Assessing changes in the genetic diversity of potato gene banks. 1. Effects of seed increase

 Effects of gene bank seed-increases on the genetic integrity of potato germ plasm is a major concern of gene bank managers. Thus the Association of Potato Inter-gene-bank Collaborators (APIC), a consortium of world potato gene bank leaders, initiated this joint research project using RAPD markers to determine genetic relationships between increased generations within accessions. Solanum jamesii (2n=2x=24) and S. fendleri (2n=4x=48), two wild potato species native to North America, were used as plant material. These species represented two major breeding systems found among Solanum species: outcrossing diploids and inbreeding disomic tetraploids, respectively. Comparisons were made between populations one generation apart and between sister populations generated from a common source. Fourteen such comparisons within S. jamesii accessions had an average similarity of 96.3%, and 21 such comparisons within S. fendleri accessions had an average similarity of 96.0%. No pairs of populations were significantly different, despite the fact that RAPD markers easily separated all of these very similar accessions within their respective species. Only one of six S. jamesii accessions analyzed showed a significant change in gene frequencies among generations. These findings indicate that there has been minimal loss or change of genetic diversity in ex situ germplasm using the gene bank techniques standard at NRSP-6 and other world potato gene banks. Received: 28 October 1996 / Accepted: 7 March 1997     

Genetic diversity of taro, Colocasia esculenta (L.) Schott, in Southeast Asia and the Pacific

The genetic diversity of 255 taro (Colocasia esculenta) accessions from Vietnam, Thailand, Malaysia, Indonesia, the Philippines, Papua New Guinea and Vanuatu was studied using AFLPs. Three AFLP primer combinations generated a total of 465 scorable amplification products. The 255 accessions were grouped according to their country of origin, to their ploidy level (diploid or triploid) and to their habitat—cultivated or wild. Gene diversity within these groups and the genetic distance between these groups were computed. Dendrograms were constructed using UPGMA cluster analysis. In each country, the gene diversity within the groups of wild genotypes was the highest compared to the diploid and triploid cultivars groups. The highest gene diversity was observed for the wild group from Thailand (0.19), the lowest for the diploid cultivars group from Thailand (0.007). In Malaysia there was hardly any difference between the gene diversity of the cultivars and wild groups, 0.07 and 0.08, respectively. The genetic distances between the diploid cultivars groups ranges from 0.02 to 0.10, with the distance between the diploid accessions from Thailand and Malaysia being the highest. The genetic distances between the wild groups range from 0.05 to 0.07. First, a dendrogram was constructed with only the diploids cultivars from all countries. The accessions formed clusters largely according to the country from which they originated. Two major groups of clusters were revealed, one group assembling accessions from Asian countries and the other assembling accessions from the Pacific. Surprisingly, the group of diploid cultivars from Thailand clustered among the Pacific countries. Secondly, a dendrogram was constructed with diploid cultivated, triploid cultivated and wild accessions. Again the division of the accessions into an Asian and a Pacific gene pool is obvious. The presence of two gene pools for cultivated diploid taro has major implications for the breeding and conservation of germplasm.     

Molecular Characterization and Comparative Analysis of Six Durum Wheat Accessions Including Graziella Ra

