利用AFLP标记分析皮燕麦种质资源遗传多样性

用20对AFLP引物对来自于国内外的177份皮燕麦(Avena.sativa L.)资源进行遗传多样性分析,共获得976条清晰条带,其中多态性条带为185条,不同引物的多态性百分率为9.3%～35.9%,平均为19.0%。不同来源组群的Shannon-Weaver多样性指数变化范围为0.19～0.3412,西欧材料最高,其次是北欧(0.3269)、日本(0.3072)、东欧(0.2949)、北美(0.2904)、黑龙江最低。主坐标和UPGMA聚类分析结果基本相同,并与地理来源有很高的一致性。全部材料总体上可分为两类,其中一类全部为国内资源,另一类包含所有国外、内蒙古和青海的材料。国内与国外材料分布相对集中,这表明国内与国外材料亲缘关系较远,交流不是很广泛。而国内不同来源的材料相互交错分布,表明国内皮燕麦资源交流充分,多样性不是很丰富,应加强国外皮燕麦的引种工作。     

Characterization of genetic diversity of nuclear and mitochondrial genomes in Daucus varieties by RAPD and AFLP

The genetic diversity of nuclear genomes of five Daucus species and seven Daucus carota L. subspecies involving 26 accessions was characterized with random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP). AFLP produced more than four times as many discrete bands per reaction compared with RAPD analysis, while both AFLP and RAPD basically led to similar conclusions. The dendrograms constructed with both RAPD and AFLP revealed that all accessions of D. carota were grouped into a major cluster delimited from other Daucus species, in good agreement with the classification by morphological char-acteristics. All accessions of cultivated carrots [(D. carota ssp. sativus (Hoffm.) Arcang.] were clustered in the same group while the variation within D. carota was relatively extensive. Genetic diversity of mitochondrial genomes was also documented with RAPD for the same accessions. The mitochondrial dendrogram differed from that of the nuclear genome, suggesting that nuclear and mitochondrial genomes of some accessions had separate evolutionary histories. Received: 20 September 1997 / Revision received: 19 January 1998 / Accepted: 28 March 1998     

Patterns of AFLP variation in a core subset of cultivated hexaploid oat germplasm

Many core collections have been developed from large collections of crop germplasm, but most of these have not been characterized, particularly using molecular techniques, for germplasm management and utilization. We have attempted to characterize a structured sample representing a world collection of 11,622 cultivated hexaploid oat accessions in the hope of understanding the genetic structure of the world collection. The amplified fragment length polymorphism (AFLP) technique was applied to screen 670 accessions representing 79 countries and one group of uncertain origin. For each accession, 170 AFLP polymorphic bands detected by five AFLP primer pairs were scored. Analyses of the AFLP data showed the effectiveness of the stratified sampling applied in capturing country-wise AFLP variation. The frequencies of polymorphic bands ranged from 0.11 to 0.99, with an average of 0.72. The majority (89.9%) of the AFLP variation resided within accessions of each country, and only 6.2% of the AFLP differences existed among accessions of major geographic regions. Accessions from the Mediterranean region were the most distinct, while those from Russia and the USA were the most diverse. The two distinct groups that were observed were separated largely on the basis of common oat and red oat. Red oat was genetically more diverse than its common and hull-less counterparts, and hull-less oat was more related to common oat than red oat. Landrace and non-landrace accessions displayed similar AFLP variation patterns. These patterns are significant for understanding the domestication of cultivated oat and are useful in classifying the intraspecific diversity of oat germplasm, developing specific core subsets of the oat collection, and exploring new sources of genes for oat improvement.     

