Genetic diversity of Bolivian wild potato germplasm: changes during ex situ conservation management and comparisons with resampled in situ populations

Potato wild relatives are important sources of novel variation for the genetic improvement of the cultivated potato. Consequently, many natural populations have been sampled and were deposited as accessions in gene banks around the world. Here we investigate to what extent the genetic variation of Bolivian wild potato species is maintained under gene bank conditions and how this diversity relates to that of current in situ populations. For this purpose, materials from seven potato species were screened for microsatellite variation. Genetic changes between different generations of ex situ germplasm were not observed for Solanum leptophyes and S. megistacrolobum, but were detected for S. neocardenasii and S. okadae, while each of the species S. acaule, S. avilesii and S. berthaultii showed stability in some cases and genetic change in others. The observed changes were ascribed to genetic drift and contamination resulting from human error during regeneration. Re-collected populations of six of the studied species showed highly significant genetic differences with the ex situ accessions that, apart from changes during ex situ maintenance, are most likely to be attributed to sampling effects during collecting and in situ genetic changes over time. The implications of the results for ex situ and in situ conservation strategies of wild potato species are discussed.     

Interspecific relationship and genetic diversity in wild beets in section Corollinae genus Beta: Isozyme and RAPD analyses

Interspecific relationship among wild beets in section Corollinae was analyzed. Isozyme allele composition supports the concept of three basic species consisting of two diploid species, Beta lomatogona and Beta macrorhiza and the tetraploid species, Beta corolliflora. The polyploid and apomictic species referred to as Beta trigyna and Beta intermedia were found as hybrids. Based on isozyme and RAPD results, B. corolliflora was also found more related to B. macrorhiza than to B. lomatogona. From the phylogenetic trees constructed from isozyme data, B. corolliflora and B. macrorhiza seem to be the end members of the evolutionary line. Analysis of genetic diversity showed that B. corolliflora was more polymorphic and heterozygous than B. lomatogona and B. macrorhiza. Differences between B. macrorhiza accessions from Turkey and Dagestan were found.     

A comprehensive collection and regeneration strategy for ex situ conservation

Because the facilities in genebanks are likely to be quite limited, it will usually be possible to raise only small populations of plants when producing fresh seed. These populations need to be large enough, however, to reducethe effects of drift on the erosion of genetical variation to an acceptable level. Calculations show that a sample size of 12 plants is probably sufficient to meet this objective provided that a biparental mating procedure is used toproduce fresh seed. It is argued that for conservation, there is little point in collecting more seed from the source populations of the species in question than can be handled when regenerating this seed. If the species is regarded asthe unit of conservation, this minimum sample size in the gene bank should determine the size of the sample collected from each population of the species. Provided that the product of this sample size and the number ofpopulations from which material is collected is not less than 172, this strategy should ensure the conservation of all or very nearly all of the polymorphic genes that are segregating in the species. A critical analysis of currentregeneration procedures shows that these are very inefficient and that much genetical variation is lost almost as soon as it is captured. Lastly, it is shown that some recent criticisms of the collection strategy proposed in earlierpapers are misplaced.     

东乡野生稻原位圃遗传多样性的微卫星标记分析

遗传多样性的分析是收集与利用种质资源的重要前提。利用微卫星标记对113份东乡野生稻(Oryza rufipogon Griff.)(简称"东野")进行多样性分析,24对SSR引物共得到114个等位基因,平均每对引物得到4.75个,表明东野具有丰富的遗传多样性。聚类分析表明,东野群体内来自同一居群的部分材料遗传距离较近,3个居群中有2个居群最小遗传距离为0,1个居群最小遗传距离为0.018,但也有些材料间的遗传距离很大,最大达0.851。东野3个居群居群内的平均遗传距离为0.171~0.435,居群间的平均遗传距离为0.432~0.652,表明东野群体内的遗传变异以居群间为主,因此必须对东野原生地的现有居群实行有力的保护。     

Ecological correlates of RAPD DNA diversity of wild barley, Hordeum spontaneum, in the Fertile Crescent

Genetic variability in RAPDs (Randomly Amplified Polymorphic DNA) was studied in 104 genotypes of wild barley, Hordeum spontaneum from 21 populations sampled in Israel, Turkey and Iran, seven population from each country. The band (= loci) frequencies were calculated for each population and correlated with ecogeographical variables. In general, high RAPD genetic diversity indices were associated with stressful environments, either with hot or cold steppes and deserts. Interpopulational genetic distances showed no association with the geographic distance between the populations' provenance. Significant Spearman rank correlations between RAPD band frequencies and ecogeographical parameters of provenance occured. Frequencies of RAPD bands were significantly correlated with the principal component factors of allozymes. The correlation data indirectly suggest that natural selection appears to be the major determinant of both RAPD and allozyme diversities both being correlated with environmental stress.     