Genetic identity and relatedness of the durum wheat Graziella Ra, four Italian commercial durum cultivars (Cappelli, Grazia, Flaminio and Svevo) and Kamut were evaluated using amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs) and α-gliadin gene sequence analysis. Our primary objective was to study molecular genetic diversity in such a set of wheats including three modern (Grazia, Flaminio and Svevo) and three older (Cappelli, Kamut and Graziella Ra) durum accessions. Specifically, we aimed at determining the relationship between the historic accession Graziella Ra and Kamut, which is considered an ancient relative of the durum subspecies. Obtained results revealed that (1) both AFLP and SSR molecular markers detected highly congruent patterns of genetic diversity among the accessions showing nearly similar efficiency; (2) for AFLPs, percentage of polymorphic loci within accession ranged from 6.57% to 19.71% (mean, 12.77%) and for SSRs, from 0% to 57.14% (mean, 28.57%); (3) principal component analysis of genetic distance among accessions showed the first two axes accounting for 58.03% (for AFLPs) and 61.60% (for SSRs) of the total variability; (4) for AFLPs, molecular variance was partitioned into 80% (variance among accessions) and 20% (within accession) and for SSRs, into 73% (variance among accessions) and 27% (within accession); (5) cluster analysis of AFLPs and SSRs datasets displayed Graziella Ra and Kamut constantly grouped into the same cluster; and (6) molecular comparison of α-gliadin gene sequences showed Graziella Ra and Kamut in separate clusters. All these findings support the hypothesis that Graziella Ra and Kamut, although very similar, at least in the little part of the genome investigated by molecular markers employed in this study, might be considered as distinct accessions.     

Patterns of genetic diversity in the Andean gene pool of common bean reveal a candidate domestication gene

Most studies on the genetic diversity of common bean (Phaseolus vulgaris L.) have focussed on accessions from the Mesoamerican gene pool compared to the Andean gene pool. A deeper knowledge of the genetic structure of Argentinian germplasm would enable researchers to determine how the Andean domestication event affected patterns of genetic diversity in domesticated beans and to identify candidates for genes targeted by selection during the evolution of the cultivated common bean. A collection of 116 wild and domesticated accessions representing the diversity of the Andean bean in Argentina was genotyped by means of 114 simple sequence repeat (SSR) markers. Forty-seven Mesoamerican bean accessions and 16 Andean bean accessions representing the diversity of Andean landraces and wild accessions were also included. Using the Bayesian algorithm implemented in the software STRUCTURE we identified five major groups that correspond to Mesoamerican and Argentinian wild accessions and landraces and a group that corresponds to accessions from different Andean and Mesoamerican countries. The neighbour-joining algorithm and principal coordinate clustering analysis confirmed the genetic relationships among accessions observed with the STRUCTURE analysis. Argentinian accessions showed a substantial genetic variation with a considerable number of unique haplotypes and private alleles, suggesting that they may have played an important role in the evolution of the species. The results of statistical analyses aimed at identifying genomic regions with consistent patterns of variation were significant for 35 loci (~20 % of the SSRs used in the Argentinian accessions). One of these loci mapped in or near the genomic region of the glutamate decarboxylase gene. Our data characterize the population structure of the Argentinian germplasm. This information on its diversity will be very valuable for use in introgressing Argentinian genes into commercial varieties because the majority of present-day common bean varieties are of Andean origin.     

Genetic diversity patterns in Phragmites australis at the population,regional and continental scales

Genetic diversity, population structure and interrelationships were investigated in eight populations of the common reed, Phragmites australis, in the Po Plain, Italy, by means of amplified fragments length polymorphisms (AFLPs) and random amplified polymorphic DNAs (RAPDs). Patterns of genetic diversity were analysed in relation to size, age and degree of human impact in the wetlands and compared with that of a distant population in Romania. Genetic distances between Po Plain clones and geographically distant clones were measured to determine the geographical extent of the gene pool.     

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

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

Simple sequence repeat diversity in diploid and tetraploid Coffea species.

Thirty-four fluorescently labeled microsatellite markers were used to assess genetic diversity in a set of 30 Coffea accessions from the CENICAFE germplasm bank in Colombia. The plant material included one sample per accession of seven East African accessions representing five diploid species and 23 wild and cultivated tetraploid accessions of Coffea arabica from Africa, Indonesia, and South America. More allelic diversity was detected among the five diploid species than among the 23 tetraploid genotypes. The diploid species averaged 3.6 alleles/locus and had an average polymorphism information content (PIC) value of 0.6, whereas the wild tetraploids averaged 2.5 alleles/locus and had an average PIC value of 0.3 and the cultivated tetraploids (C. arabica cultivars) averaged 1.9 alleles/locus and had an average PIC value of 0.22. Fifty-five percent of the alleles found in the wild tetraploids were not shared with cultivated C. arabica genotypes, supporting the idea that the wild tetraploid ancestors from Ethiopia could be used productively as a source of novel genetic variation to expand the gene pool of elite C. arabica germplasm.     

