Chloroplast and nuclear DNA variation in common wheat: insight into the origin and evolution of common wheat

To understand the origin and evolution of common wheat, chloroplast (ct) and nuclear DNA variations were studied in five hexaploid and three tetraploid wheat subspecies. Based on chloroplast simple sequence repeats at 24 loci, they were classified into two major plastogroups. Plastogroup I consisted of 11 plastotypes, including the major plastotype H10 that occurred at the highest frequency (59%) in common wheat. Plastogroup II consisted of five plastotypes and occurred in eight out of 27 accessions of T. aestivum ssp. spelta and one accession of ssp. aestivum. As for nuclear DNA variations, AFLP data using 10 primer sets revealed two major clades of a phylogenetic tree constructed by UPGMA (unweighted pair-group method with arithmetic mean), one consisting of common wheat and the other of emmer wheat. The clade of common wheat was further divided into two major and six minor subclades. One of the major subclades consisted only of non-free-threshing ssp. spelta accessions, which were grouped into two clusters, one consisting only of accessions with plastogroup I ctDNA and the other with both plastogroups I and II. T. aestivum ssp. macha, another non-free-threshing common wheat, formed the other cluster. Taken together, our data indicate the existence of at least two maternal lineages in common wheat and support the hypothesis that European spela wheat originated in Europe separately from other groups of common wheat.     

The use of RAPD analysis to classify Triticum accessions

 Crop germplasm collections contain a considerable percentage of misclassified accessions which may affect the use of germplasm for agricultural crop improvement. The objective of this study was to determine if random amplified polymorphic DNA (RAPD) analysis could be used to reclassify misclassified Triticum accessions. Twelve accessions suspected to be misclassified, based on morphological characters, as either macha or vavilovii wheat were studied using RAPD and cytological analyses. In the RAPD analysis, a dendrogram, based on Jaccard genetic similarity coefficients, grouped 5 dicoccum-like, 1 timopheevii-like, and 6 monococcum-like accessions with Triticum dicoccum, T. timopheevii, and T. monococcum accessions, respectively. These results were confirmed by the cytological analysis. A RAPD marker specific to the D genome was also detected. This study suggests that RAPD analysis can be used to classify germplasm and to distinguish some species in Triticum. Received: 12 June 1998 / Accepted: 18 August 1998     

Analysis of intraspecific divergence of hexaploid wheat Triticum spelta L. by chromosome C-banding

Intraspecific divergence of hexaploid wheat Triticum spelta was studied by chromosome C-banding in 41 accessions of different geographic origins. The spelt accessions did not differ in karyotype structure or heterochromatin distribution from common wheat, but showed greater intraspecific polymorphism for chromosome rearrangements (translocations, inversions) and banding patterns. On evidence of C-banding patterns, spelt was assumed to occupy an intermediate position between tetraploid and hexaploid wheat species. Accessions of the Asian spelt subspecies had more diverse banding patterns than European accessions. A relatively high frequency of chromosome rearrangements was observed in Iranian accessions. Visual analysis revealed high uniformity of chromosome banding patterns in T. spelta populations of Afghanistan, Spain, and Germany (Bavarian group), suggesting a significant role of the founder effect in their evolution.     

Stripe rust analysis of D-genome synthetic wheats (2n = 6x = 42, AABBDD) and their molecular diversity

Stripe or yellow rust caused by Puccinia striiformis f. sp. tritici is a threat to many of the existing cultivars of Pakistan. Many attempts are being made to evolve new varieties resistant to stripe rust to reduce the losses caused by this disease. For this purpose, novel genes are needed to incorporate into the existing cultivars. These genes are found in the wild progenitors of wheat that are D-genome donors to wheat. As a result of extensive research, wheat synthetic hexaploids have been developed. These synthetics have resistances against biotic as well as abiotic stresses including the yellow rust. A group of such synthetics has been identified which seems resistant to this destructive disease. This group was tested under field conditions to identify resistance against stripe rust. The same population was analysed at molecular level to explore the genetic diversity for rust resistance. Genetic diversity among 34 selected synthetic hexaploid wheats was studied by random amplified polymorphic DNA (RAPD) analysis. A set of 12 RAPD primers was applied, and the level of polymorphism was found to be 46.67%. The coefficients in the range of 71–100% were detected by genetic similarity matrix based on Nei and Li's index. These coefficients were used for constructing a dendrogram using unweighted pair group of arithmetic means. Synthetic hexaploid line 34 was found to exhibit maximum genetic distances among the 34 selected lines. The same accession also showed excellent phenotypic characters with above average grain weight. These synthetic hexaploids carrying genetic potential for stripe rust resistance and morphological traits should be useful for improvement of existing wheat cultivars.     