Leaf area expansion and net photosynthetic rate of three bromegrass (Bromus) species

This study measured individual leaf area expansion rate and leaf net photosynthetic rate (P _N) of meadow bromegrass (Bromus riparius Rehm.), smooth bromegrass (Bromus inermis Leyss.) and hybrid bromegrass (B. riparius × B. inermis). Smooth bromegrass expanded individual leaf area 1.5 times faster than meadow bromegrass and hybrid bromegrass. P _N was highest in smooth bromegrass, intermediate in hybrid bromegrass, and lowest in meadow bromegrass. Rapid growth of meadow bromegrass following defoliation compared to smooth bromegrass and hybrid bromegrass could not be explained by higher rates of these measured characteristics.     

AFLP analysis of somaclonal variations in Eucalyptus globulus

DNA variations of forty-eight Eucalyptus globulus plants, regenerated by successive culture from seven different explants were assessed by AFLP analysis using 18 primer combinations. At least one variation showed 66.7 % of the analyzed plants, and the numbers of polymorphic bands per plant ranged from 1 to 22. The proportion of polymorphic fragments did not correlate with the numbers of the regenerated plants. However, the more times of successive culture were done the more of polymorphic bands were found within the groups. On average, between 97.39 and 99.88 % of all fragments were shared within the same group. AMOVA analysis showed 39.33 % of the variation was found among the accessions that originated from different calli while 60.67 % was from same calli.     

Genetic and epigenetic instabilities induced by tissue culture in wild barley (<Emphasis Type="Italic">Hordeum brevisubulatum</Emphasis> (Trin.) Link)

A simple tissue culture protocol was developed for efficient plant regeneration from young inflorescence-derived calli in wild barley, Hordeum brevisubulatum (Trin.) Link, an important pasturage grass. Genetic and epigenetic instabilities in the regenerated plants (regenerants) were assessed by three molecular markers AFLP, S-SAP and MSAP. Two pools of calli derived from young inflorescences of a single donor plant and 44 randomly chosen regenerants were subjected to AFLP analysis. Results showed that 74 out of 793 scored bands were polymorphic among the studied samples, giving rise to a genetic variation frequency of 9.3%. The number of variant bands as compared to the donor plant varied greatly among the regenerants, with a small number of regenerants accumulated a large number of variant bands (maximum 55), while the majority of regenerants showed only 2–3 variant bands. A subset of regenerants together with the two pools of calli were selected for S-SAP and MSAP analysis to detect possible retrotranspositional activity of a prominent retroelement family, BARE-1, in the genomes of Hordem species, and possible alterations in cytosine methylation. S-SAP analysis showed that of the 768 scored bands, 151 were polymorphic among the analyzed samples, giving rise to a genetic variation frequency of 19.7%, albeit no evidence for retrotranspositional event was obtained based on locus-specific PCR amplifications. MSAP analysis revealed that tissue culture has caused cytosine methylation alterations in both level and pattern compared with the donor plant. Sequencing of selected variant bands indicated that both protein-coding genes and transposon/retrotransposons were underlying the genetic and epigenetic variations. Correlation analysis of the genetic and epigenetic instabilities indicated that there existed a significant correlation between MSAP and S-SAP (r = 0.8118, 1,000 permutations, P < 0.05), whereas the correlation between MSAP and AFLP (r = 0.1048) is not statistically significant. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Xiaoling Li and Xiaoming Yu contributed equally to this work.     

