Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces assessed by Random Amplified Polymorphic DNA (RAPD) markers

Genetic diversity in 12 landraces of bambara groundnut (Vigna subterranea), an indigenous African legume, was evaluated using Random Amplified Polymorphic DNA (RAPD) markers. DNA from individuals of each landrace was also analysed to determine the level of heterogeneity within landraces. RAPDs revealed high levels of polymorphism among landraces. The percentage polymorphism ranged from 63.2% to 88.2% with an average of 73.1% for the 16 RAPD primers evaluated. The construction of genetic relationships using cluster analysis groups the 12 landraces in two clusters. RAPDs are useful for the genetic diversity studies in V. subterranea and can identify variation within landraces.     

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.     

Diversity in reproductive characteristics of potato landraces and cultivars for producing true seed

Potato production from true seed, or true potato seed (TPS) is not a new system for this vegetatively propagated crop. Andean farmers have grown potatoes in the cool highlands from true seed for many centuries. TPS appears today as a promising technology in the warm tropics, where diseases impede the production of pathogen-free potato propagules. However, the identification of suitable genetic resources for potato seed production requires the selection of clones that lack antagonism between tuber growth and seed embryo development. Furthermore, the potential TPS parents need to possess characteristics of a sexually propagated crop that is grown for the harvest of its vegetative part, i.e., the tuber. This new process of domestication requires a change in the selection methods, which starts by assessing the potential of available potato clones for both reproductive characteristics and agronomic traits, particularly those of the tuber. Tetraploid landraces and cultivars of the pathogen-tested collection of the Centro Internacional de la Papa were assessed for reproductive and agronomic characteristics during three consecutive years in San Ramón, a Peruvian location in the warm lowland tropics. The clones showed significant variation for all characteristics recorded. The Shannon–Weaver diversity index (H) was highest for flowering duration (0.617) and intensity (0.600). The lowest H was calculated for bee attraction in this location. The overall H was not significantly affected by the year-to-year variation, but some of the characteristics recorded (e.g. flowers per inflorescence, anther type, style length, plus fruit and berry set) showed distinct H according to the year of assessment. Some of the cultivars with promising TPS traits, as determined by their reproductive characteristics, also had outstanding tuber set, weight and yield. Furthermore, hybrid offspring from the selected clones from the pathogen-tested elite sample, did show high tuber yield with appropriate tuber set and reproductive traits as shown by progeny testing. Hence, the approach followed for identifying parental sources as discussed in this article appears to be appropriate.     

Genetic diversity and similarity of pear (<Emphasis Type="Italic">Pyrus</Emphasis> L.) cultivars native to East Asia revealed by SSR (simple sequence repeat) markers

Simple sequence repeat (SSR) markers were used to assess genetic diversity and relationship of Pyrus L. cultivars native mainly to East Asia. A total of 168 putative alleles were generated from six primer-pairs (BGA35, KU10, BGT23b, NH004a, NH011b and NH015a). All the SSR markers showed a high level of genetic polymorphism with a mean of 28 putative alleles per locus and the heterozygosity of 0.63. The Dice’s similarity coefficient between cultivars ranged from 0.02 to 0.98 and Occidental pears generally had low affinities to Asian pears. Ten major groups were generated from all the accessions by UPGMA clusters analysis. Chinese sand pears consisted of four groups with Chinese white pears and Japanese pears, of which Chinese sand pears occurred in all four groups, presenting a large genetic diversity, Chinese white pears were included in three groups, and Japanese pears only fell into one group. In the dendrogram, Chinese sand pears and Chinese white pears did not form discrete group, even subgroups. Some Japanese pear cultivars had high affinities to Chinese sand pear cultivars. These findings supports the authors’ previous viewpoints of Chinese white pears as a variety or an ecotype of Chinese sand pears (P. pyrifolia var. sinensis (Lindley) Y. Teng et K. Tanabe) and the progenitor of Japanese pears coming from China. Cultivars of P. ussuriensis Maxim. were clustered together with one clone of P. hondoensis Nakai et Kikuchi, a relative species of P. ussuriensis. Cultivars of P. communis L. and other Occidental species formed three independent groups and were distant from most Asian pears, except for P. betulaefolia Bge.     