Genotyping of <Emphasis Type="Italic">Triticum</Emphasis> ssp. Hexaploid Species Samples with ISSR-Markers

The genetic improvement of soft wheat (Triticum aestivum L.) and other hexaploid wheat species (T. spelta, T. spherococcum, T. petropavlovskyi, and T. compactum) is important. This can be done by transferring genes of interest (resistance to biotic and abiotic factors). For this purpose, phylogenetic connections of the studied genotypes should be investigated. This problem can be solved by using a multilocus system based on ISSR markers. The marker system is highly polymorphic and convenient for analysis. The study presents the results of a comparison of 20 different hexaploid wheat genotypes based on ISSR markers. In addition, the level of polymorphism was determined and a dendrogram reflecting the phylogenetic connections between the studied genotypes was constructed. It was shown that the species located next to each other according to the systematics turned out to be more remote after the ISSR-marker analysis, and, vice versa, the species that were systematically more distant showed a higher level of kinship.     

Applicability of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers

 Inter-simple sequence repeat polymorphic DNA (ISSR) was evaluated for its applicability as a genetic marker system in wheat. PCR was carried out with primers that annealed to simple sequence repeats. The resultant products were subjected to agarose-gel electrophoresis, and the banding patterns were compared among six wheat accessions containing diploid, tetraploid, and hexaploid members. Out of 100 examined, 33 primers produced distinguishable as well as polymorphic bands in each of the six accessions. Although most of the primers that gave distinct bands (30 primers out of 33) contained dinucleotide repeats, each of the primers with tri-, tetra-, and penta-nucleotide motifs also yielded discrete bands. Primers based on (AC)_n repeats gave the most polymorphic bands. In total, 224 polymorphic bands were found in the comparison between Einkorn wheats whereas, on the average, 120 polymorphic bands were detected between common wheats. ISSR primers produced several times more information than RAPD markers. The extent of band polymorphism was similar to that of RFLP markers, and greater than that of RAPDs. The genetic relationships of wheat accessions estimated by the polymorphism of ISSR markers were identical with those inferred by RFLP and RAPD markers, indicating the reliability of ISSR markers for estimation of genotypes. These polymorphic bands are potential candidates as novel markers for use in linkage-map construction in wheat. The characteristic features of ISSR markers, i.e. polymorphism, generation of information and ease of handling, suggest their applicability to the analysis of genotypes as well as to the construction of PCR-based genome maps of wheats. Received: 15 September 1996 / Accepted: 25 October 1996     

Phylogenetic relationships and intraspecific variation of D-genome Aegilops L. as revealed by RAPD analysis