AFLP variation in 25 Avena species

Current molecular characterization of ex situ plant germplasm has placed more emphasis on cultivated gene pools and less on exotic gene pools representing wild relative species. This study attempted to characterize a selected set of germplasm accessions representing various Avena species with the hope to establish a reference set of exotic oat germplasm for oat breeding and research. The amplified fragment length polymorphism (AFLP) technique was applied to screen 163 accessions of 25 Avena species with diverse geographic origins. For each accession, 413 AFLP polymorphic bands detected by five AFLP primer pairs were scored. The frequencies of polymorphic bands ranged from 0.006 to 0.994 and averaged 0.468. Analysis of molecular variance revealed 59.5% of the total AFLP variation resided among 25 oat species, 45.9% among six assessed sections of the genus, 36.1% among three existing ploidy levels, and 50.8% among eight defined genome types. All the species were clustered together according to their ploidy levels. The C genome diploids appeared to be the most distinct, followed by the Ac genome diploid A. canariensis. The Ac genome seemed to be the oldest in all the A genomes, followed by the As, Al and Ad genomes. The AC genome tetraploids were more related to the ACD genome hexaploids than the AB genome tetraploids. Analysis of AFLP similarity suggested that the AC genome tetraploid A. maroccana was likely derived from the Cp genome diploid A. eriantha and the As genome diploid A. wiestii, and might be the progenitor of the ACD genome hexaploids. These AFLP patterns are significant for our understanding of the evolutionary pathways of Avena species and genomes, for establishing reference sets of exotic oat germplasm, and for exploring new exotic sources of genes for oat improvement.     

Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance, and near-isogenic line analysis

Amplified fragment length polymorphism (AFLP) analysis is a PCR-based technique capable of detecting more than 50 independent loci in a single PCR reaction. The objectives of the present study were to: (1) assess the extent of AFLP variation in cultivated (Gycine max L. Merr.) and wild soybean (G. soja Siebold & Zucc.), (2) determine genetic relationships among soybean accessions using AFLP data, and (3) evaluate the usefulness of AFLPs as genetic markers. Fifteen AFLP primer pairs detected a total of 759 AFLP fragments in a sample of 23 accessions of wild and cultivated soybean, with an average of 51 fragments produced per primer pair per accession. Two-hundred and seventy four fragments (36% of the total observed) were polymorphic, among which 127 (17%) were polymorphic in G. max and 237 (31%) were polymorphic in G. soja. F₂ segregation analysis of six AFLP fragments indicated that they segregate as stable Mendelian loci. The number of polymorphic loci detected per AFLP primer pair in a sample of 23 accessions ranged from 9 to 27. The AFLP phenotypic diversity values were greater in wild than in cultivated soybean. Cluster and principal component analyses using AFLP data clearly separated G. max and G. soja accessions. Within the G. max group, adapted soybean cultivars were tightly clustered, illustrating the relatively low genetic diversity present in cultivated soybean. AFLP analysis of four soybean near-isogenic lines (NILs) identified three AFLP markers putatively linked to a virus resistance gene from two sources. The capacity of AFLP analysis to detect thousands of independent genetic loci with minimal cost and time requirements makes them an ideal marker for a wide array of genetic investigations.     

Loss of Genetic Diversity of Domesticated Panax notoginseng F H Chen as Evidenced by ITS Sequence and AFLP Polymorphism: A Comparative Study with P. stipuleanatus H Tsai et K M Feng

Abstract: In the present study, we evaluated the genetic diversity of Panax notoginseng F H Chen, a domesticated species, and P. stipuleanatus H T Tsai et K M Feng, an endangered wild species in southeastern Yunnan and adjacent areas in Vietnam, using sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA and amplified fragment length polymorphism (AFLP) markers. Twenty‐four accessions from three plantations of P. notoginseng and 51 samples from eight populations of P. stipuleanatus were assayed. A total of 694 bp of partial sequences of 18S, ITS 1, 5.8S, ITS2, and partial sequences of 26S were obtained. No sequence variation was detected within P. notoginseng and nine sites (1.30%) were variable in P. stipuleanatus. Two‐thirds of the variable sites were found between Langqiao and other populations. In P. notoginseng, four pairs of AFLP primer combinations generated 312 bands, of which 240 (76.9%) were polymorphic and 60.15% of the polymorphisms were harbored within plantations. Approximately 41.0% and 66.9% of bands were polymorphic in population D7 and 5589, respectively. In P. stipuleanatus, the same four primer combinations produced 346 bands, of which 334 (96.5%) were polymorphic and approximately 62.14% of polymorphisms were maintained within populations. Considerable variations were observed. The percentage of polymorphic bands ranged from 50.2% to 84.9% and the average over populations was 70.9%. Cluster analysis did not show correlation of genetic differentiation with the distinctive leaf morphology of P. stipuleanatus(i.e. one form with bipinnatifid leaflets and the other with undivided leaflets). Because over 40% of genetic variations were maintained among populations and because of the very restricted distribution of P. stipuleanatus, all natural populations of this species should be conserved in situ. Considering that there are variations in P. notoginseng within and among plantations, we suggest establishing a genetic resource conservation garden or reintroducing P. notoginseng into its native habitats in southwestern China. Such reintroduction should be carefully executed after large‐scale screening of genetic variation within the species. ( Managing editor: Li‐Hui ZHAO ¹ )     