Analysis of genetic diversity in a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP

Sweet potato (Ipomoea batatas L.) is the fifth most important crop in the developing countries after rice, wheat, maize and cassava. The amplified fragment length polymorphism (AFLP) method was used to study the genetic diversity and relationships of sweet potato accessions in the germplasm collection of Sokoine University of Agriculture, Morogoro and Sugarcane Research Institute, Kibaha, Tanzania. AFLP analysis of 97 sweet potato accessions using ten primer combinations gave a total of 202 clear polymorphic bands. Each one of the 97 sweet potato accessions could be distinguished based on these primer combinations. Estimates of genetic similarities were obtained by the Dice coefficient, and a final dendrogram was constructed with the un-weight pair-group method using arithmetic average. AFLP-based genetic similarity varied from 0.388 to 0.941, with a mean of 0.709. Cluster analysis using genetic similarity divided the accessions into two main groups suggesting that there are genetic relationships among the accessions. Principal Coordinate analysis confirmed the pattern of the cluster analysis. Analysis of molecular variance revealed greater variation within regions (96.19%) than among regions (3.81%). The results from the AFLP analysis revealed a relatively low genetic diversity among the germplasm accessions and the genetic distances between regions were low. A maximally diverse subset of 13 accessions capturing 97% of the molecular markers diversity was identified. We were able to detect duplicates accessions in the germplasm collection using the highly polymorphic markers obtained by AFLP, which were found to be an efficient tool to characterize the genetic diversity and relationships of sweet potato accessions in the germplasm collection in Tanzania.     

Simple sequence repeats marker polymorphism in emmer wheat (<Emphasis Type="Italic">Triticum dicoccon</Emphasis> Schrank): Analysis of genetic diversity and differentiation

Genetic diversity was investigated in 73 accessions of emmer wheat (Triticum dicoccon Schrank) from 11 geographical regions using a set of 29 simple-sequence repeat (SSR or microsatellite) markers, representing at least two markers for each chromosome. The SSR primers amplified a total of 357 different alleles with an average of 12.31 alleles per locus. The number of fragments detected by each primer ranged between 6 (Xgwm1066) and 21 (Xgwm268). Null alleles were detected in nine of the 29 primers used. A high level of gene diversity index was observed. Across the 29 primers, gene diversity ranged from 0.60 (Xgwm46) to 0.94 (Xgwm655), with a mean of 0.82. There was a highly significant correlation (r=0.882; p<0.01) between gene diversity index and the number of loci, showing the number of loci per se is a strong indicator of diversity. Analysis of genetic diversity within and among eleven geographical regions revealed most of the genetic diversity of the total sample resided within regions. The coefficient of gene differentiation (Gst = 0.27) showed that the genetic variation within and among the 11 geographical regions was 73 and 27%, respectively. High value of mean number of alleles per locus was found in Iran (4.86) followed by Morocco (4.10) and Armenia (4.03). On the contrary, lower mean number of alleles per locus was detected in Yemen (2.83). The average gene diversity index across regions ranged from 0.52 (Slovakia) to 0.67 (Morocco) with an average of 0.60. Multivariate techniques of principal component analysis and clustering were employed to examine genetic relationship among the 73 emmer wheat accessions vis-à-vis geographical regions of collections. The genetic distance coefficients for all possible 55 pairs of regional comparisons ranged from 0.63 (between Iran and Armenia, Georgia and Azerbaijan, Georgia and Slovakia) to 0.97 (between Morocco and Yemen, Spain and Georgia, and Turkey and Iran) with a mean of 0.82. From the PCA results, a two dimensional plot of PC1 versus PC2 was constructed. The scatter plot of the first two principal components which explained altogether 27% of the total variation depicted the presence of a clear pattern of geographical differentiation except in few cases like accessions from Caucasian region. Similar pattern of genetic relationships among accessions was observed in cluster analysis. The study provided genetic information of emmer wheat in relation to geographical regions of origin. The information could be utilized in crop improvement, germplasm conservation programs, and in further investigation.     

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.     

RAPD markers efficiently distinguish heterogenous populations of wild potato (Solanum)

Genetic characterization of germplasm is important for setting objective guidelines for conservation. One common problem found in genebanks is determining the value of populations with insufficient or unreliable data regarding their geographic origin. In this study, a genetic analysis based on RAPD markers was conducted to characterize a `mystery' population of Solanum sucrense, a polysomic tetraploid potato (2n=4x=48), for which adequate documentation was lacking. The comparative analysis of genetic similarities between this mystery population and each one of 30 other S. sucrense populations in the genebank revealed that all populations within this species, including the mystery population, are significantly different from being duplicates, and are therefore worthy of separate conservation. RAPD markers also distinguished the mystery population from closely related tetraploid species S. oplocense, S. gourlayi and S. tuberosum ssp. andigena, suggesting that it is also not a duplicate of a population of these species. If RAPDs can clearly differentiate populations within highly heterogeneous tetraploids like S. sucrense, they should be generally useful for determining germplasm organization within potato species.     

