Genetic Diversity among Syrian Cultivated and Landraces Wheat Revealed by AFLP Markers

Genetic diversity among some important Syrian wheat cultivars was estimated using Amplified Fragment Length Polymorphism (AFLP) markers. Five Triticum aestivum L. and 10 Triticum turgidum ssp. durum were analyzed with 11 EcoRI–MseI primer pair combinations. Of the approximately 525 detected AFLP markers, only 46.67% were polymorphic. Cluster analysis with the entire AFLP data divided all cultivars into two major groups reflecting their origins. The first one contained T. aestivum L. cultivars, and the T. turgidum ssp. durum cultivars and landraces were grouped in the second. Narrow genetic diversity among all cultivars was detected with an average genetic similarity of 0.884. The lowest similarity index (0.9) was found between Cham5 and Hamary (durum wheat), whereas this value was 0.93 between Salamony and Bouhouth 4 (T. aestivum L.). The narrow genetic diversity level indicates that these genotypes could be originated from the same source. AFLP analysis provides crucial information for studying genetic variation among wheat cultivars and provides important information for plant improvement.     

Analysis of Genetic Diversity in the Brassica napus L. Gene Pool Using SSR Markers

Genetic diversity throughout the rapeseed (Brassica napus ssp. napus) primary gene pool was examined by obtaining detailed molecular genetic information at simple sequence repeat (SSR) loci for a broad range of winter and spring oilseed, fodder and leaf rape gene bank accessions. The plant material investigated was selected from a preliminary B. napus core collection developed from European gene bank material, and was intended to cover as broadly as possible the diversity present in the species, excluding swedes (B. napus ssp. napobrassica (L.) Hanelt). A set of 96 genotypes was characterised using publicly available mapped SSR markers spread over the B. napus genome. Allelic information from 30 SSR primer combinations amplifying 220 alleles at 51 polymorphic loci provided unique genetic fingerprints for all genotypes. UPGMA clustering enabled identification of four general groups with increasing genetic diversity as follows (1) spring oilseed and fodder; (2) winter oilseed; (3) winter fodder; (4) vegetable genotypes. The most extreme allelic variation was observed in a spring kale from the United Kingdom and a Japanese spring vegetable genotype, and two winter rape accessions from Korea and Japan, respectively. Unexpectedly the next most distinct genotypes were two old winter oilseed varieties from Germany and Ukraine, respectively. A number of other accessions were also found to be genetically distinct from the other material of the same type. The molecular genetic information gained enables the identification of untapped genetic variability for rapeseed breeding and is potentially interesting with respect to increasing heterosis in oilseed rape hybrids.     

Evaluation of Genetic Diversity Among Bulgarian Winter Wheat (Triticum aestivum L.) Varieties During the Period 1925–2003 Using Microsatellites

Simple sequence repeats (SSRs) were used to study the genetic diversity within old and modern Bulgarian winter wheat (Triticum aestivum L.) varieties released in 20th century. A set of 91 varieties were screened by 19 wheat microsatellite markers (WMS), covering 17 wheat chromosomes, and one secalin-specific marker for rye chromosome arm 1RS. A total of 136 allelic variants were detected at 22 loci, ranging from 2 to 11, with an average of 6.8 alleles per marker. For 7 markers, null alleles were detected. The occurrence of rare alleles (frequency <2%) was observed for 13 markers. The polymorphism information content (PIC) values of the markers ranged from 0.10 (WMS0165 on 4AS) to 0.81 (WMS0437 on 7DL) with an average of 0.51. Approximately 74% of the varieties, mostly non-commercial, showed heterogeneity, with an average level of 10.1%. For the majority of markers, the relative frequencies of alleles varied considerably among different groups of varieties, revealing the effects of different selection between breeding centres. Some alleles, present in old genotypes, were lost, and new alleles have been introduced into modern varieties. Genetic diversity values over different periods of release were high, starting at 0.64 for varieties developed before 1960 to reach 0.71 in 1990s, revealing no declining trends in the diversity due to breeding activity. The cluster analysis discriminated all varieties (except for two) and revealed distinct groups of old and modern varieties, released from the main breeding centres in Northern, Southern and Western Bulgaria.     