RAPD analysis was carried out to study the genetic variation and phylogenetic relationships of polyploid Aegilops species, which contain the D genome as a component of the alloploid genome, and diploid Aegilops tauschii, which is a putative donor of the D genome for common wheat. In total, 74 accessions of six D-genome Aegilops species were examined. The highest intraspecific variation (0.03-0.21) was observed for Ae. tauschii. Intraspecific distances between accessions ranged 0.007-0.067 in Ae. cylindrica, 0.017-0.047 in Ae. vavilovii, and 0.00-0.053 in Ae. juvenalis. Likewise, Ae. ventricosa and Ae. crassa showed low intraspecific polymorphism. The among-accession difference in alloploid Ae. ventricosa (genome DvNv) was similar to that of one parental species, Ae. uniaristata (N), and substantially lower than in the other parent, Ae. tauschii (D). The among-accession difference in Ae. cylindrica (CcDc) was considerably lower than in either parent, Ae. tauschii (D) or Ae. caudata (C). With the exception of Ae. cylindrica, all D-genome species--Ae. tauschii (D), Ae. ventricosa (DvNv), Ae. crassa (XcrDcrl and XcrDcrlDcr2), Ae. juvenalis (XjDjUj), and Ae. vavilovii (XvaDvaSva)--formed a single polymorphic cluster, which was distinct from clusters of other species. The only exception, Ae. cylindrica, did not group with the other D-genome species, but clustered with Ae. caudata (C), a donor of the C genome. The cluster of these two species was clearly distinct from the cluster of the other D-genome species and close to a cluster of Ae. umbellulata (genome U) and Ae. ovata (genome UgMg). Thus, RAPD analysis for the first time was used to estimate and to compare the interpopulation polymorphism and to establish the phylogenetic relationships of all diploid and alloploid D-genome Aegilops species.     

A comparison of RAPD and isozyme analyses for determining the genetic relationships among Avena sterilis L. accessions

Isozyme analysis is a valuable tool for determining genetic relationships among breeding lines and populations. The recently developed DNA technologies which can assay a greater proportion of the plant genome are providing a plentiful array of additional genomic markers. The objective of this research was to compare random amplified polymorphic DNA (RAPD) versus isozyme-based estimation of relationships among 24 accessions of a hexaploid wild oat, Avena sterilis L. The accessions were evaluated for variation in 23 enzyme systems and by 21 10-mer primers. A total of 77 polymorphic isozyme bands and 115 polymorphic RAPD bands were observed. Two matrices of genetic distances were estimated based on band presence/ absence. These matrices were subsequently utilized in cluster analysis and principal coordinate analysis. Both isozymes and RAPDs were proficient at distinguishing between the 24 accessions. The correspondence between the elements of both distance matrices was moderate (r=0.36**). Nevertheless, the overall representation of relationships among accessions by cluster analysis and ordination was in considerable agreement. The two techniques contrasted most notably in pair-by-pair comparisons of relationships. RAPD analysis resulted in a more definitive separation of clusters of accessions. The most significant impact of the DNA-based markers probably will be the more accurate determination of relationships between accessions that are too close to be accurately differentiated by isozymes.The research reported in this publication was funded by the North Carolina Agricultural Research Service, the North Carolina Biotechnology Center, and by a Heisenberg Fellowship (HE 1497/3-2) provided by the German Research Council to Manfred Heun     

粘类非1BL/1RS小麦CMS基因定向选择及其育性特性的研究

对携有不同不育基因的4个粘类小麦雄性不育系进行了定向选择与鉴定,并对其育性特性进行研究,以选育更具应用价值的粘类非1BL/1RS小麦雄性不育系,推动三系杂交小麦的实际应用.结果表明:(1)根尖体细胞随体鉴定和A-PAGE技术分析筛选出的SP4、莫迦小麦为非1BL/1RS类型,其它供试不育系均属于1BL/1RS类型;(2)减数分裂及成熟花粉粒形态观察,粘类非1BL/1RS小麦雄性不育系其不育性是在整个配子发育过程中连续产生的,且在B型不育细胞质背景下,SP4和莫迦小麦的花粉细胞学形态与在K、Ven型2种不育细胞质背景下的不同,B型不育细胞质背景下SP4和莫迦不育系的花粉萌发率比K、Ven型不育细胞质背景下的花粉萌发率高;(3)以不同来源不育基因培育成的粘类K、Ven型非1BL/1RS不育系育性恢复性测定发现,SP4、莫迦小麦2种雄性不育系育性恢复性有一定差异,莫迦小麦不育类型育性恢复性高于SP4.     