Genetic diversity and intra-specific phylogeny of Triticum turgidum L. subsp. dicoccon (Schrank) Thell. revealed by RFLPs and SSRs

Today, emmer wheat, T. turgidum subsp. dicoccon, widely grown in the past is a candidate crop for sustainable agriculture in Italy. As part of a research project aimed at the enhanced use of the hulled wheat germplasm, molecular characterization was carried out to understand the genetic structure of the crop and to identify accessions of interest. A collection of 194 accessions was analyzed with 15 microsatellite loci (SSRs), while only a sample of 38 accessions was tested with 19 RFLP probes. The marker loci were selected on the basis of their independent genomic distribution. Genetic distances and allelic frequencies were calculated for each marker class. The genetic relationships were visualized with dendrograms. RFLP loci were, on average, less polymorphic than SSRs. An average Dice's genetic distance of 0.22 for RFLPs vs 0.38 for SSRs was detected, while an expected average heterozygosity per locus of 0.23 for RFLPs vs 0.26 for SSRs was also estimated. With a least number of 10 loci per marker class it was possible to identify each genotype. The most diverse accessions had different geographic origins. Germplasms from Italy and Ethiopia appear to belong to a more primitive genepool, given that a group of accessions from these countries were genetically differentiated from a Russian-Iranian group.     

Evaluation of genetic diversity of bread wheat landraces from Pakistan by AFLP and implications for a future collection strategy

We used amplified-fragment-length polymorphism (AFLP) markers to evaluate genetic variation in a set of bread wheat (Triticum aestivum L.) landraces and improved materials. Landraces collected from different geographic and agro-ecological zones in Pakistan in 1987, 1989 and 1991 were separated into two groups based on their geographic origins: northern (Himalaya) and south-western (Balochistan) Pakistan. Six AFLP primer combinations detected 453 AFLP markers in the 43 landrace accessions and four high-yield varieties (HYVs). Of these, 225 (49.67%) were rare (shared with < 5% of all accessions). Among these rare alleles, 23 (10.22%) were common in the Himalaya (shared with > 10% of accessions collected there) but were not found in Balochistan. We conclude that there is a higher probability of collecting rare alleles at overall, but which are in contrast locally common ones in the Himalayan region. Gene diversity was 0.17 in the Himalayan group and 0.15 in the Balochistan group. Considerable genetic variability was found in both groups. Accessions from different agro-ecological zones were indistinguishable by cluster analysis, indicating intensive seed trading within the country. Cluster analysis indicated that the landraces and the HYVs are genetically distinct; suggesting that genetic erosion of wheat landraces has been unlikely taken in place. This study provides an example of how analysis of existing materials and data, can serve as a basis for future collection planning and conservation policies.     

Characterization of a flint maize (Zea mays var. indurata) Italian landrace, II. Genetic diversity and relatedness assessed by SSR and Inter-SSR molecular markers

A comparative characterization of 10 field populations of the maize (Zea mays var. indurata) landrace Nostrano di Storo was carried out using different types of PCR-based markers. The inbred line B73 and three synthetics (VA143, VA154 and VA157) selected from as many landraces were also used. Genetic diversity and relatedness were evaluated over 84 SSR and 53 I-SSR marker alleles using a total of 253 individual DNAs. Up to 23 alleles per SSR locus were scored while the average effective number of alleles per population was 6.99. Nei's total genetic diversity as assessed with SSR markers was H_T = 0.851 while the average diversity within populations was H_S = 0.795. The overall Wright's fixation index F_ST was as low as 0.066. Thus, more than 93% of the total variation was within population. Unique alleles over all SSR loci were found for six populations. An average of 17.7 marker alleles per I-SSR primer were scored with an effective number of marker alleles per locus of 1.34. The Shannon's diversity information index over all populations and I-SSR loci was 0.332, varying from 0.286 to 0.391. The extent of differentiation between populations was as low as G_ST = 0.091. Dice's genetic similarity matrices were estimated for both SSR and I-SSR markers. The mean genetic similarity coefficients within and between populations were respectively 0.269 and 0.217, for SSR markers, and 0.591 and 0.564, for I-SSR markers. UPGMA dendrograms displayed all field populations but one clustered into a distinct group, in which the synthetic VA154, selected from the Marano Vicentino landrace, was also included. One field population and the other two synthetics were clustered separately as well B73. The matrix correlation assayed by the Mantel's correspondence test was as high as 0.908. Findings suggest that, although a high variability can be found among plants, most plant genotypes belong to the same landrace called Nostrano di Storo. Although gene flow from commercial hybrids might have occurred, the large number of polymorphisms and the presence of both unique alleles and alleles unshared with B73 and synthetics are the main factors underlying the value of this flint maize landrace as a source of genetic variation and peculiar germplasm traits. Because of its exclusive utilization for human consumption, such a molecular marker characterization will be a key step for obtaining the IGP mark and so promote the in situ conservation and protection of the landrace Nostrano di Storo.     