Genetic Diversity Among Brazilian Cultivars and Landraces of Tomato Lycopersicon Esculentum Mill. Revealed by RAPD Markers

Random amplified polymorphic DNA markers (RAPD) were used to estimate the variability of 35 tomato accessions (Lycopersicon esculentum Mill.). A total of 257 reproducibly scorable bands were obtained from 20 primers, 78.6% of which were polymorphic. The percentage distribution of RAPD markers shows a bimodal distribution, and the frequency of rare alleles is similar in commercial and landrace accessions. Genetic distances among accessions were calculated and a dendrogram showing the genetic relationships among them was constructed allowing for the separation of four groups. Twenty out of 23 Brazilian landraces fell within one group, whereas commercial cultivars were distributed in the four groups. AMOVA analysis of RAPD data showed that, despite the high within Brazilian landraces and commercial cultivars variation, these two groups are significantly different, indicating that landraces can be a source of variation for breeding programs.     

Genetic Diversity and Phylogenic Relations Among Sahelian Sorghum Accessions

To establish the genetic relationship among Sahelian sorghum [Sorghum bicolor (L.) Moench S.L.] landraces from Burkina Faso were submitted to electrophoretic analysis for 10 enzymatic systems and 18 loci. Four enzymatic systems (ADH, LAP, MDH, PGD) and five loci revealed polymorphism both within and among landraces. Thirty-eight per cent of the landraces were monomorphic in all the 18 loci. The genotypic frequencies in most of the landraces deviated markedly from Hardy–Weinberg proportions due to a major heterozygote deficit, the landrace being homozygous or a mixture of homozygotes. Multivariate analysis yielded three main groups, containing native landraces and five minors, containing introduced cultivars, randomly distributed over the territory. The pattern of allelic occurrence was random and unrelated to external selection pressures. The major diversity among landraces appears to be from genetic shift caused by farmers’ selection of their seeds. It could also be due to the low rates of outcrossing (19%) and migration (0.06) prevailing in the set.     

Cultivation and Taxonomic Classification of Wheat Landraces in the Upper Panjsher Valley of Afghanistan After 23 Years of War

After 23 years of war, current information about the biodiversity of crops in the Hindukush mountains of Afghanistan is scarce. This study aimed at assessing the genetic composition of farmers wheat (Triticum spp.) populations through a survey of 21 randomly chosen cereal fields on both sides of the Panjsher river in the upper Panjsher valley of Northern Afghanistan. A stratified sampling of wheat heads according to morphological differences was followed by estimates of field size and grain yield and a formal interview with the landowner about the cropping sequence and the inputs used. About 75% of the cereal fields were cropped in rotation systems with faba bean (Vicia faba L.), barley (Hordeum vulgare L.), potato (Solanum tuberosum L.), maize (Zea mays L.) or fallow. Manure application at between 2.3 and 5.3 t ha⁻¹ was the major source of nutrient inputs at grain yield levels between 1.2 and 4.7 t ha⁻¹. The morphological characterization of the collection revealed 19 taxonomically different varieties of bread wheat (Triticum aestivum L.) but also barley and triticale (Triticosecale Wittm.) grown in mixtures. Populations within one field consisted of up to seven botanical wheat varieties. Farmers did not differentiate between morphological differences within such mixtures but identified their populations instead according to grain color, cooking properties and resistance to mildew and frost. Triticum aestivum var. subferrugineum was the most widespread wheat variety and no effects of altitude on biodiversity of wheat was noted across the transect. Particularly interesting was the occurrence of T. aestivum var. subferrugininflatum and var. subgraecinflatum which so far have only been reported from Mongolia. The finding of triticale indicated the active seed exchange with lowland or long-distance seed sources.     

