergeneric hybridizations have been performed between cultivated species and between cultivated species and their wild relatives. Furthermore, interspecific and intergeneric hybrids have been successfully produced using embryo rescue techniques. In this paper, we review the interspecific and intergeneric incompatibilities between Brassicaceae crops and their wild relatives, and the production, characterization, and improvement of synthetic amphidiploid lines, alien gene introgression lines, alloplasmic lines, monosomic alien chromosome addition lines, and monosomic alien chromosome substitution lines. The goal is to provide useful materials to support practical breeding strategies and to study the genetic effects of individual chromosomes on plant traits, the number of genes that control a trait, their linkage relationships, and genetic improvement in Brassicaceae crops.     

Genetic diversity of flax accessions originating in the Alpine region: a case study for an ex situ germplasm evaluation based on molecular marker

Agro-biodiversity is currently experiencing severe genetic erosion due to mankind’s unsustainable activities. Because of initiatives following the goal of the conservation of biological diversity, so far seven million crop accessions are being conserved ex situ in gene banks worldwide. Many of these accessions are landraces being rich in gene diversity, silently awaiting their proper characterisation. This is a very critical part of any long-term strategy to enhance the productivity and resilience of crops and agricultural systems and—most importantly—to ensure the preservation of our cultural and biological heritage. In this study of an ex situ germplasm evaluation we analysed 27 flax (Linum usitatissimum L.) accessions originating in the Alpine region, provided by five local gene banks/providers. Based on genomic microsatellite markers (gSSRs), a varying extent of accession-specific gene diversity (expected heterozygosity, H_E) was revealed ranging from 0.05 to 0.51. Admixture of individuals between accessions was uncovered, pointing towards past processes related to gene bank management activities (e.g. intentional selection, unintentional cross-pollination during regeneration) or towards the evolution of the landrace itself (e.g. same regional origin, traditional naming), highlighting the co-existence of cultural and biological diversity. Such an genetic analysis of accessions stored ex situ not only produces valuable agronomic and breeding data, but also is useful for the clarification of past processes leading to duplicates within and between collections or mislabelling, contributing to the potential for rationalisation of collections, which in turn can help ensure that the limited resources available for regeneration are used most efficiently and effectively.     

Genomic variation and genetic relationships in Ipomoea spp.

Random amplified polymorphic DNA (RAPD) markers were used to develop genetic fingerprints and analyse genetic relationships among 29 Ipomoea accessions from different geographical locations around the world, including unique wild species, and reproducible profiles were obtained for all accessions using random decamer primers. The primers generated 46 polymorphic markers, one primer alone having 10 products, enabling the discrimination of all 29 accessions. A high level of genetic variability in sweet potato collections was suggested by the degree of polymorphism. Half of the Japanese land races were closely related while accessions from Papua New Guinea and The Philippines were distinct and exhibited the greatest genetic diversity. The wild species Ipomoea gracilis and Ipomoea tiliacea formed a group distinct from the cultivated sweet potato. The wild tetraploid accession K233 and the species Ipomoea trifida were progressively more related genetically to the cultivated sweet potato and are the probable progenitors of Ipomoea batatas, and may be suitable as germplasm for genetic enhancement. RAPDs proved to be useful for sweet potato systematics and should be valuable for germplasm management, gene tagging and efficient choice of parents in breeding programmes.     

The need for characterisation and evaluation of germplasm: kiwifruit as an example

Genetic diversity provides the raw material for breeding and plant improvement. Breeders of plant species that have little or no history of improvement tend to make the greatest use of collections of raw or unimproved germplasm. Kiwifruit (Actinidia) are one such crop in that they have been subjected to little selection pressure and are still very similar to plants in the wild. To take advantage of the diversity in the genus Actinidia, breeders need to know the extent of the diversity and also need to be able to identify the plants with which they are working. Voucher specimens should be prepared for all plants used in experimental studies. A good understanding of the reproductive biology of Actinidia should facilitate incorporation of wild germplasm into kiwifruit breeding programmes. The HortResearch Actinidia collection has already proved its worth with the development of valuable new kiwifruit cultivars.     