Rice genetic diversity at farm and village levels and genetic structure of local varieties reveal need for in situ conservation

Rice genetic diversity partitioning between farms, varieties and, within-variety diversity, were analysed in two villages of Maritime Guinea with contrasted agroecological conditions. One thousand and two hundred individual plants belonging to 45 accessions collected in eight farms were genotyped using 10 SSR markers. The molecular variance was evenly shared between and within accessions, while the farm effect was almost nil. Local varieties had a multi-line genetic structure. The number of multilocus genotypes was proportional to the utilisation rate of the variety in the village. The F _ST values between different accessions of each variety were significant which indicated low genetic consistency in the variety names. This varietal structure could mainly be explained by the migration phenomenon and the high varietal turnover. Compared to allelic diversity, multilocus genotypic diversity seemed to be the most suitable indicator of the quantitative distribution of diversity at different management scales (accession, farm and village). The within- and between-farm F _ST values were in the same order of magnitude. The within-farm diversity was not farm-specific but quantitatively high, i.e. up to 50% of the total genotypic diversity of a given village. Given the relative importance of the within-variety diversity, the in situ approach stands out as the most effective solution. As farms do not host specific diversity the in situ approach could be implemented by working with a small number of farms.     

A problem of the rich: Prioritizing local plant genetic resources for ex situ conservation in Israel

A priority list of 323 plant species was created through a consultative process for ex situ conservation in the recently inaugurated Israel Plant Gene Bank (IGB). The IGB is set up to preserve plant genetic resources and the endangered genetic variability of the Israeli flora. Upon its inauguration, we consulted with the country’s leading plant breeders and botanists in an attempt to create a list of the most important plant species to be included in the initial collections. The list includes crop wild relatives (CWRs), selected according to their contribution to humans: edible plants (grains, vegetables, oil); forage plants; species with potential industrial and biotechnological applications (e.g. spices, medicinal plants, aromatic plants, fibers, dyes), and species with horticultural and forestry potential. We further ranked the species on the basis of assessed values for each of seven characteristics: distribution range in the country; abundance; rarity of the growing habitats; endemism; red number index—representing imminent threat of extinction; availability of samples in Israeli collections, and genetic relationship to cultivated crops. The sum of the assessed values for these seven characteristics was used to group the species on the list into four main prioritized-collection schemes. Statistical analysis indicated that all attributes had similar influence on the collecting prioritization scheme. In general, rare species with low abundance in their growing habitats were ranked in the highest priority group, while highly distributed species were sorted together into a lower priority group. The prioritization scheme will be used to optimize the collection in the IGB with the aim of establishing its collecting activities.     

Genetic diversity in Ethiopian barley in relation to altitude

Summary A representative sample of the Ethiopian barley collection, maintained at the Ethiopian Plant Genetic Resources Centre (PGRC/E), was studied for its phenotypic diversity for some agronomic characters, i.e. kernel row number, spike density, spikelets per spike, caryopsis type, kernel colour, thousand grain weight, days to maturity and plant height. The diversity was estimated by using the Shannon-Weaver diversity index (H) for each of the characters to examine overall genetic divergence between accessions on the basis of administrative regions, ecogeographical zones as well as altitudinal ranges within Ethiopia. Most of the variation was due to differences among characters and only a relatively small fraction due to differences between regions. However, almost all characters are considerably influenced by altitude within the regions. The mean diversity index for all characters increases with altitude, reaches a maximum between 2,400 and 2,800 m, and decreases beyond that altitude.     

The Vigna angularis complex: Genetic variation and relationships revealed by RAPD analysis, and their implications for in situ conservation and domestication

The present study, using RAPD analysis, was undertaken to characterize genetic variation in three forms of V. angularis, cultivated, wild and weedy forms, and their relationships. The materials used consisted of 171 individuals (plants) or cultivars from 23 populations including 5 wild populations, 6 weedy populations, 6 cultivated populations and 6 populations with plants having wild and weedy or intermediate morphology, denoted here as complex populations. The materials used were collected on Honshu Island, Japan and seeds collected directly from the field were germinated for DNA extraction. In addition, 6 landrace accessions of V. angularis from the genebank were also analyzed. Genetic variation was highest in the wild form (H_g= 0.132; GD = 0.388), followed by the weedy form (H_g= 0.124; GD = 0.341) and the least in the cultivated form (H_g= 0.079; GD = 0.274). Intra-population genetic variation was high in the weedy and in the wild populations. However, inter-population was greater than intra-population genetic variation for all groups of populations studied in the V. angularis complex. 93% of the total diversity in the present study was exhibited by plants from complex populations and specific RAPD bands were found in these populations. Our results provide evidence that complex populations would be a logical focus for efforts to conserve the V. angularis complex in situ. Our results suggest that weedy populations are usually an ecotype of the wild form adapted to a different habitat.     