Segregation analysis of heading traits in hexaploid wheat utilizing recombinant inbred lines

The purpose of this study was to analyze the genetic segregation of heading traits in wheat using recombinant inbred lines (RILs) of hexaploid wheat, derived from Triticum aestivum cv. Chinese Spring and T. spelta var. duhameliamum. The population was examined under controlled environmental conditions as well as in the field. This strategy differentiated the effect of three genetic factors (vernalization requirement, photoperiod sensitivity and narrow-sense earliness) and identified their interactions. Correlation analysis showed that photoperiod sensitivity and narrow-sense earliness are critical for heading time in the field. Single-marker analysis using 322 molecular markers segregating among RIL detected a total of 38 linked markers for each genetic factor and heading in the field. In interval analysis, two Vrn genes (Vrn-B1 and Vrn-D1) and Ppd-B1 were mapped on chromosomes 5B, 5D and 2B, respectively. It was noticed that Vrn-B1 on 5B from the spelt wheat conferred a strong-spring habit equivalent to the homologous Vrn-A1. Quantitative trait locus analysis also showed that Ppd-B1 was not detected under the short-day condition without vernalization treatment, and that there were two types of genes for photoperiod sensitivity, dependent on and independent of vernalization treatment.     

Genetic diversity and relationships among germplasm of Jatropha curcas L. revealed by RAPDs

Variation is the phenomenon where individuals of a population differ from each other. The variation or diversity can have morphological manifestation or genetic basis. Individual identification based on morphological record is the most common practice in Jatropha. Therefore, in order to find a proper method for estimation of genetic diversity and genetic relationships among different germplasm of Jatropha curcas L., random amplified polymorphic DNA (RAPD) technique based on polymerase chain reaction (PCR) was used for described purpose. Out of 55 decamer primers tested, 26 primers produced good amplification products. A total of 6,011 amplification products were scored from which only 1,859 bands (30.92%) were found to be polymorphic and the size of bands ranged from 300 to 2,500 bp. Unweighted pair group method using arithmetic average cluster analysis revealed clear genetic difference among J. curcas germplasm. The scientific data presented in this study suggests that RAPD-PCR could be used as a valuable tool for estimation of genetic diversity and genetic relationship among germplasm of J. curcas L.     

Genetic diversity of Persian shallot (Allium hirtifolium Boiss.) populations based on morphological traits and RAPD markers

Mooseer or Persian shallot (Allium hirtifolium Boiss.) is a bulbous perennial herb belonging to Alliaceae family. Genetic diversity of 16 mooseer populations collected from different parts of Iran were evaluated using 14 morphological traits as well as antioxidant activities and RAPD markers. Statistical analysis showed significant differences among populations for all morphological traits. In a principal component analysis, four components showed 77.5 % of the total morphological variation. Based on the morphological traits, populations were divided into five groups by clustering. Antioxidant capacities differed among all populations, with the Sahneh and Nahavand populations having the highest and the lowest activities, respectively. Genetic diversity of populations was also investigated through RAPD technique using 14 random primers. Cluster analysis based on RAPD markers plus 47 % coefficient of similarity divided the genotypes into six distinct groups. The highest and lowest similarities between populations were detected to be 0.63 and 0.21, respectively. These results indicated that the assessment of genetic diversity in Iranian mooseer populations could be appropriately carried out using RAPD technique which correlates with morphological traits.     

苏铁属植物RAPD反应体系的优化及部分种类亲缘关系的探索

通过优化苏铁属植物的RAPD反应体系,进而探讨苏铁属部分种类的亲缘关系。结果表明,Mg~(2+)、dNTP、Taq酶及随机引物浓度在RAPD反应中有重要影响,而模板DNA浓度有一个很大的适应范围。适合苏铁属植物RAPD分析的反应体系:20μL反应体系中,含有10 mmol/L Tris-HCl(pH8.3)、50 mmol/L KCl、2.0mmol/L MgCl_2、200μmol/L dNTP、0.3μmol/L随机引物、模板DNA 50ng、Taq酶1.0 U。聚类分析结果基本反应了苏铁属各个种间的亲缘关系,证明了RAPD适用于苏铁属种间亲缘关系分析。RAPD聚类分析结合形态学研究表明:海南苏铁、台湾苏铁、广东苏铁、滇南苏铁和仙湖苏铁之间的亲缘关系较远,支持各自成为独立的种。     