Genetic diversity in perennial ryegrass and white clover among old Dutch grasslands as compared to cultivars and nature reserves

To support conservation policies for old Dutch grasslands that are still in agricultural use, morphological variation and AFLP-based (amplified fragment length polymorphism-based) genetic diversity was studied in perennial ryegrass and white clover populations and compared with the diversity in reference varieties. In addition, AFLP variation was also studied in grasslands located in nature reserves. From principal component analysis (PCA), it appeared that date of ear emergence in perennial ryegrass and characters related to plant vigour in white clover were the main morphological characters separating the reference varieties from the old Dutch grassland populations, and some of the grassland populations from each other. In both species, intrapopulation variation was lower for the reference varieties. Lower heterogeneity within the reference varieties was also found in the AFLP analysis. All common AFLP's observed in old Dutch grasslands could also be found in the reference varieties and nature reserves. Only a small number of low-frequency alleles found in old Dutch grasslands were absent from the other two groups. However, band frequencies of markers could vary considerably between populations, which may have been caused by selection. Analysis of the AFLP data by PCA distinguished the majority of reference varieties from the old Dutch grasslands, and showed genetic differentiation only between some grasslands. Comparison of old Dutch grasslands with grasslands in nature reserves indicated that basically the same range of genetic variation is covered by the two groups. Our study indicates that the Netherlands harbour a more or less continuous population for major parts of the diversity of perennial ryegrass and white clover. It was concluded that no specific conservation measures are presently needed to maintain genetic diversity of perennial ryegrass and white clover occurring in old Dutch grasslands.     

AFLP analysis of the diversity and phylogeny of Lens and its comparison with RAPD analysis

AFLP and RAPD marker techniques have been used to evaluate and study the diversity and phylogeny of 54 lentil accessions representing six populations of cultivated lentil and its wild relatives. Four AFLP primer combinations revealed 23, 25, 52 and 48 AFLPs respectively, which were used to partition variation within and among Lens taxa. The results of AFLP analysis is compared to previous RAPD analysis of the same material. The two methods provide similar conclusions as far as the phylogeny of Lens is concerned. The AFLP technique detected a much higher level of polymorphyism than the RAPD analysis. The use of 148 AFLPs arising from four primer combinations was able to discriminate between genotypes which could not be distinguished using 88 RAPDs. The level of variation detected within the cultivated lentil with AFLP analysis indicates that it may be a more efficient marker technology than RAPD analysis for the construction of genetic linkage maps between carefully chosen cultivated lentil accessions.     

Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, <Emphasis Type="Italic">Helianthus annuus</Emphasis> L

Crop germplasm collections are valuable resources for ongoing plant breeding efforts. To fully utilize such collections, however, researchers need detailed information about the amount and distribution of genetic diversity present within collections. Here, we report the results of a population genetic analysis of the primary gene pool of sunflower (Helianthus annuus L.) based on a broad sampling of 433 cultivated accessions from North America and Europe, as well as a range-wide collection of 24 wild sunflower populations. Gene diversity across the cultivars was 0.47, as compared with 0.70 in the wilds, indicating that cultivated sunflower harbors roughly two-thirds of the total genetic diversity present in wild sunflower. Population structure analyses revealed that wild sunflower can be subdivided into four genetically distinct population clusters throughout its North American range, whereas the cultivated sunflower gene pool could be split into two main clusters separating restorer lines from the balance of the gene pool. Use of a maximum likelihood method to estimate the contribution of the wild gene pool to the cultivated sunflower germplasm revealed that the bulk of the cultivar diversity is derived from two wild sunflower population genetic clusters that are primarily composed of individuals from the east-central United States, the same general region in which sunflower domestication is believed to have occurred. We also identified a nested subset of accessions that capture as much of the allelic diversity present within the sampled cultivated sunflower germplasm collection as possible. At the high end, a core set of 288 captured nearly 90% of the alleles present in the full set of 433, whereas a core set of just 12 accessions was sufficient to capture nearly 50% of the total allelic diversity present within this sample of cultivated sunflower.     