A phenotypic diversity analysis of foxtail millet (Setaria italica (L.) P. Beauv.) landraces of Chinese origin

A total of 23 381 foxtail millet landraces of Chinese origin were analysed for seven qualitative traits and four quantitative traits. The Shannon-Weaver diversity index was used to estimate the phenotypic diversity of each characteristic on the basis of administrative provinces and ecogeographical regions. Hierarchical analysis of variance indicated that most of the variation was due to differences among characteristics. Only the diversity indices for leaf color of seedlings, starch composition and 1000-grain weight showed significant differences among regions. In relative terms, a greater genetic divergence was found in some provinces of southern China, where foxtail millet is not a major crop.     

Genetic Survey of Chinese and Swedish Oilseed Rape (Brassica napus L.) by Simple Sequence Repeats (SSRs)

Eleven Chinese and twelve Swedish rapeseed (Brassica napus) genotypes were analysed by PCR with 41 microsatellite primers, generating a total of 50 loci. For these 50 loci, the number of alleles ranged from 1 to 14, and the average number of alleles per loci was 2.7. As an example of simple sequence repeat (SSR) scoring in Metaphor agarose gel, a single marker could distinguish 14 different DNA profiles. Based on cluster analysis (UPGMA), the dendrogram clearly distinguished three clusters, a cluster with exclusively Swedish genotypes, and two clusters with Chinese genotypes. The genetic diversity within the Chinese genotypes was broad compared to the genetic diversity within the Swedish material. The genetic similarity within the Swedish breeding lines ranged from 69.5 to 95.6%, while that of Chinese genotypes ranged from 57.1 to 81.6%. The results in this report will permit to establish a set of microsatellite primers that can be used for selecting appropriate parents for Brassica napus hybrids and for monitoring hybridity level.     

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 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.     

绿色豌豆蚜不同地理种群的遗传多样性

豌豆蚜是我国苜蓿上危害最为严重的害虫之一。利用微卫星标记研究了我国绿色型豌豆蚜10个地理种群的遗传相似性、基因分化、遗传距离与地理距离和海拔之间的关系及其基因结构。选取15对引物扩增300个个体,共检测到41个多态性条带,多态性条带百分率(PPB)为100%。10个豌豆蚜地理种群观测等位基因数(Na)为1.592 7,有效等位基因数(Ne)为1.356 9,Nei’s基因多样性指数为0.206 6,Shannon-Wiener指数(I)为0.307 6。新疆维吾尔自治区、陕西省、河南省种群的遗传多样性较高,内蒙古自治区、山东省、青海省种群相对较低。然而,10个地理种群豌豆蚜(绿色型)的遗传分化较高(Gst=0.399 6)。种群聚类分析结果显示,全部豌豆蚜种群明显聚为两大类群,山东省、河南省种群为一大类群,其余为另一大类群。Mentel检测表明,遗传分化与地理距离、海拔无显著相关性。我国豌豆蚜种群具有非常丰富的遗传多样性,应加强豌豆蚜的监测和治理。     

Evaluation of Genetic Diversity of Wild Rice (Oryza rufipogon Griff.) in Myanmar using Simple Sequence Repeats (SSRs)

As a part of an in situ survey of wild rice (Oryza rufipogon Griff.) in Myanmar (Burma), 16 strains of wild rice were collected, and analyzed for allelic diversity over 74 loci with simple sequence repeat (SSR) markers to obtain a basic information for their conservation. Three each of indica and japonica cultivars were added for a comparison. In the six cultivars and 16 strains of wild rice, three to 15 alleles were detected per locus with an average of 7.9. The wild rice revealed a large number of unique alleles throughout their chromosomes with much wider ranges of variation than those detected in the six cultivars of O. sativa L.. The alleles found in the wild rice were classified into those specific to wild rice, common to wild rice and cultivars, and those similar to indica or japonica cultivars. According to the classification, the genotype of each of the 16 strains of wild rice was schematically depicted. The genetic variation among individual strains within a collection site was larger than the variation among the collection sites.     

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.