Genetic variation of the durum wheat landrace Haurani from different agro-ecological regions

The durum wheat landrace Haurani (Triticum durum Desf.) is grown under contrasting climatic regions of Syria from Deir Ezzor, in the North-East (230 m altitude, 150 mm mean annual rainfall), to Qunaytra, in the South-West (1060 m altitude, 825 mm mean annual rainfall). In order to assess the genetic variation between and within Haurani populations, samples from eight provinces of Syria (Daraa, Damascus, Qunaytra, Deir Ezzor, Hassakeh, Aleppo, Homs and Hama) were analysed by RFLPs and seed storage proteins of glutenin subunits as markers. The analyses showed the presence of genetic polymorphisms in all populations with the highest values in those from Homs and Hassakeh. Moreover, the results point out differences in genetic distances between populations; some populations were further apart, such as Damascus and Aleppo, whereas others were closer to each other, for instance Homs and Hama. Cluster analysis identified two distinct groups of populations, characterized by geographical proximity, with similar rainfall and altitude. It is suggested that the similarity of landraces at locations close to each other might be the result of more frequent seed exchanges between farmers or of gene flow due to 5% estimated outcross rate of Haurani.     

Analysis of Microsatellite Diversity in Ethiopian Tetraploid Wheat Landraces

The extent and patterns of microsatellite diversity in 141 Ethiopian tetraploid wheat landraces consisting of three species Triticum durum Desf., T. dicoccon Schrank and T. turgidum L. were analyzed using 29 microsatellite markers. A high level of polymorphism and a large number of alleles unique for each species were detected. Compared to emmer (T. dicoccon) and poulard (T. turgidum) wheats, a higher genetic diversity was observed in T. durum. The A-genome was more polymorphic than the B-genome in all the three species. Microsatellites with (GA) _n -repeats had a higher number of alleles than (GT) _n -repeats. A species pairwise comparison was made to determine the percentage of shared alleles and a large number of common alleles among species were observed. Average gene diversity, across the 29 microsatellite loci, was 0.684 for T. durum, 0.616 for T. dicoccon and 0.688 for T. turgidum. Genetic distances were lower between T. durum and T. turgidum (0.26) than between T. durum and T. dicoccon (0.34) or between T. turgidum and T. dicoccon (0.38). A significant correlation (p < 0.01) was found between the number of alleles per locus and the gene diversity in all the three species. Allelic frequency variation was highest between T. turgidum and T. dicoccon (10.62%) and lowest between T. durum and T. turgidum (4.86%). A genetic similarity coefficient of 0.34, 0.46 and 0.37 was found in T. durum, T. dicoccon, and T. turgidum, respectively. The dendogram, which was constructed on the basis of a similarity matrix using the UPGMA algorithm, distinguished all accessions represented in the study.     

Analysis of Genetic Variability in a Sample of the Durum Wheat (Triticum durum Desf.) Spanish Collection Based on Gliadin Markers

In this work gliadin proteins were used to analyse the genetic variability in a sample of the durum wheat Spanish collection conserved at the CRF-INIA. In total 38 different alleles were identified at the loci Gli-A1, Gli-A3, Gli-B5, Gli-B1, Gli-A2 and Gli-B2. All the gliadin loci were polymorphic, possessed large genetic diversity and small and large differentiation within and between varieties, respectively. The Gli-A2 and Gli-B2 loci were the most polymorphic, the most fixed within varieties and the most useful to distinguish among varieties. Alternatively, Gli-B1 locus presented the least genetic variability out of the four main loci Gli-A1, Gli-B1, Gli-A2 and Gli-B2. The Gli-B1 alleles coding for the gliadin γ-45, associated with good quality, had an accumulated frequency of 69.7%, showing that the Spanish germplasm could be a good source for breeding quality. The Spanish landraces studied showed new gliadin alleles not catalogued so far. These new alleles might be associated with specific Spanish environment factors. The large number of new alleles identified also indicates that durum wheat Spanish germplasm is rather unique.     

