Genetic diversity of wild banana (<Emphasis Type="Italic">Musa balbisiana</Emphasis> Colla) in China as revealed by AFLP markers

Wild banana Musa balbisiana Colla is one of the progenitors of cultivated bananas and plantains. It is native to Southeast Asia and the western Pacific. South China represents the northern limit of its distribution range. The genetic diversity of Musa balbisiana was assessed by the amplified fragment length polymorphism (AFLP) fingerprinting in 15 populations of China. Four primer pairs produced 199 discernible loci. High levels of genetic diversity were detected, with P = 78.5%, H _E = 0.241, and H _pop = 0.3684 at population level, and P = 100%, H _T = 0.3362 and H _sp = 0.5048 at species level. Significant genetic differentiation among populations was detected based on Hickory’s analysis (27.6%), Shannon’s diversity index (27.0%) and AMOVA (27.1%). The AFLP results are discussed and compared with data obtained by microsatellites method. The estimates of genetic diversity and differentiation between each pair of populations computed with microsatellites and AFLP markers were not significantly correlated. Conservation strategies for Musa balbisiana in China are proposed.     

Genetic diversity and relationships among safflower (<Emphasis Type="Italic">Carthamus tinctorius</Emphasis> L.) analyzed by inter-simple sequence repeats (ISSRs)

Genetic diversity and relationships among 48 safflower accessions were evaluated using 22 inter-simple sequence repeats (ISSR) primers. A total of 429 bands were amplified, and 355 bands (about 82.7%) were polymorphic. Five to forty-one polymorphic bands could be amplified by each primer, with an average of 16.1 polymorphic bands per primer. The results showed that the polymorphism of the safflower germplasm was higher at the DNA level. All the 48 accessions could be distinguished by ISSR markers and were divided into 9 groups based on ISSR GS by using UPGMA method. The genetic relationships among the accessions from different continents were closer. Comparatively, the genetic diversity of the accessions originated from Asia was higher, from Europe assembled. The results also showed that the genetic variation of accessions from Indian and Middle Eastern safflower diversity centers were relatively higher. ISSR is an effective and promising marker system for detecting genetic diversity among safflower and give some useful information on its phylogenic relationships.     

Genetic diversity of 38 spinach (<Emphasis Type="Italic">Spinacia oleracea</Emphasis> L.) germplasm accessions and 10 commercial hybrids assessed by TRAP markers

Target region amplification polymorphism (TRAP) markers were used to assess genetic variability among 38 germplasm accessions and 10 commercial hybrids of spinach (Spinacia oleracea L.), an economically important leafy vegetable crop in many countries. Germplasm accessions with different geographic origins and 10 commercial hybrids were examined. For assessing genetic diversity within accessions, DNA was extracted from 12 individual seedlings from six germplasm accessions and two hybrids. A relatively high level of polymorphism was found within accessions based on 59 polymorphic TRAP markers generated from one fixed primer derived from the Arabidopsis-like telomere repeat sequence and two arbitrary primers. For evaluating interaccession variability, DNA was extracted from a bulk of six to 13 seedlings of each accession. Of the 492 fragments amplified by 12 primer combinations, 96 (19.5%) were polymorphic and discriminated the 48 accessions from each other. The average pair-wise genetic similarity coefficient (Dice) was 57.5% with a range from 23.2 to 85.3%. A dendrogram indicated that the genetic relationships among the accessions were not highly associated with the geographic locations in which the germplasms were collected. The seven commercial hybrids were grouped in three separate clusters, suggesting that the phenotype-based breeding activities tended to reduce the genetic variability. This preliminary study demonstrated that TRAP markers are effective for fingerprinting and evaluating genetic variability among spinach germplasms. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. The U.S. Government's right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

Genetic diversity trend of common wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) in China revealed with AFLP markers