微卫星标记分析广西水牛遗传多样性

为研究广西沼泽型水牛(Bubalus bubalis)核基因组的多态性,采用23对荧光标记微卫星引物,对随机抽取的60个广西本地水牛样本进行了PCR检测。结果表明,23对引物中,有19对可以获得特异性产物且存在多态,平均有效等位基因数为4.0189,基因座ILSTS086含有13个等位基因;各微卫星基因座的平均杂合度变化范围为0.1852~0.4722,ILSTS019基因座平均杂合度最高(0.4722),而ILSTS017平均杂合度最低(0.1852);群体基因平均多态信息含量(PIC)为0.6639,19个标记中有18个PIC大于0.5,属高度多态位点。     

Patterns of morphological diversity in tetraploid wheat (Triticum turgidum L.) landraces from Ethiopia

Thirty‐four tetraploid (2n = 4x = 28) wheat (Triticum turgidum L.) landrace populations collected from four regions in Ethiopia, and consisting of 4099 entries were characterized for glume colour, glume pubescence, beak awn, seed colour and spike density. The main objective was to analyse the diversity and distribution of these traits on the basis of administrative regions and altitudinal gradients. The Shannon‐Weaver Diversity Index (H') was used to estimate the magnitude of diversity. With the exception of spike density, all characters were polymorphic in all regions and most altitude groups. However, clinal patterns were observed in only a few cases. At the population level, the mean H’ varied from completely monomorphic (H’ = 0.00) to highly polymorphic (H’ = 0.80 ± 0.07). The highest diversity was found in regions with relatively better climatic conditions and in optimal altitude ranges. On country basis, seed colour (H’ = 0.98) and spike density (H’ = 0.43) displayed the highest and the lowest diversity indices, respectively. Spike density was the only character that exhibited significant differences (P<0.01) both “between regions”; and “between altitude groups”;. Across characters, most of the variance was due to the lowest hierarchy, the “within‐population”; component. The “between region”; and “between altitude group”; variances were significant, but spike density alone was responsible for the differences. The overall mean H’ for Ethiopia was 0.77 + 0.09 and did not seem to have reduced appreciably within the past 25 years or so, when compared to previous estimates.     

广西那坡县风水林植物物种多样性及其保育对策

采用线路踏查法和样方法相结合,调查了位于广西西南部那坡县8个屯的风水林。结果表明:(1)共有维管束植物241种,隶属于79科163属;(2)风水林为典型的热带季雨林,多数保护较好;(3)种子植物区系以热带亚热带成分占优势;(4)8个村屯的乔木层以及林下植物物种多样性差异较大。最后提出风水林植物物种多样性保育的对策。     

Genetic diversity in grasspea (Lathyrus sativus L.)

Genetic diversity was investigated in 348 accessions and subaccessions of grasspea (Lathyrus sativus L.) from 10 geographical regions. Polymorphism for 20 isozymes of 13 enzyme systems was studied to estimate the genetic diversity. The Near East and North Africa regions included the most variability for these isozyme systems, suggesting that the center of diversity (center of origin) for grasspea is in this general area. The lowest variability was found in accessions and subaccessions from South America, followed by those from Sudan–Ethiopia. Diversity was measured for individual loci over regions and EST-1 and SKDH had the highest genetic diversity. The closest genetic diversity was observed for LAP-2, followed by AAT-1 and PGM. The closest genetic distance existed between populations from the Near East and North Africa. Populations from South Asia and Sudan–Ethiopia, though geographically widely separated, exhibited a closer genetic distance from each other than from other regions.     