M‐AFLP‐based protocol for microsatellite loci isolation in Cynara cardunculus L. (Asteraceae)

Nine microsatellite markers for Cynara cardunculus L. were developed using a two‐step ‘primer extension’ procedure, based on microsatellite‐amplified fragment length polymorphism (M‐AFLP) technique. In the first step, highly enriched SSR gel profiles were produced and, from the derived sequences of selected bands, forward primers directed towards the microsatellite motif were designed. In the second step, the opposite microsatellite flanking sequence was isolated using a nested approach on a restricted‐ligated genomic fraction. Polymorphism was explored in 24 plants of wild cardoon (Cynara cardunculus L. var. sylvestris) as well as two accessions of both globe artichoke (Cynara cardunculus L. var. scolymus), and cultivated cardoon (Cynara cardunculus L. var. altilis).     

Amplified fragment length polymorphism for genetic diversity assessment in globe artichoke

Globe artichoke (Cynara cardunculus L. var. scolymus L.) is a diploid (2n=2x=34), predominantly cross-pollinated plant native to the Mediterranean basin, and Italy contains the richest primary cultivated gene pool. Commercial production is mainly based on perennial cultivation of vegetatively propagated clones that are highly heterozygous and segregate widely when progeny-tested. Analysis of the artichoke genome by means of molecular markers has been limited to a few studies; here we report on the genetic relatedness among 118 artichoke accessions, including clones belonging to the same varietal type, two accessions of cultivated cardoon (C. cardunculus L. var. altilis DC.) and four accessions of wild cardoon [C. cardunculus L. var. sylvestris (Lamk) Fiori] as measured by amplified fragment length polymorphism (AFLP). Eight primer combinations yielded a total of 667 bands, of which 519 were polymorphic. Genetic similarities among accessions were calculated according to Jaccards Similarity Index and used to construct a dendrogram based on the unweighted pair group method using arithmetic averages. Our results demonstrate that AFLP markers can be useful in evaluating Cynara cardunculus genetic diversity and in classifying accessions to phylogenetic groups based on their genetic similarity values. Genetic variation among artichoke clones belonging to the same varietal type was in some cases higher than that found among accessions differently named and coming from different areas. The lowest Jaccards Similarity Index found within a varietal type can be considered as a threshold for the identification of accessions which share an analogous genetic background. This will enable the selection of representatives in order to develop and manage a germplasm core collection as well as the identification of suitable material for future artichoke breeding efforts.Communicated by J.S. Heslop-Harrison     

Inhibition of germination and α-amylase induction by 6-methoxy-2-benzoxazolinone in twelve plant species

6-Methoxy-2-benzoxazolinone (MBOA) inhibited germination of rice (Oryza sativa L.), wheat (Triticum aethiopicum Jakubz), rye (Secale cereale L.), onion (Allium cepa L.), wild oat (Avena fatua L.), barnyard grass [Echinochloa crus-galli (L.) Beauv.], ryegrass (Lolium rigidum Gaudin), cress (Lepidium sativum L.), lettuce (Lactuca sativa L.), tomato (Lycopersicum esculentum Mill.), carrot (Daucus carota L.) and amaranth (Amaranthus retroflexus L) and the inhibition increased with increasing MBOA concentrations. MBOA also inhibited the induction of α-amylase in these plant seeds and the inhibition increased with increasing MBOA concentrations. There were variations in sensitivity of these plant species to MBOA, and species of family Poaceae (barnyard grass, wild oat, rice, rye, ryegrass, and wheat) were less sensitive to MBOA than the other plant species.     