A total of 242 accessions of common wheat (Triticum aestivum L.) released in China since the 1940s were evaluated with AFLP (amplified fragment length polymorphism) technique. Genetic diversity was analyzed using five pairs of polymorphic primer combinations with 245 polymorphic bands. The highest genetic diversity was found in the accessions of the 1950s, and in the next place was that in the 1940s. The genetic diversity began to descend in the 1960s, and fell to the lowest in the 1970s. After that, the genetic diversity came back to some extent in the 1980s, however, it became much lower in the 1990s compared with that in the 1940–1950s. Landraces and introduced accessions from foreign countries showed greater genetic diversity in comparison to improved varieties. In addition, greater genetic diversity was observed in winter wheat. It was emphasized that great attention should be paid on further exploration of genetic diversity in wheat breeding program.     

Genetic diversity of cowpea [<Emphasis Type="Italic">Vigna unguiculata</Emphasis> (L.) Walp.] in four West African and USA breeding programs as determined by AFLP analysis

Cowpea is an important grain legume and hay crop of many tropical and subtropical regions, especially in the dry savanna region of West Africa. The cowpea gene pool may be narrow because of a genetic bottleneck during domestication. Genetic variation within specific breeding programs may be further restricted due to breeding methods, ‘founder effects’ and limited exchange of germplasm between breeding programs. Genetic relationships among 60 advanced breeding lines from six breeding programs in West Africa and USA, and 27 landrace accessions from Africa, Asia, and South America were examined using amplified fragment length polymorphism (AFLP) markers with six near infrared fluorescence labeled EcoRI + 3/1bases/MseI + 3/1bases primer sets. A total of 382 bands were scored among the accessions with 207 polymorphic bands (54.2%). Despite a diverse origin, the 87 cowpea accessions shared a minimum 86% genetic similarity. Principal coordinates analysis showed clustering of breeding lines by program origin, indicating lack of genetic diversity compared to potential diversity. Accessions from Asia and the Americas overlapped and were distinct from West African breeding lines, indicating that germplasm from Asia and the Americas have common origins outside West Africa. US and Asian breeding programs could increase genetic variability in their programs substantially by incorporating germplasm from West Africa, while national programs in West Africa should consider introgression of Asian germplasm and germplasm from other parts of Africa into their programs to ensure long-term gains from selection.     

Dispersal of durum wheat [<Emphasis Type="Italic">Triticum turgidum</Emphasis> L. ssp. <Emphasis Type="Italic">turgidum</Emphasis> convar. <Emphasis Type="Italic">durum</Emphasis> (Desf.) MacKey] landraces across the Mediterranean basin assessed by AFLPs and microsatellites

A comprehensive characterization of crop germplasm is critical to the optimal improvement of the quality and productivity of crops. Genetic relationships and variability were evaluated among 63 durum wheat landraces from the Mediterranean basin using amplified fragment length polymorphisms (AFLPs) and microsatellites markers. The genetic diversity indices found were comparable to those of other crop species, with average polymorphism information content (PIC) values of 0.24 and 0.70 for AFLP and microsatellites, respectively. The mean number of alleles observed for the microsatellites loci was 9.15. Non-metric multi-dimensional scaling clustered the accessions according to their geographical origin with the landraces from the South shore of the Mediterranean Sea closely related. The results support two dispersal patterns of durum wheat in the Mediterranean basin, one through its north side and a second one through its south side.     

Genetic diversity of <Emphasis Type="Italic">Nelumbo</Emphasis> accessions revealed by RAPD