Value of permanent grassland habitats as reservoirs of Festuca pratensis Huds. and Lolium multiflorum Lam. populations for breeding and conservation

European natural and semi-natural grassland form reservoirs of genetic resources containing highly adapted and variable ecotype populations of forage plants. Variation within these reservoirs is stimulated by variation in natural and anthropogenic site-related factors. Changes in agricultural practices lead to the loss of many characteristic habitats. In order to preserve resources for breeding, targeted conservation strategies for germplasm in gene banks (ex-situ) or on site (in-situ) are needed. In order to define site-related criteria for the potential of habitats to preserve valuable resources for breeding and conservation, 38 different habitats across Switzerland were selected to collect Festuca pratensis Huds. and Lolium multiflorum Lam. ecotype populations. Phenotypic variation and population differentiation of 60 single plants were evaluated in a field experiment using 16 morpho-physiological traits. For F. pratensis, ecotype populations and cultivars were clearly separated and there was a significant correlation between diversity of morphological traits and geographic location of sampling sites. For L. multiflorum no clear separation of ecotype populations and cultivars was observed suggesting gene flow from adjacent temporary leys into permanent grassland. Several ecotype populations were superior to cultivars in important traits such as early heading or resistance to winter damage, indicating the importance of natural habitats as a reservoir of genetic resources for breeding. In conclusion, maintenance of permanent grassland in contrasting environments appears to be a promising strategy for preserving valuable genetic variation of forage grasses. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular markers for late blight resistance breeding of potato: an update

Late blight is the most devastating disease of the potato crop that can be effectively managed by growing resistant cultivars. Introgression of resistance (R) genes/quantitative trait loci (QTLs) from the Solanum germplasm into common potato is one of the plausible approaches to breed resistant cultivars. Although the conventional method of breeding will continue to play a primary role in potato improvement, molecular marker technology is becoming one of its integral components. To achieve rapid success, from the past to recent years, several R genes/QTLs that originated from wild/cultivated Solanum species were mapped on the potato genome and a few genes were cloned using molecular approaches. As a result, molecular markers closely linked to resistance genes or QTLs offer a quicker potato breeding option through marker‐assisted selection (MAS). However, limited progress has been achieved so far through MAS in potato breeding. In near future, new resistance genes/QTLs are expected to be discovered from wild Solanum gene pools and linked molecular markers would be available for MAS. This article presents an update on the development of molecular markers linked to late blight resistance genes or QTLs by utilization of Solanum species for MAS in potato.     

Molecular markers in Brassica oilseed breeding: current status and future possibilities

As PCR techniques have developed over the last 15 years, a wealth of new DNA marker technologies have arisen which have enabled the generation of high‐density molecular maps for all the major Brassica crop species. Molecular markers have also been heavily used in analyses of genetic diversity in Brassica crops. The majority of the work utilizing molecular markers in Brassica oilseed breeding has to date been based on genetic mapping using various DNA marker systems in segregating populations generated for specific investigations of particular traits of interest. For numerous qualitative traits, traditional mapping approaches have led to the development of marker‐assisted selection strategies in oilseed Brassica breeding, and in some cases to map‐based cloning of the responsible genes. For quantitative traits, however, it has become apparent that traditional mapping of quantitative trait loci (QTL) is often not sufficient to develop effective markers for trait introgression or for identification of the genes responsible. In this case, allele‐trait association studies in non‐structured genetic populations represent an interesting new approach, provided the degree of gametic phase disequilibrium between the QTL and the marker loci is sufficient. Because Brassica species represent the closest crop plant relatives to the model plant Arabidopsis thaliana, significant progress will be achieved in the coming years through integration of candidate gene approaches in crop brassicas, using the detailed information now available for the Arabidopsis genome. Integration of information from the model plant with the increasing supply of data from physical mapping and sequencing of the diploid Brassica genomes will undoubtedly give great insight into the genetics underlying both simple and complex traits in oilseed rape. This review describes the current use of available genetic marker technologies in oilseed rape breeding and provides an outlook for use of new technologies, including single‐nucleotide polymorphism markers, candidate gene approaches and allele‐trait association studies.     

Genetic diversity of Chinese Spring Soybean Germplasm Revealed by SSR Markers

To use, maintain and increase crop germplasm collections efficiently, it is important to assess the diversity of these collections. In this study, 1383 accessions of Chinese spring sowing soybean ( Glycine max ) were used for SSR analysis. In total, 1111 alleles were detected among these collections with an average number of alleles (NA) of 18.52 per locus. The genetic diversity index (PIC value) varied from 0.456 to 0.928 with an average of 0.815. Intensive breeding of cultivars have led to a decrease of genetic diversity. Random-repeated sampling within landraces of different geographical regions suggested that the ranking of both average NA and PIC values among different geographical regions were North spring soybean (Nsp) > South spring soybean (Ssp) > Northeast spring soybean (NEsp), but because of the uneven distribution of SSR variation patterns, the differences between them did not reach a significant level. There was a relationship between genetic distances and geographical distances among soybean populations from different regions, indicating a certain degree of geographical differentiation among Chinese soybean germplasm collections.