Genetic diversity in Eastern U.S. soft winter wheat (Triticum aestivum L. em. Thell.) based on RFLPs and coefficients of parentage

 Genetic diversity in a set of 11 red and 11 white wheat lines from the Eastern U.S. soft wheat germplasm pool was measured using restriction fragment length polymorphism (RFLP) assay and coefficients of parentage (COP) analysis. On average, 78% of all bands revealed by three enzymes with 48 RFLP clones were monomorphic. Average pairwise genetic similarity (GS) was 0.97 when data from all enzymes were pooled. Probe Polymorphic Information Content (PIC) indexes ranged from 0 to 0.73 with a mean of 0.2. Fewer than 55% of the probes revealed any polymorphism. The frequency of polymorphism in the Eastern U.S. soft white winter (SWW) wheat gene pool was much lower than that observed in the Eastern U.S. soft red winter (SRW) wheat gene pool. SWW lines formed a single group on a dendrogram based on cluster analysis of RFLP-derived GS estimates, while SRW lines did not form a single group. COP values for all pairs of the Eastern U.S. soft wheat lines ranged from 0.02 to 0.9 with a mean of 0.21. SWW wheat lines traced to 53 ancestral lines and had an average COP of 0.51. The SRW wheat gene pool had more complex parentages (mean COP=0.15 and a total of 65 ancestral lines). COPs were correlated with RFLP-based GS for all line pairs (r=0.73, P<0.01). However, correlations between the two similarity measures were substantially lower when the SRW and SWW wheat gene pools were considered individually (r values of 0.23 and 0.28, respectively). The actual GS among unrelated lines in the U.S. Eastern soft wheat gene pool appears to be higher than that observed for unrelated landraces from Southwest Asia (0.96 vs. 0.905), suggesting that the ancestral landrace parents of this gene pool were themselves drawn from a base population where inbreeding, i.e., F, was greater than zero. Received:18 April 1996 / Accepted: 6 September 1996     

Analysis of tetraploid Elymus species using wheat microsatellite markers and RAPD markers.

An analysis of Amplification fragment polymorphism of DNA from 27 accessions of 19 tetraploid Elymus species was carried out using 18 wheat microsatellite (WMS) primer pairs and 10 decamer primers. Ten WMS primer pairs produced multiple polymorphism on all accessions tested. Two independent phenograms, one based on WMS-PCR and one on RAPDs, separated the 19 tetraploid species into two main groups, viz., the SH genome species group and the SY genome species group. The results coincide with the genomic classification of these species and hence support previous studies showing that Elymus is not a monophyletic genus. The assays indicated that accessions within a species cluster together, which concurs with the morphological classification. Interspecific and intraspecific polymorphisms were detected by the WMS-PCR and RAPD analyses. Variation was observed among accessions of Elymus caninus. The WMS-PCR detected a much higher level of polymorphism than the RAPD analysis. WMSs seem to be more efficient markers than RAPD markers for studying the population diversity of Elymus species. The potential of cross-species amplification of microsatellite markers as an additional source for genetic analysis and applications in Elymus is discussed in the context of these results.     

SEED PROTEIN PROFILES AND THE ORIGIN OF THE HEXAPLOID WHEATS

Protein profiles of Triticum and Aegilops species were obtained by electrophoresis of crude seed extracts on polyacrylamide gels. All subspecies of the hexaploid T. aestivum (AABBDD) showed a very uniform profile that could be closely simulated only by the pattern produced by a protein mixture (2:1) from specific profile types of the ancient tetraploid cultivar T. dicoccum (AABB) and the wild diploid Ae. squarrosa (DD). An exceptional hexaploid pattern occurred only in some accessions of T. aestivum ssp. macha. These results confirm the parentage of the aestivum hexaploids in general as T. dicoccum and Ae. squarrosa and more specifically identify the type of the D-genome donor. They suggest that these wheats, excepting the aberrant macha types, had essentially a monophyletic origin in southwestern Asia. They favor the hypotheses that the cultivated aestivum wheats were derived from the so-called primitive spelta complex primarily by mutation of a single gene governing the free threshing character and that alpine spelta represents an element displaced from the area of endemism.     