Genetic diversity in Ethiopian hexaploid and tetraploid wheat germplasm assessed by microsatellite markers

The genetic diversity of a subset of the Ethiopian genebank collection maintained at the IPK Gatersleben was investigated applying 22 wheat microsatellites (WMS). The material consisted of 135 accessions belonging to the species T. aestivum L. (69 accessions), T. aethiopicum Jacubz. (54 accessions) and T. durum Desf. (12 accessions), obtained from different collection missions. In total 286 alleles were detected, ranging from 4 to 26 per WMS. For the three species T. aestivum, T. aethiopicum and T. durum on average 9.9, 7.9 and 7.9 alleles per locus, respectively, were observed. The average PIC values per locus were highly comparable for the three species analysed. Considering the genomes it was shown that the largest numbers of alleles per locus occurred in the B genome (18.4 alleles per locus) compared to A (10.1 alleles per locus) and D (8.2 alleles per locus) genomes. Genetic dissimilarity values between accessions were used to produce a dendrogram. All accessions could be distinguished, clustering in two large groups. Whereas T. aestivum formed a separate cluster, no clear discrimination between the two tetraploid species T. durum and T. aethiopicum was observed.     

Protein Heterogeneity in European Wheat Landraces and Obsolete Cultivars: Additional Information II

The endosperm storage protein of 46 European wheat (Triticum aestivum L.) landraces and obsolete cultivars have been fractionated by SDS-PAGE to determine the composition of high molecular weight glutenin subunits (HMW-GS) composition. It has been discovered that about 46% of the wheats were heterogeneous, comprising 2–11 different glutenin profiles. Eighteen of them were observed to be homogeneous. A total of 13 HMW-GS alleles, including 3 at the Glu-A1, 8 at the Glu-B1, and 3 at the Glu-D1 loci were revealed. HMW-GS null controlled by locus Glu-A1, subunits 7 + 8 by Glu-B1, and 2 + 12 by Glu-D1 predominated. However low frequented alleles such as 17 + 18, 20, 6, and 7 were observed. Furthermore, other new alleles encoding HMW-GS at the locus Glu-B1 have been found in one of France cultivar (Saumur d’Automne). The glutenin-based quality score ranged from 4 to 10.     

Assessing Genetic Diversity of Chinese Cultivated Barley by STS Markers

To assess the genetic diversity among China’s cultivated barley, sequence tagged site (STS) marker analysis was carried out to characterize 109 morphologically distinctive accessions originating from five Chinese eco-geographical zones. Fourteen polymorphic STS markers representing at least one in each chromosome were chosen for the analysis. The 14 STS markers revealed a total of 47 alleles, with an average of 3.36 alleles per locus (range 2–8). The proportion of polymorphic loci per population averaged 0.84 (range 0.71–1.00); the mean gene diversity averaged 0.39 (range 0.28–0.49). The means of P and H_e were highest in the Yangtze reaches and Southern zone (P = 1.00; H_e = 0.46) and lowest (P = 0.71 He = 0.28) in the Yellow river reaches zone. The STS diversity in different zones is quite different from the morphology diversity. The STS variation was partitioned into 17% among the zone and 83% within the zone. Both cluster and principal coordinate analyses clearly separated the accessions into a dispersed group (mostly two-rowed barley with a lower mean GS value) and a concentrated group (mostly six-rowed barley with a higher mean GS value) according to the spike characteristic with only a few exceptions. The accessions from the Qinghai-Tibet plateau formed a distinctive subgroup and can be distinguished from the concentrated group. The role of Tibet in the origin and evolution of cultivated barley has been discussed.     

Genetic Diversity within and Between Populations of Lathyrus genus (Fabaceae) Revealed by ISSR Markers

In order to evaluate the genetic diversity in Lathyrus genus, the Inter Simple Sequence Repeats method (ISSR) was exploited in five populations. These consisted of two cultivated species belonging to section Lathyrus (L. sativus L. and L. cicera L.) and a wild one belonging to the section Clymenum (L. ochrus DC.). Two 3′anchored ISSR primers and two unanchored ones, generated a total of 60 useful polymorphic DNA bands. Our data provide evidence of high molecular polymorphism at the intra- and the inter-specific levels showing that both wild and cultivated forms constitute an important pool of diversity. Moreover, among the generated DNA bands, a 500 bp band, totally absent in the banding patterns of the section Clymenum, appears to be a molecular marker of section Lathyrus. Results provided for lineage and suggest recent origin of these species that might have evolved from a common ancestor producing both L. ochrus species and the two other species L. sativus and L. cicera. These relationships support previous studies based on morphological variation and molecular analysis.     