Total 65 lotus accessions in genus Nelumbo mainly collected from China, were subjected to random amplified polymorphic DNA (RAPD) markers to estimate the genetic diversity and to test the genetic basis of the relationships between morphotypes and molecular markers. Seventeen primers generated a total of 195 highly reproducible and discernible loci, among which 173 were polymorphic. Percent polymorphism varied from 66.7 to 100 with an average of 88.72, and five primers out of them, OPC05, OPG10, OPN20, OPP09 and OPS17, showed 100% polymorphism. A relatively high genetic diversity was detected among all the samples with the similarity coefficient values ranging from 0.45 to 0.85, and Nei’s gene diversity (h) 0.30, and Shannon index (I) 0.46. The UPGMA dendrogram clustered 65 accessions in four clusters and the clustering pattern showed two groups, N. nucifera ssp. nucifera and those accessions related to the American lotus, and some special cultivars, landraces, hybrids and the American lotus. Principal Coordinate Analysis (PCA) further indicated that the genetic diversity of Nelumbo accessions was not evenly distributed, instead, was presented by a clustered distribution pattern. Similar to the results revealed by the dendrogram, two main groups representing the two subspecies of N. nucifera, as well as some special landraces, cultivars of Chinese lotus, the Japanese lotus and hybrids out of the two groups were obtained. Neither the UPGMA dendrogram nor the PCA analysis exhibited strict relationship with geographic distribution and morphotypes among the accessions.     

Genetic diversity of HMW glutenin subunit in Chinese common wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) landraces from Hubei province

The high molecular weight (HMW) glutenin subunit composition of 111 common landraces of bread wheat collected from Hubei province, China has been determined by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). Ninety six of the accessions were homogeneous for HMW glutenin subunit composition and 15 were heterogeneous. For the Glu-1 loci, 16 alleles were detected, 3 at the Glu-A1locus, 9 at the Glu-B1and 4 at the Glu-D1. Three novel alleles were identified, two at the Glu-B1 and one at the Glu-D1locus. Combination of these 16 alleles resulted in 14 different HMW subunit patterns. The distribution of HMW glutenin subunit alleles in a subset of 105 of the 111 accessions representing six populations was assessed both at the individual population and whole population levels. The results demonstrated that the distribution of allelic patterns varied among populations. Taken together, 62.5% of the alleles detected were considered to be rare alleles while the Glu-A1c (null), Glu-B1b (1Bx7 + 1By8) and Glu-D1a (1Dx2 + 1Dy12) alleles were found most frequently in the six populations. The subset exhibited relatively high genetic diversity (A = 5.33, P = 1.00, Ae = 1.352 and He = 0.238) with 81.5% of the diversity being within populations and 18.5% between populations.     

Comparison of genetic variation among accessions of <Emphasis Type="Italic">Aegilops tauschii</Emphasis> using AFLP and SSR markers

Genetic diversity of 54 accessions of Aegilops tauschii from five countries was assessed using sequence-tagged microsatellites (or simple sequence repeats, SSRs) and amplified fragment length polymorphisms (AFLPs). In the case of AFLP analysis, a total of 256 amplification products obtained, 234 of them were polymorphic across all the 54 accessions. A total of 224 fragments were obtained from the 24 SSR primers and 219 of fragments were polymorphic across all the genotypes screened. Based on both AFLP and SSR markers, the highest percentage of polymorphisms were obtained in Iranian and accessions of unknown origin. The highest polymorphic information content (PIC) value was observed for SSRs (0.82) while the highest marker index (MI) value was for AFLPs (8.5) reflecting the hyper-variability of the first and the distinctive nature of the second system. Principal co-ordinate analysis (PCO) revealed congruent patterns of genetic relationships for both data sets, but did not group accessions strictly according to their geographical origins. Poor correlation was found between AFLP and SSR marker loci. This low association may be due to low number of AFLP and SSR markers. These results show that molecular markers can help to organize the genetic variability and expose useful diversity for breeding purposes.     