Genetic relationship in ecotypes of Leymus chinensis revealed by polymorphism of amplified DNA fragment lengths

Leymus chinensis (Trin.) Tzvel is a perennial grass in the tribe Gramineae and important forage in Northern China. Knowledge of its genetic diversity is a prerequisite for using modern breeding techniques. Amplified fragment length polymorphism (AFLP) was first used to evaluate the genetic relationship among and within three ecotypes. Distinct clusters were produced based on AFLP markers. All accessions from the same ecotype were grouped in a cluster except accessions 6. According to AFLP profile ecotype-specific bands differ from each other. The genetic differentiation within the ecotype of the species was much smaller than that among ecotypes. Self-incompatibility in this species contributes to evident genetic differentiation together with environment. These results indicate that ecotypes were distinguished visually similarly to genetic variation. Published in Russian in Fiziologiya Rastenii, 2006, Vol. 53, No. 5, pp. 764–770. The text was submitted by the authors in English.     

AFLP analysis of genetic relationships among the cultivated eggplant, Solanummelongena L., and wild relatives (Solanaceae)

The AFLP technique of DNA analysis was evaluated as a tool for assessing genetic relationships among the cultivated eggplant, S. melongena, and related species [Solanum L. subgenus Leptostemonum (Dunal) Bitter, section Melongena (Mill.) Dunal, series Incaniformia Bitter]. Genetic distances based on the AFLP data were estimated for 49 samples of 36 distinct accessions. Phenetic trees were constructed using Jaccard’s coefficient and UPGMA, and other clustering methods: they all had very high co-phenetic correlation values, and were found to be consistent with previous trees based on other data types, in particular ITS-1 sequences, isozymes and morphology, carried out on the same accessions. These results indicated that the AFLP technique is both an efficient and effective tool for determining genetic relationships among species of Solanum. A new classification is proposed for series Incaniformia. Received: 11 January 1999 / Accepted: 30 January 1999     

Isolation and characterization of microsatellite markers in the sacred lotus (Nelumbo nucifera Gaertn.)

The sacred lotus (Nelumbo nucifera Gaertn.) is an aquatic plant of economic and ornamental importance in China. From an (AG)_n‐enriched genomic library, 24 microsatellites were isolated and identified by using the (fast isolation by the AFLP of sequences containing repeats) FIASCO protocol. Eleven loci showed polymorphism with two to six alleles per locus. These markers yielded 42 alleles in a survey of 32 accessions of the sacred lotus. Eleven effective primer pairs of simple sequence repeats were designed and will be used as genetic markers to evaluate the fine‐scale population structure of the sacred lotus in the future.     

Isozyme variation in germplasm accessions of the wild oat Avena sterilis L.