RAPD Polymorphism of the White-Flowered Gourd (Lagenaria siceraria (Molina) Standl. Landraces and its Wild Relatives in Kenya

The present study was performed to investigate genetic diversity of Kenyan landraces of the white-flowered gourd (Lagenaria siceraria), which exhibits tremendous morphological variation. RAPD analyses were performed on 53 landraces of the cultivated species L. siceraria and 42 accessions of three wild species (40 L. sphaerica, 1 L. abyssinica, and 1 L. breviflora). A total of 432 polymorphic bands were detected using 54 primers. The four species were clearly differentiated from one another. Intra-specific variations were investigated with L. siceraria and its wild relative L. sphaerica. Landraces of the cultivated species collected from different ethnic communities or regions were differentiated. Morphological variations were not associated with RAPD variations. Bitter landraces collected in Maasai communities showed two specific RAPD bands. In the wild species, accessions collected from the eastern and western sides of the Great Rift Valley were genetically differentiated from each other. In both species, genetic and geographical distance matrices computed among all pairs of accessions were significantly correlated, implying that the observed geographical variation can be explained by the 'Isolation by distance model'. Progeny plants derived from a common mother in L. siceraria showed a low level of segregation in RAPD pattern, suggesting that collected landraces are cultivated, maintaining their inherent traits although they are monoecious and insect-pollinated, whereas the wild relative L. sphaerica showed a higher level of segregation. The morphological diversity observed among landraces of L. siceraria is the result of human selection and their genetic identities are maintained by inbreeding probably resulting from frequent self-pollination.     

Genetic Variation and Relationships of Pedigree-Known Oat, Wheat, and Barley Cultivars Releaved by Bulking and Single-Plant Sampling

Applications of bulking procedures have played an increasingly important role in molecular characterization of plant germplasm, but little attention has been made to address the effectiveness of detecting genetic variation and inferring genetic relationships via bulking. An analysis was performed here to compare the genetic variation detected and genetic relationships inferred via bulking and single-plant sampling of five oat (Avena sativa L.), wheat (Triticum aestivum L.), and barley (Hordeum vulgare L.) cultivars with known pedigrees using amplified fragment length polymorphism (AFLP) markers. Three AFLP primer pairs were applied to screen one bulk and eight single-plant samples of each cultivar and up to 140 AFLP bands were scored for each sample. Analyses of these AFLP data showed bulking revealed AFLP variation up to 21.4% less than corresponding single-plant sampling for these crop species and also introduced up to 2.2% upward and 5.1% downward biases in detecting AFLP variations for each cultivar. The genetic relationships inferred by bulking using the Dice's coefficient, the simple matching coefficient, and the Jaccard's coefficient were largely the same, but differed from those in single-plant samples employing average Dice's coefficient, average simple matching coefficient, and AMOVA-based distance method. All of the inferred genetic relationships were not congruent to the known pedigrees. Clearly, substantial biases could exist in detection of AFLP variation and in inference of genetic relationships from bulk samples, even for closely related germplasm, and more efforts to assess the effectiveness of bulking in inferring genetic variation and relationships are needed for more informative molecular characterization of plant germplasm.     