Genetic diversity in selected, historical US sugarbeet germplasm and Beta vulgaris ssp. maritima

 Diversity among sugar beet accessions released over the first 50 years of public breeding in the United States was examined to ascertain a baseline of genetic diversity and to gauge the effect of breeding on the loss or gain of diversity over this time period. Accessions were chosen as released germplasm from the major breeding stations contributing to the US germplasm pool and their presumed ancestors from Europe, including representatives for the wild forms Beta vulgaris ssp. maritima. Sixty nine polymorphic RAPD fragments were used for gene frequency analysis, and heterozygosity was determined within and among groups of accessions related either by breeding station or simply inherited agronomic characters for monogerm seed and restoration of fertility in a cytoplasmic male-sterile background. In general, heterozygosity within releases declined with time, but total genetic diversity in the US germplasm pool remained constant. Breeding for the agronomic characters had a marked influence in reducing diversity. Received: 20 October 1998 / Accepted: 28 October 1998     

RFLP diversity of common bean (Phaseolus vulgaris) in its centres of origin.

Eighty-five wild and cultivated accessions of common bean (Phaseolus vulgaris L.), representing a wide geographic area in the centres of domestication were tested for restriction fragment length polymorphisms (RFLPs). Genomic DNA was digested with one of three restriction enzymes (EcoRI, EcoRV, and HindIII) and hybridized to 12 probes distributed throughout the common bean genome. Accessions could be classified into two major groups with a distinct geographical distribution in Middle America and the Andes. Within each gene pool, cultivated accessions clustered together with wild forms from the same geographical area supporting the multiple domestications hypothesis for this crop. Estimates of Nei's genetic distances among the cultivated races from the two different gene pools varied from 0.12 to 0.56 and among races from the same gene pool from 0.04 to 0.12, suggesting that the divergence in Phaseolus vulgaris has reached the subspecies level. The level of genetic diversity (Ht = 0.38) was twice the value obtained with isozyme analysis. Genetic diversity within races (Hs = 0.27) was four to five times higher compared with isozymes, but genetic diversity between races (Dst = 0.11) was similar for both categories of markers. These results corroborate previous studies on the characterization of genetic diversity in common bean that clearly showed two distinct gene pools, Middle American and Andean. Moreover, RFLP markers are superior to isozymes because they provide better coverage of the genome and reveal higher level of polymorphisms.     

Genetic diversity of the Khakass gene pool: Subethnic differentiation and the structure of Y-chromosome haplogroups

The structure of Khakass gene pool has been investigated: Y-chromosome haplogroup compositions and frequencies were described in seven population samples of two basic subethnic groups, Sagai and Kachins, from three geographically separated regions of the Khakass Republic. Eight haplogroups were detected in the Khakass gene pool: C3, E, N*, N1b, N1c, R1a1a, and R1b1b1. The haplogroup spectra and the genetic diversity by haplogroups and YSTR haplotypes differed significantly between Sagai and Kachins. Kachins had a low level of gene diversity, whereas the diversity of Sagai was similar to that of other South-Siberian ethnic groups. Sagai samples from the Askizskii district were very similar to each other, and so were two Kachin samples from the Shirinskii district, while Sagai samples from the Tashtypskii district differed considerably from each other. The contribution of intergroup differences among ethnic groups was high, indicating significant genetic differentiation among native populations in Khakassia. The Khakass gene pool was strongly differentiated both by haplogroup frequencies and by YSTR haplotypes within the N1b haplogroup. The frequencies of YSTR haplotypes within the chromosome Y haplogroups N1b, N1c, and R1a1 were determined and their molecular phylogeny was investigated. Factor and cluster analysis, as well as AMOVA, suggest that the Khakass gene pool is structured by territory and subethnic groups.     