Diversity for abiotic and biotic stress resistance in the wild annual Cicer species

Data on 228 accessions of eight annual wild Cicer species and 20 cultivated chickpea check lines were evaluated for diversity in response to six of the most serious biotic and abiotic stresses which reduce crop yield and production stability of chickpea, i.e., ascochyta blight, fusarium wilt, leaf miner, bruchid, cyst nematode, and cold. Relative frequencies of score reactions to the above six stresses were recorded from all the annual wild Cicer species and the cultivated taxon. Patterns of distribution and amount of variation of the resistance reactions differed between stresses and species. C. bijugum, C. pinnatifidum and C. echinospermum showed accessions with at least one source of resistance (1 to 4 score reactions) to each stress. Overall, C. bijugum showed the highest frequencies of the highest categories of resistance. Next in performance was C. pinnatifidum followed by C. judaicum, C. reticulatum and C. echinospermum. Furthermore, C. bijugum had the highest number of accessions with multiple resistance to the six stresses; two accessions were resistant to five stresses and 16 to four. According to the Shannon-Weaver diversity indices (H), five species showed discrete mean diversity indices which varied from 0.649 in C. pinnatifidum to 0.526 in C. judaicum, whereas C. chorassanicum, C. cuneatum and C. yamashitae showed the lowest Hs, which were respectively 0.119, 0.174 and 0.216. Pair-wise correlations among the six biotic and abiotic stresses showed the possibility of combining these resistances. Interestingly, multiple resistant accessions were predominantly of Turkish origin.     

Genetic diversity and local population structure of fragmented populations of Trillium camschatcense (Trilliaceae)

Trillium camschatcense, a long-lived common woodland herb, has been experiencing intensive habitat fragmentation over the last century in eastern Hokkaido, Japan. We examined the genetic diversity and population genetic structure of 12 fragmented populations with different population sizes using allozyme electrophoresis. The percentage of polymorphic loci and mean number of alleles per locus were positively related to population size, probably due to the stochastic loss of rare alleles (frequency of q<0.1) in small populations. Populations with 350 flowering plants or fewer had lost almost all of their rare alleles. While the heterozygosity and inbreeding coefficient were not related to population size, some small populations showed relatively high inbreeding coefficients. In spite of the low genetic differentiation among overall populations (F_ST=0.130), local population structuring was recognized between the two geographically discontinuous population groups. Within groups, sufficient historical gene flow was inferred, whereas a low dispersal ability of this species and geographical separation could produce apparent differentiation between groups.     

Geographical, altitude and agro-ecological differentiation of isozyme and hordein genotypes of landrace barleys from Ethiopia: implications to germplasm conservation

An analysis of the variability of genes encoding six isozyme systems (15 loci) and two storage proteins (2 loci) in landrace barley from Ethiopia is reported. The materials consisted of populations collected from sites as low as 1650 and as high as 3750 meters, covering a wide range of agro-ecological conditions and geographical areas. Of the 17 loci 7 were polymorphic and 10 monomorphic when the 95% criterion of polymorphism was applied. Despite the disproportionate monomorphic loci, polymorphism was detected in all populations when this criterion is used. The populations were found to possess fairly low mean number of alleles per locus (A = 1.5), low mean value of expected heterozygosity (H = 0.134) and a fairly high mean percentage of polymorphic loci (P = 35.3%). The mean F_ST= 0.474 for the populations is typical of inbreeding species. The result indicated that allelic richness is concentrated in altitude class 3 (2500–3000 m) followed by altitude class 1 (<2000 m). Altitude class 2 (2000–2500) holds an intermediate place though it is the highest in terms of expected heterozygosity (H = 0.245). Higher genetic diversity is concentrated in some geographical regions such as Shewa, Arsi, Bale compared to others (Welo, Gamu Gofa, Gojam). Genetic differentiation among the agro-ecological zones was more profound than both among the altitudes and among regions. Correlation analysis between phenotypic diversity (Shannon-Weaver diversity index) and expected heterozygosity (H) for isozyme/hordein loci revealed non significant associations except with respect to agro-ecological zones. In general, it was detected that sites in highland areas in central and northern regions may be more desirable for in situ conservation than sites in peripheral regions in terms of isozyme/hordein diversity and current rate of varietal replacement.     

Isozyme studies of genetic diversity and evolution in Hippophae

Summary To provide information on the genetic variation, differentiation and evolution in Hippophae seed samples of 25 populations from China, Finland and Russia were electrophoretically analyzed. Of six loci investigated, four were good genetic markers for identifying species and subspecies. The percentages of polymorphic loci per population were 40.3% and 62.5% at 0.95 and 0.99 polymorphic criteria respectively. The mean number of alleles per locus per population was 2.1. Total genetic diversity in the material was 0.4614. Genetic diversity partitioning showed that there was a large amount of diversity residing within geographical populations (0.1354), between subspecies within species (0.1046) and between species (0.2566) but not between geographical populations (0.0114). There were nearly twice as many negative fixation indices as positive ones in Hippophae populations. The phylogenetic tree agreed very well with botanic classifications of the species and subspecies and their geographical distributions, and quantitatively presented the genetic relationships of 25 populations. A detailed view of the evolutionary stages in Hippophae showed clearly a general decline of similarity as evolutionary divergence continued, which further explained the evolution process in Hippophae.     