Intra-specific DNA polymorphism in pineapple (<Emphasis Type="Italic">Ananas comosus</Emphasis> (L.) Merr.) assessed by AFLP markers

Pineapple (Ananas comosus (L.) Merr.) cultivars, often derived from somatic mutations, are propagated vegetatively. It has been suggested by isozyme data that there is little genetic variation among Smooth Cayenne cultivars. A thorough investigation of the genetic variation within the cultivated speciesAnanas comosus, particularly among commercial cultivars, will provide critical information needed for crop improvement and cultivar protection. One-hundred and forty-eight accessions ofA. comosus and 14 accessions of related species were evaluated with AFLP markers. The average genetic similarity ofA. comosus was 0.735 ranging from 0.549 to 0.972, suggesting a high degree of genetic variation within this species. With AFLP markers, discrete DNA fingerprints were detected for each commercial cultivar, breeding line, and intra-specific hybrid. Self-incompatibility, high levels of somatic mutation, and intraspecific hybridization may account for this high degree of variation. However, major cultivar groups of pineapple, such as Cayenne, Spanish, and Queen, could not be distinctively separated. These cultivar groups are based on morphological similarity, and the similar appearance can be caused by a few mutations that occurred on different genetic background. Our results suggest that there is abundant genetic variation within existing pineapple germplasm for selection, and discrete DNA fingerprinting patterns for commercial cultivars can be detected for cultivar protection. The genetic diversity and relationships of fourAnanas species are also discussed.     

Assessing genetic diversity of Polish wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis>) varieties using microsatellite markers

Fifty-three wheat cultivars have been genotyped using 24 SSR (simple sequence repeat) markers in order to evaluate genetic similarities among Polish wheats, i.e. 53 spring and winter cultivars; ‘Chinese Spring’ was taken as reference. ll but one SSR marker allowed to identify DNA polymorphisms, giving in total 166 alleles (including nulls), from 3 to 13 alleles per marker with mean of 7.22. Based on marker data, genetic similarities were calculated and a dendrogram was created. ‘Spring’ cultivars were less diverse than winter ones, showing the biggest similarity to ‘Chinese Spring’. Four sister cultivars (Nutka, Tonacja, Zyta and Sukces), formed a cluster of very similar materials, of which Zyta and Sukces had the highest similarity indices. Parental lines Jubilatka and SMH 2182 were more distant from each other (genetic similarity of 0.227). It was possible to differentiate all the wheats using only four SSR markers: Xgwm186, Xgwm389, Xgwm459 and Xgwm577.     

Genetic diversity changes and relationships in spring barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) germplasm of Nordic and Baltic areas as shown by SSR markers

To examine changes in the level of and pattern in variability in 197 Nordic and Baltic spring barley cultivars over time we used 21 mapped barley simple sequence repeats (SSRs). A total number of 191 alleles were found from 22 SSR loci. The number of alleles per locus ranged from 2 to 23, with average of 8.63 107 alleles were rare (frequency <0.05) among the cultivars and only one allele was frequently observed (frequency >0.95). The gene diversity between loci in Nordic and Baltic material varied between 0.033 and 0.891. Average gene diversity was 0.623. The SSR data separated two-rowed and six-rowed cultivars. According to analysis of molecular variance (AMOVA) differentiation in two-rowed vs six-rowed accounted for 23.6% of the total variation. Overall no significant decrease of average gene diversity over time could be found. However, differences were observed when spring barleys from northern (north of ∼58°) and southern (south of ∼58°) parts of the Nordic and Baltic area were compared. For the southern ecogeographical region significant decrease of genetic diversity was observed in the middle of the 20th century, whereas no significant changes in the northern part were found. We found larger differentiation between modern and old cultivars in the South compared to the ones in North parts of the region. The magnitude of changes in genetic diversity differed also with the country of origin. Danish cultivars had a significant decrease in diversity in the middle of century, whereas changes in Finland, Norway and Sweden were not significant.     