A genetic bottleneck in the ’evolution under domestication’ of upland cotton Gossypium hirsutum L. examined using DNA fingerprinting

Reliable information about the evolutionary and genetic relationships of various germplasm resources is essential to the establishment of rational strategies for crop improvement. We used AFLPs to study the genetic relationships of 43 cultivars of Gossypium hirsutum representative of the genomic composition of modern ’Upland’ cotton. The study also included representatives of the related tetraploid species Gossypium barbadense, as well as the diploid species Gossypium raimondii, Gossypium incanum, Gossypium herbaceum and Gossypium arboreum. We tested 20 primer combinations that resulted in a total of 3,178 fragments. At the species level, and above, genetic similarities based on AFLPs were in agreement with the known taxonomic relationships. Similarity indices ranged from 0.25 to 0.99. Representatives of the G. hirsutum germplasm resources utilized in North America, including secondary accessions collected by breeders in Central America (’Acala’, ’Tuxtla’, ’Kekchi’) and the southwestern US (’Hopi Moencopi’), formed a single cluster with exceedingly limited genetic diversity (with many pairwise similarity indices >0.96) We concluded that these accessions were derived from the same genetic pool. The early maturing or ’latifolium’ or ’Mexican Highlands’ cultigens from which these cultivars were derived appear to have had extremely limited genetic diversity, perhaps as a result of a severe genetic bottleneck resulting from the selection pressures of domestication. Outside of the major G. hirsutum cluster, well-supported phylogenies were inferred. Inside this cluster, phylogenies were obscured by limited diversity, reticulation and lineage sorting. The implications of these findings for cotton improvement are discussed. Received: 23 May 2000 / Accepted: 23 January 2001     

Molecular genetic diversity of the Turkish national hazelnut collection and selection of a core set

European hazelnut (Corylus avellana L.) is an economically and nutritionally important nut crop with wild and cultivated populations found throughout Europe and in parts of Asia. This study examined the molecular genetic diversity and population structure of 402 genotypes including 143 wild individuals, 239 landraces, and 20 cultivars from the Turkish national hazelnut collection using simple sequence repeat (SSR) markers. A total of 30 SSR markers yielded 407 polymorphic fragments. Diversity analysis of the Turkish hazelnut genotypes indicated that they fell into three subpopulations according to ad hoc statistics and neighbor-joining algorithm. Although all cultivars clustered together, they overlapped with the wild accessions and landraces. Thus, the dendrogram, principal coordinate, and population structure analyses suggest that they share the same gene pool. A total of 78 accessions were selected as a core set to encompass the molecular genetic and morphological diversity present in the national collection. This core set should have priority in preservation efforts and in trait characterization.     

Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs

 RFLPs, AFLPs, RAPDs and SSRs were used to determine the genetic relationships among 18 cultivated barley accessions and the results compared to pedigree relationships where these were available. All of the approaches were able to uniquely fingerprint each of the accessions. The four assays differed in the amount of polymorphism detected. For example, all 13 SSR primers were polymorphic, with an average of 5.7 alleles per primer set, while nearly 54% of the fragments generated using AFLPs were monomorphic. The highest diversity index was observed for AFLPs (0.937) and the lowest for RFLP (0.322). Principal co-ordinate analysis (PCoA) clearly separated the spring types from the winter types using RFLP and AFLP data with the two-row winter types forming an intermediate group. Only a small group of spring types clustered together using SSR data with the two-row and six-row winter varieties more widely dispersed. Direct comparisons between genetic similarity (GS) estimates revealed by each of the assays were measured by a number of approaches. Spearman rank correlation ranked over 70% of the pairwise comparisons between AFLPs and RFLPs in the same order. SSRs had the lowest values when compared to the other three assays. These results are discussed in terms of the choice of appropriate technology for different aspects of germplasm evaluation.     