Summary Optimal exploitation of crop genetic resources requires a knowledge of the range and structure of the variation present in the gene pool of interest. Avena sterilis L., the cultivated oat progenitor, contains a store of genetic diversity that is readily accessible to the oat breeder. The objectives of the present paper were: (1) to evaluate isozyme polymorphisms in a sample of A. sterilis accessions from the U.S. National Small Grains Collection, (2) to analyze the distribution of isozyme diversity across the geographic range of the accessions, (3) to classify the accessions into groups based on isozyme variation, and (4) to suggest strategies for efficient sampling of this germplasm collection. One thousand and five accessions from 23 countries and 679 collection sites were screened for variation using 23 enzyme systems. Due to limited information about the genetic relationship among individual members of families of isozymes in hexaploid oat species, data were recorded solely for band presence. The frequencies of bands in accessions from the various countries were used to calculate the probability of genotypic identity (I_x.y), the probability of a unique genotype (U_x.y), and an adjusted polymorphic index (H_x). Accessions from Turkey and Lebanon had the largest polymorphic index values, Turkish and Moroccan accessions displayed the greatest numbers of bands. Accessions from Iran, Turkey, Iraq, and Lebanon had the largest mean probabilities of containing unique genotypes. Based on isozyme data, Turkey appeared to represent the center of diversity in this germplasm collection. Band frequencies calculated among countries were used in a principal component analysis. Accessions from Israel and Morocco clustered together; accessions from Iran, Iraq, Turkey, and Ethiopia formed another group; and Algerian accessions formed an outlying group. Several isozyme bands had a regional distribution. These results suggested that choosing accessions from countries based on their groupings in the principal component analysis should secure a greater range of diversity than sampling from the collection at random. Cluster analyses based on Jaccard's distances calculated for all pairwise combinations of the 1005 accessions revealed six broad genetic groups of accessions. Groups 1 and 6 contained accessions from many countries and encompassed half of all accessions. Groups 2 and 4 were heavily populated by accessions from Israel and Morocco. Groups 3 and 5 were composed almost exclusively of accessions from Iran, Iraq, and Turkey. By selecting representative accessions from these six groups, oat breeders could most effectively sample the range of genetic variation in this A. sterilis collection.     

Genomic characterization of natural and somaclonal variations in bananas (<Emphasis Type="Italic">Musa</Emphasis> spp.)

Unexpected variations can occur during natural and in vitro propagation of bananas (banana and plantain) to generate off-types. The molecular basis of such variations is not well-understood. This study aimed to characterize the functions of genomic regions varying within clones grown naturally or in vitro. Fifty-four simple sequence repeat (SSR) markers and six primer combinations of EcoR I/Msp I-amplified fragment length polymorphism (AFLP) were used to analyze accessions of the AA, BB, AB, AAA, AAB, and ABB groups of Musa, and polymorphic regions were sequenced to characterize candidate genes. One SSR locus with significant similarity to an arcelin gene revealed a deletion in a subculture regenerant. In AFLP analysis, 24 (6.15%) of 390 bands accounted for within-clone variations, with 0.5% and 5.65% occurring in natural and in vitro propagated plants, respectively. Sequence homology searches revealed that most polymorphic regions were related to cytochrome P450, cell-wall biosynthesis, and senescence genes. The importance of these candidate genes is discussed. The plants harboring the variations were field-established to relate molecular variations to phenotypic changes. Sixteen of the sequences registered in Genbank (ET165586 to ET165601) and select PCR primers from this study can be further tested for variations between normal clones and off-types in Musa.     

Single‐molecule real‐time sequencing reveals diverse allelic variations in carotenoid biosynthetic genes in pepper (Capsicum spp.)

The diverse colours of mature pepper (Capsicum spp.) fruit result from the accumulation of different carotenoids. The carotenoid biosynthetic pathway has been well elucidated in Solanaceous plants, and analysis of candidate genes involved in this process has revealed variations in carotenoid biosynthetic genes in Capsicum spp. However, the allelic variations revealed by previous studies could not fully explain the variation in fruit colour in Capsicum spp. due to technical difficulties in detecting allelic variation in multiple candidate genes in numerous samples. In this study, we uncovered allelic variations in six carotenoid biosynthetic genes, including phytoene synthase (PSY1, PSY2), lycopene β‐cyclase, β‐carotene hydroxylase, zeaxanthin epoxidase and capsanthin‐capsorubin synthase (CCS) genes, in 94 pepper accessions by single‐molecule real‐time (SMRT) sequencing. To investigate the relationship between allelic variations in the candidate genes and differences in fruit colour, we performed ultra‐performance liquid chromatography analysis using 43 accessions representing each allelic variation. Different combinations of dysfunctional mutations in PSY1 and CCS could explain variation in the compositions and levels of carotenoids in the accessions examined in this study. Our results demonstrate that SMRT sequencing technology can be used to rapidly identify allelic variation in target genes in various germplasms. The newly identified allelic variants will be useful for pepper breeding and for further analysis of carotenoid biosynthesis pathways.     