Genetic Diversity Among Traditional Ethiopian Highland Maize Accessions Assessed by Simple Sequence Repeat (SSR) Markers

Over the past three centuries, maize has become adapted to complex environmental conditions in the highlands of Ethiopia. We analyzed 62 traditional Ethiopian highland maize accessions, using 20 simple sequence repeat (SSR) markers and 15 morphological traits, to assess genetic diversity and relationships among these accessions and to assess the level of correlation between phenotypic and genetic distances. The accessions varied significantly for all of the measured morphological traits. The average number of alleles per locus was 4.9. Pair-wise genetic dissimilarity coefficients ranged from 0.27 to 0.63 with a mean of 0.49. Ward minimum variance cluster analysis showed that accessions collected from the Northern agroecology were distinct from the Western and Southern agroecologies. However, there was no differentiation between the Western and Southern accessions. This suggested gene flow between these regions. The relationship between morphological and SSR-based distances was significant and positive (r = 0.43, p = 0.001). The high genetic diversity observed among these set of accessions, suggests ample opportunity for the development of improved varieties for different agroecologies of Ethiopia. From conservation perspective, sampling many accessions from all agroecologies would be an effective way of capturing genetic variation for future collections and conservation.     

Microsatellite Markers Revealed the Genetic Diversity of an Old Japanese Rice Landrace ‘Echizen’

Landraces of rice (Oryza sativa L.) are valuable sources of genetic variation that have been lost in advanced cultivars. Seeds of a rice landrace stored for almost 100 years were found on Sado Island in Niigata prefecture, Japan. This report aims to present basic data on the genetic variation of this landrace, which was known as ‘Echizen’. Five samples of ‘Echizen’, consisting of two old samples, one sample maintained on farm, and two lines regenerated from old seeds were compared with other advanced cultivars and landraces using 19 microsatellite markers. Among the five samples of Echizen, the two stored samples showed greater diversity than the other samples. Cluster analysis based on the UPGMA method also showed that old Echizen was a diverse landrace that could cover the genetic diversity of most Japanese rice cultivars.     

A note about Triticum in Oman

Little is known about the diversity of wheat (Triticum spp.) in Oman. Results of a survey conducted in two remote mountain oases of northern Oman indicate that there exists considerable morphological variation within and among the five traditional landraces of wheat cultivated. Within two of the landraces grown on irrigated terraces, sized between 2 and 100 m², two new botanical wheat varieties (Triticum aestivum var. baladseetense and var. maqtaense) were identified of which the agronomic properties, in particular tolerance to drought and heat, and the nutritional value require further investigation.     

Genetic diversity of Pakistan wheat germplasm as revealed by RAPD markers

Wheat breeding in Pakistan started in 1930s before partition in the United India and so far has released more than 68 cultivars, but no systematic analyses of the genetic diversity of Pakistan wheat have been made. Twenty Pakistan wheat cultivars released from 1933 to 2002 were examined for genetic diversity and relationships using random amplified polymorphic DNA (RAPD) markers. Forty-two RAPD primers were applied and 184 polymorphic bands were generated for each cultivar. Most of the cultivars were genetically interrelated, although six of them displayed some genetic distinctness. The RAPD variation observed among these cultivars was low. Only 40.7% of the total scorable bands were polymorphic, and 26.1% of the polymorphic bands were observed most frequently (f = 0.95) among the 20 cultivars. The proportions of polymorphic bands for each cultivar ranged from 0.67 in ‘Yecora’ to 0.84 in ‘C-250’ with an average of 0.76. About 1.4% of the RAPD variation might have been fixed over the 69 years of wheat breeding, but such fixation was not statistically significant. These results are significant for future improvement and conservation of Pakistan wheat.     

Detection of genetic diversity in Libyan wheat genotypesusing wheat microsatellite markers

Twenty-four wheat microsatellites (WMS) wereused to estimate the extent of genetic diversity among 15 Libyanwheat genotypes. The WMS used determined 26 loci located on 20different chromosomes, and were capable of detecting 116 alleles withan average of 4.5 alleles per locus. Only two markers located on 2DSand 4DL, were monomorphic. The results indicated that the B genome(5.9 alleles per locus) was more variable than the A and Dgenomes (4.1 and 2.7 alleles per locus, respectively).Furthermore, the results obtained suggest that a relatively smallnumber of primers can be used to distinguish all genotypes used andto estimate their genetic diversity. Genetic dissimilarity valuesbetween genotypes, calculated by the WMS derived data, were used toproduce a dendrogram. The diversity within the analysed germplasm isdiscussed.