Genetic structure and diversity analysis of the primary gene pool of chickpea using SSR markers

Members of the primary gene pool of the chickpea, including 38 accessions of Cicer arietinum, six of C. reticulatum and four of C. echinospermum grown in India were investigated using 100 SSR markers to analyze their genetic structure, diversity and relationships. We found considerable diversity, with a mean of 4.8 alleles per locus (ranging from 2 to 11); polymorphic information content ranged from 0.040 to 0.803, with a mean of 0.536. Most of the diversity was confined to the wild species, which had higher values of polymorphic information content, gene diversity and heterozygosity than the cultivated species, suggesting a narrow genetic base for cultivated chickpea. An unrooted neighbor-joining tree, principal coordinate analysis and population structure analysis revealed differentiation between the cultivated accessions and the wild species; three cultivated accessions were in an intermediate position, demonstrating introgression within the cultivated group. Better understanding of the structure, diversity and relationships within and among the members of this primary gene pool will contribute to more efficient identification, conservation and utilization of chickpea germplasm for allele mining, association genetics, mapping and cloning gene(s) and applied breeding to widen the genetic base of this cultivated species, for the development of elite lines with superior yield and improved adaptation to diverse environments.     

小麦地方品种繁殖更新过程中的遗传多样性变化分析

采用分别保存于长期库及中期库的3个小麦地方品种的6份材料,进行了9项农艺性状及35个与农艺性状相关的微卫星标记检测,每份材料选取30个单株进行遗传多样性与遗传结构分析。结果表明:(1)更新前,3个小麦地方品种均为遗传异质性群体,在SSR位点上的异质度分别为57.14%、48.57%和5.71%。(2)在农艺性状表现上,只有温泉小麦3在株高和穗粒数上更新后比更新前显著增加,其他材料无显著差异。(3)在SSR位点多态性表现上,3个品种在更新后均发生了遗传多样性变化,8个与粒重、产量、生育期性状相关位点存在等位位点丢失现象,其中2个与粒重、生育期相关位点频率变化显著。(4)综合农艺性状调查与SSR分子标记检测结果发现,3个品种更新前后在多样性指数上无显著差异,遗传分化系数Gst分别为0.0269、0.0324和0.0380,即更新前后遗传差异分别为2.69%、3.24%和3.80%。上述结果建议,经繁殖更新的小麦种质资源能够比较完好地保持其遗传多样性和遗传结构。对于遗传异质性小麦地方品种在繁殖更新后存在遗传多样性丢失的危险,为了保证更新前后的遗传完整性,建议在繁殖更新过程中每个品种至少应保持300个单株的群体。     

Genetic diversity of Southeastern Nigerien date palms reveals a secondary structure within Western populations

Date palm (Phoenix dactylifera L.) is mainly cultivated for its edible fruit and is of great socio-economic importance for the populations of arid zones. Analysis of the date palm genetic diversity in the Old World had revealed a strong genetic structure with the existence of two gene pools, one Eastern comprising Asia and Djibouti, and one Western, consisting of North African accessions. So far, mainly date palm populations from countries within the Maghreb and the Middle East were characterized, but no information from the Sahel was included. Here, we present the genetic diversity of date palms from Southeastern Niger. The DNA of 113 date palm accessions were analyzed and compared with a database containing the genetic information of 248 accessions from the Old World. The diversity generated from microsatellite markers was compared to that of the same loci of both the Eastern and Western genetic pools. Our results show that date palms from Southeastern Niger constitute a unique group with a high level of genetic diversity. Moreover, even though this group is included in the Western genetic pool, it shows a specific originality which differentiates it from other Western populations. It also shows one of the lowest admixture levels of the Western pool. Global analysis showed a secondary genetic structure within the Western pool highlighting a new genetic group located in Southeastern Niger that distinguishes itself from the North African group.