Analysis of the wild potato germplasm of the series Acaulia with AFLPs: implications for ex situ conservation

The wild potato germplasm of the series Acaulia maintained at the Centre for Genetic Resources, The Netherlands, currently consists of 314 accessions. This collection comprises seed samples of the species Solanum acaule (ssp. acaule, ssp. aemulans, ssp. palmirense and ssp. punae) and Solanum albicans collected from South America. In order to validate taxonomic classification, to investigate the extent of redundancy and to study the distribution of genetic diversity across the collection area, the entire collection was analysed with two AFLP primer pairs on two plants per accession. Within the entire sample a total number of 130 polymorphic bands were scored for the two primer pairs. An UPGMA cluster analysis grouped the majority of plants according to the species and subspecies. A total number of 16 misclassifications were identified, including four cases that did not seem to belong to the series Acaulia. Two accessions were found to consist of plants of different AFLP clusters. AFLP data also allowed the taxonomic classification of the subspecies of 97 accessions that previously were described as S. acaule only. For 126 accessions the two individuals studied displayed identical AFLP profiles. Forty six of these 126 accessions shared their profiles with both or single plants of other accessions. These were all tested for identical profiles for a third primer pair, resulting in 15 duplication groups consisting of a total number of 22 accessions and 14 single plants. Analyses of molecular variance (AMOVA) were performed to examine the distribution of genetic variation. Comparison of geographic distances between the collection site of plants and the number of AFLP polymorphisms revealed no consistent relationship between geographic distance and genetic diversity. AFLP analysis appeared to be an efficient method to verify taxonomic classification and to identify redundancies in the wild germplasm of the series Acaulia. Implications of the results for the ex situ conservation of wild potato germplasm are discussed. Received: 6 November 2000 / Accepted: 20 April 2001     

Comparative AFLP mapping in two hexaploid oat populations

Amplified fragment length polymorphisms (AFLPs) can be used to quickly develop linkage maps in plant species and are especially useful for crops with large genomes like oat (Avena sativa L., 2n=6x=42). High reproducibility and consistency are crucial if AFLP linkage maps are employed for comparative mapping. We mapped AFLP markers in combination with restriction fragment length polymorphism (RFLP) markers in two recombinant inbred populations of hexaploid oat in two laboratories to test the consistency of AFLP markers in a polyploid crop. Eight primer combinations produced 102 and 121 scoreable AFLP markers in the respective populations. In a population from the cross Kanota×Ogle, AFLP markers were placed onto a RFLP reference map consisting of 32 linkage groups. Nineteen linkage groups from another population from the cross Kanota×Marion were assigned to the reference map using AFLP and RFLP markers homologous to those used in the Kanota× Ogle cross. Reproducibility of AFLP assays was high in both laboratories and between laboratories. The AFLP markers were well-distributed across the genome in both populations. Many AFLP markers tended to extend the distance between adjacent RFLP markers in linkage analysis. Of the 27 polymorphic AFLPs common in both populations, 20 mapped to homologous linkage groups, 4 were unlinked in at least one population, and 3 mapped to different linkage groups in the two crosses. We believe that 1 of the 3 markers that mapped to a different linkage group in the two populations mapped to homoeologous linkage groups. The linkage map of hexaploid oat is not yet complete, and genomic rearrangements such as translocations exist among cultivars and are likely to account for the remaining two non-syntenous mapping results. AFLPs provide not only a fast and powerful tool for mapping but could be useful in characterizing genomic structural variations among germplasms in hexaploid oat. Received: 17 December 1999 / Accepted: 28 July 2000