Morphological and molecular variation among populations of octoploid Fragaria virginiana and F. chiloensis (Rosaceae) from North America

Relationships among 37 North American octoploid strawberry populations were studied by evaluating 44 morphological traits and 36 randomly amplified polymorphic DNA (RAPD) markers. Both data sets were analyzed by principal components analysis and UPGMA clustering based on genetic distances. Morphological data defined five groups: east of the Missouri River (Fragaria virginiana ssp. virginiana), the Black Hills (F. virginiana ssp. virginiana and ssp. glauca), from the eastern Cascades to the eastern Rocky Mountains (F. virginiana ssp. glauca), the western Cascades and Olympic Peninsula (F. virginiana ssp. platypetala), and the Pacific coast (F. chiloensis). Canonical discriminant analysis clearly discriminated populations into these provenances, suggesting that these groups are morphologically distinct. RAPD data defined three groups, one with F. virginiana ssp. virginiana and ssp. glauca, another with F. chiloensis, and a third with F. virginiana ssp. platypetala. The latter was more similar to F. chiloensis than F. virginiana, suggesting it is likely a subspecies of F. chiloensis. All octoploid North American strawberries have likely derived from a common ancestor and have differentiated into F. chiloensis and F. virginiana by adapting to moister and drier environments, respectively.     

RAPD analysis reveals genetic variability among sexual and Apomictic Paspalum dilatatum poiret biotypes

Paspalum dilatatum is a valuable forage grass in the subtropics. This species consists of several sexual (tetraploid) and apomict (penta- and hexaploid) biotypes. It has been proposed that the presence of a genome of unknown origin, the X genome, is responsible for apomixis in penta- and hexaploid biotypes. Here we evaluated the utility of random amplified polymorphic DNA (RAPD) markers for discriminating sexual and apomictic P. dilatatum biotypes. DNA samples from nine accessions, including P. intermedium, P. juergensii, and P. dilatatum (ssp. flavescens, and the common and Uruguayan biotypes) were analyzed with 86 RAPD primers. Three hundred sixty-two fragments were scored and genetic similarity estimates revealed that the penta- and hexaploid biotypes were highly similar (S(D) > or = 0.913). Forty RAPDs were unique to the penta- and hexaploid biotypes. Overall RAPD markers were useful for assessing genetic variation among closely related P. dilatatum genotypes as well as generating putative X genome markers.     

Genetic diversity among European cultivated spelt revealed by microsatellites

Spelt and common wheat constitute two of the six groups of the hexaploid wheats with an AABBDD genome. Spelt culture has been progressively replaced by that of common wheat which out-yields spelt under high-input conditions. In the last decades, spelt breeders intended to introduce the yield-potential and bread-making qualities of common wheat into spelt, by frequent crossings between accessions of these two different groups. The present study aims at determining the genetic basis of modern spelt cultivars in terms of intra-group variability and inter-group (spelt vs common wheat) distances, by using microsatellite markers developed for common wheat. The allelic composition of 30 spelt and nine common wheat accessions was determined at 17 microsatellite loci. The coefficient of co-ancestry (ƒ) and the genetic distances (1 - proportion of shared alleles) based upon allelic composition were calculated for all pairs of accessions. Two dendrograms were constructed using the UPGMA method. Amplification products were found for all loci on most accessions. A total of 113 alleles was identified, of which 60.2% were specific to spelt or common wheat. The correlation between (1 –ƒ ) and the genetic distance was high (0.701***). The mean pairwise genetic distance was 0.656 ± 0.181 over the 39 accessions, 0.706 ± 0.14 among common wheat and 0.573 ± 0.172 among spelt. The mean genetic distance between spelt and wheat was 0.782 ± 0.113. The two dendrograms were in accordance with each other and clearly separated the spelt from the common wheat accessions. It is concluded that microsatellites developed for common wheat and distances based on the proportion of shared alleles are powerful tools for reconstructing phylogenies in spelt, and that the genetic basis of modern spelt cultivars is narrow despite frequent crosses made with bread wheat. Received: 26 January 2000 / Accepted: 26 May 2000