A preliminary study of the genetic diversity of Bolivian oca (<Emphasis Type="Italic">Oxalis tuberosa</Emphasis> Mol.) varieties maintained<Emphasis Type="Italic"> in situ</Emphasis> and<Emphasis Type="Italic"> ex situ</Emphasis> through the utilization of ISSR molecular markers

ISSR molecular markers have been used to investigate genetic diversity of oca (Oxalis tuberosa Mol.), an Andean neglected tuber crop species. Sampling procedure allowed a preliminary study of the genetic diversity at the intra- and intervarietal levels. Twenty tuber lots conserved in situ in the microcentre of Candelaria and ex situ in the Toralapa Centre (Bolivia) were identified. Four ISSR primers amplified a total of 25 fragments of which 17 (68%) were polymorphic. These experiments show that the structure of oca varieties is mainly based upon vernacular names with a greater differentiation among tuber lots than within them, supporting agromorphological data. ISSR technique enlightened the existence of heterogeneous varieties in oca and divergence between in situ and ex situ conservation strategies. These observations are potentially linked to the different ways of management of tubers in these two conservation systems.     

Analysis of Genetic Variation Among Accessions of <Emphasis Type="Italic">Pueraria montana</Emphasis> (Lour.) Merr. var. <Emphasis Type="Italic">lobata</Emphasis> and <Emphasis Type="Italic">Pueraria phaseoloides</Emphasis> (Roxb.) Benth. based on RAPD Markers

Pueraria montana var. lobata and P. phaseoloides originating from tropical Asia and parts of Oceania are ecologically and economically important legumes that are used as green manure, cover crop or forage plants. Conservation and use of plant genetic resources require an understanding of the extent and distribution of genetic diversity in any given region. In this study, genetic variation of five P. montana var. lobata and 16 P. phaseoloides accessions was analysed developing a random amplified polymorphic DNA (RAPD) marker methodology for Pueraria species and thereby creating basic data for follow-up research and the development of conservation strategies. Seeds were collected from native populations in Bac Kan Province, a mountainous region in Northeast Vietnam. P. montana var. lobata presented a high level of variation with 54.3% of the detected markers being polymorphic, whereas P. phaseoloides exhibited an intermediate to high level of variation (45.5%). The P. montana var. lobata accessions clustered in congruence with their eco-geographical origin. For P. phaseoloides no correspondence between sampling sites and genetic differentiation was found. Inter-population differentiation was measured as Jaccard's similarity coefficient (JSC). Mean JSC amounted to 0.35 in P. montana var. lobata and 0.52 in P. phaseoloides. Results are compared to other genetic studies of herbaceous legumes and conservation strategies are suggested.     

Genetic diversity of <Emphasis Type="Italic">rbc</Emphasis>L gene in <Emphasis Type="Italic">Elymus trachycaulus</Emphasis> complex and their phylogenetic relationships to several Triticeae species

Elymus trachycaulus complex species are known for their morphological variability, but little is known about their genetic basis. The phylogenetic relationships among the E. trachycaulus complex, and their systematic relation to other species in Triticeae remain unknown. Nucleotide diversity of ribulose-1,5 bisphosphate-carboxylase (rbcL) gene in E. trachycaulus complex species and several other Triticeae was first characterized and compared. A primary conclusion of the present study is that nucleotide diversity for rbcL gene in E. trachycaulus species was detected with the estimates of nucleotide diversity θ = 0.00039 and π = 0.00043. The estimate of nucleotide diversity in rbcL gene for species with different genome constitution here ranged from 0.00099 (π) and 0.00099 (θ) for the species with Ns genome to 0.00226 (π) and 0.00291 (θ) for the species with St genome. The phylogenetic relationships of these species were assessed using these rbcL sequences. A total of 47 variable positions including 19 parsimony-informative sites were detected among 24 accessions of 18 species/subspecies. The species with St, H/I and Ns genomes well separated from each other, and formed a three distinct clades with higher bootstrap values support for both Parsimony and NJ analyses. The St genome containing species is sister group of H/I genome containing species. Our result confirms that Pseudoroegneria is the maternal genome donor to these Elymus species studied here, regardless of their distribution. Elymus trachycaulus complex are more related to each other than to E. glaucescens, E. patagonicus, and E. solandri. This study suggested that Elymus species with StH genomes may form from multiple closely related sets of donors.     