Genetic diversity for root-knot nematode resistance in white clover and related species

A total of 237 Plant Introduction in eleven Trifolium species were evaluated for resistance to Meloidogyne arenaria (Neal) Chitwood race 1, M. hapla Chitwood, M. incognita (Kofoid & White) Chitwood race 3, and M. javanica (Treub) Chitwood. Plants were infected with 1500 nematode eggs collected from 'Rutgers' tomato (Lycoperiscon esculentum Mill.) roots with 0.5% NaOCl. Ratings of galling severity and egg mass production were assigned to each plant 8 wk after inoculation. Host plant reaction was classified as immune, highly resistant, resistant, moderately resistant, intermediate, moderately susceptible, susceptible, and highly susceptible according to the resistance index . More than 95% of 171 white clover accessions were moderately to highly susceptible to all four nematodes species. The best white clover accessions were only moderately resistant to either M. arenaria (PI 291843 and PI 306286) or M. hapla (PI 100250 and PI 204930). Accessions with moderate resistance or resistance to root-knot nematodes were found among relatives of white clover, with T. ambiguum M. Bieb. exhibiting the greatest resistance level. Among the other Trifolium species evaluated, T. carolinianum Michx. PI 516273 was immune or highly resistant to all four nematode species while accessions of T. hirtum All. showed a wide range of reaction to root-knot nematodes. Identified germplasm of white clover relatives with resistance to root knot nematodes should be useful for the selection of parents in white clover breeding programs.     

Genetic diversity of core and peripheral Sitka spruce (Picea sitchensis (Bong.) Carr) populations: implications for conservation of widespread species

This study investigated levels of genetic diversity and population differentiation among Sitka spruce (Picea sitchensis) populations classified as core or peripheral based on ecological niche, and continuous or disjunct based on species distribution. Large numbers of trees (N = 200) were sampled from each of eight populations to evaluate the distribution of rare as well as common alleles across the species range. Codominant alleles for eight sequence-tagged site loci were classified based on frequency and geographic distribution in order to develop appropriate sampling strategies to target specific classes of alleles. An important finding of this study is the similarity in genetic diversity as measured by expected heterozygosity between core populations (mean H_E = 0.58) and peripheral populations (mean H_E = 0.56). However, there was significant inbreeding in peripheral (F_IS = 0.17) but not in core (F_IS = 0.03) populations. Large differences in gene flow estimates were observed between core (Nm = 9.0) and peripheral populations (Nm = 3.5). Irrespective of population classification, over 75% of the alleles were common and widespread. Only one allele was classified as rare and localized, and this allele was limited to one core, disjunct and two peripheral, disjunct populations. There was stronger evidence of past bottlenecks in peripheral, disjunct populations than in core, continuous populations. Results are used to suggest sampling strategies for capture of maximum level of genetic diversity and conservation of rare alleles. The conservation of peripheral, particularly disjunct, populations as well as populations in putative glacial refugia may present the best opportunity for conserving rare alleles.     

Isoenzyme differences between the wild diploid and tetraploid wheats

Variability of acid phosphatase (ACP), esterase (EST), and superoxide dismutase (SOD) isoenzymes among 660 accessions of wild diploid wheats Triticum boeoticum (475) and T. urartu (185) and among 35 accessions of wild tetraploid wheats T. araraticum (21) and T. dicoccoides (14) was studied with the use of polyacrylamide gel electrophoresis. The wild diploids are differentiated by the electrophoretic variants of ACP-B, ACP-C, EST-A, EST-B, EST-C, EST-D, and SOD-B. Triticum urartu matches the A genome of wild tetraploid wheats T. araraticum and T. dicoccoides by allozymes of ACP-B, ACP-C and SOD-B, but differs distinctly by the monomorphic allozyme EST-A66. Triticum boeoticum fits the A genome of polyploid wheats by allozymes of EST-A and EST-B, but differs in allozymes of ACP-B and SOD-B. Thus, none of the two contemporary diploid wheats corresponds exactly to the A genome of wild tetraploid wheats by all diagnostic isoenzymes. Triticum boeoticum and T. arararicum share EST-C46 and EST-D71, whereas T. urartu and T. dicoccoides are fixed for silent EST-C0 and share EST-D73, suggesting independent origin of the two tetraploid wheats with a contribution from ancestral forms of both diploids.