Evaluation of genetic diversity in Turkish melons (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.) based on phenotypic characters and RAPD markers

The genetic relationships among 56 melon (Cucumis melo L.) genotypes collected from various parts of Turkey were determined by comparing their phenotypic and molecular traits with those of 23 local and foreign melon genotypes to investigate the taxonomic relationships and genetic variation of Turkish melon germplasm. Sixty-one phenotypic characters and 109 polymorphic RAPD markers obtained from 33 primers were used to define the genetic similarity among the melon genotypes by dendrograms or two and three dimensional scaling. There were high correlations (r ≥ 0.97) among the four resulting matrices used in molecular characterization. The correlations between phenotypic (Euclidean) and molecular Euclidean, Jaccard, Simple matching, and Nei analyses were r = 0.41, r = −0.40, r = −0.43 and r = −0.40, respectively. Related genotypes or genotypes collected from similar regions were partitioned to similar clusters. Both analyses (phenotypic and molecular) indicated that non-sweet melon types were dissimilar from sweet types and diversity of Turkish melon genotypes was higher than that of sweet foreign cultivars examined, but similar to that of the reference accessions employed. It was also observed that sweet Turkish melon genotypes belonging to groups inodorus and group cantalupensis were highly variable and could have intermated or have crossed with other non-sweet types.     

Genetic structure of quinoa (<Emphasis Type="Italic">Chenopodium quinoa</Emphasis> Willd.) from the Bolivian altiplano as revealed by RAPD markers

Quinoa (Chenopodium quinoa Willd.) is a pseudocereal originated from the Andes important for small farmers’ food security as well as for commercial production. Recently, it has been claimed that in Bolivia genetic erosion could result from the marginalization of the crop in the north and from its commercial standardization in the south. The aim of this study was to quantify the hierarchical structure of the genetic variation present in eight quinoa field populations, consisting of cultivated and weedy individuals, representative of the altiplano and interandean valleys of Bolivia. Randomly amplified polymorphic DNA markers show that quinoa has a strong population structure and a high intra-population variation. An effect of geographical structure of the populations was highlighted, due to population isolation, not simply linked to distance but more probably to climatic and orographic barriers present in the studied zone. The population structure is also reinforced by the limited seed exchanges among farmers as revealed by field interviews. This population structure appears related to three major biogeographic zones: the northern and central altiplano, the interandean valley, and the southern Salar. Intrapopulation genetic diversity was higher than that expected for a mainly autogamous species, and higher than that reported in anterior studies based on germplasm collections. These results are commented in view of current knowledge on phylogeny and reproductive biology of the species, and their implications regarding genetic resources management are discussed.     

Characterization of intergeneric hybrids of <Emphasis Type="Italic">Erianthus rockii</Emphasis> and <Emphasis Type="Italic">Saccharum</Emphasis> using molecular markers

Erianthus rockii, a wild relative of sugarcane, is drought and cold tolerant, and both are potentially important agronomic traits to the sugarcane industry worldwide. As such it is of interest as a source of parental germplasm to sugarcane breeders and is currently being used in sugarcane introgression programs in both China and Australia. To date morphological characters have been used to verify the putative hybrids produced. Two crosses were generated between two different Saccharum species and two E. rockii accessions. Over 400 AFLP markers were used to identify the intergeneric hybrid progeny as well as determine hybrid diversity. Both crosses generated hybrids but efficiency levels were very different and are probably related to the different Saccharum parent used in each cross. Cross 1 was between a Saccharum officinarum and E. rockii and generated 100% hybrid progeny. Cross 2, however, was between a sugarcane hybrid (S. officinarum × Saccharum spontaneum) and E. rockii and only 10% of the progeny were intergeneric hybrids. Inheritance of markers in the progeny was analysed and for both crosses there were equal numbers of markers from both parents indicating n + n transmission of chromosomes. This is the first verification of E. rockii hybrids with molecular markers. It may now be possible to exploit genes of value from E. rockii in sugarcane breeding programs.