Fine-scale geographical structure of genetic diversity in inland wild beet populations

Introgression arising from crop-to-wild gene flow provides novel sources of genetic variation in plant species complexes. Hybridization within the Beta vulgaris species complex is of immediate concern; crop lineages ( B .  vulgaris ssp. vulgaris ) hybridize easily with their wild relatives ( B .  vulgaris ssp. maritima ) thereby threatening wild beet gene diversity with genetic swamping. Hybridization 'hotspots' occur in European seed production areas because inland ruderal wild beets occur and reproduce in sympatry with cultivated beets. We studied gene flow occurring between seed-producing cultivars and ruderal wild B .  vulgaris in southwestern France to determine whether feral beets, arising from unharvested cultivated seed, represent an opportunity for crop-to-wild gene flow. We surveyed 42 inland ruderal beet populations located near seed production fields for nucleo-cytoplasmic variation and used a cytoplasmic marker diagnostic of cultivated lines. Occurrence of cultivated-type cytoplasm within ruderal populations clearly reflected events of crop seed escape. However, we found no genetic signatures of nuclear cultivated gene introgression, which suggests past introgression of cultivated cytoplasm into a wild nuclear background through seed escape rather than recent direct pollen flow. Overall, patterns of genetic structure suggested that inland ruderal wild beet populations act as a metapopulation, with founding events involving a few sib groups, followed by low rates of seed or pollen gene flow after populations are established. Altogether, our results indicate that a long-lived seed bank plays a key role in maintaining cultivated-type cytoplasm in the wild and highlight the need for careful management of seed production areas where wild and cultivated relatives co-occur.     

Evolutionary dynamics of mitochondrial plasmids in natural populations of Silene vulgaris

Although plasmid-like mitochondrial DNA molecules have been investigated in a number of cultivated plant species, knowledge about their occurrence and behavior in natural plant populations is scarce. In the bladder campion, Silene vulgaris, a common weed of northern Europe, mt-plasmids of three different sizes were detected in a survey of S. vulgaris populations in southern Sweden. Two of the three plasmids usually occurred together within individual plants and showed large variation in frequency between populations. From F(ST)-estimates of plasmids, mitochondrial markers, and nuclear markers it was concluded that the plasmids are predominantly maternally inherited in their natural habitat, as observed in greenhouse experiments. The association between mt-plasmids and mitochondrial haplotype was strong, but not complete, in the natural material. These results indicate that the mt-plasmids of S. vulgaris have evolved toward almost strict maternal inheritance.     

一株高脂土壤小球藻的分离鉴定及脂质分析

对采自山西省庞泉沟国家自然保护区的土壤中的藻种进行分离鉴定, 获得了一株优良的高脂绿藻。经显微形态观察鉴定, 该藻株的形态特征属于小球藻属Chlorella (Chlorellasp. PQG67)。进一步对其rbcL和18S rDNA基因序列进行分析并构建系统树, 结果表明基因序列与普通小球藻Ch. vulgaris同源并聚为一支, 确定其为一株普通小球藻Ch. vulgaris PQG67。在不同光照强度下连续培养后测定其油脂含量稳定在30%左右, 在不同NaCl浓度胁迫条件下可达40%以上, 并通过叶绿素荧光值测量探索该藻株生长趋势。通过傅立叶变换红外光谱图对其油脂积累过程分析, 显示该藻株脂类成分在1634/cm附近, 有vC=O伸缩振动谱带, 随着培养时间的延长, 脂质含量的相对强度也在增加。可见该藻株具有较高的生长速率及产油能力, 是一株具产业化应用潜力的优良产油藻株。     

ALLOZYME VARIATION IN OLD WORLD RACES OF SORGHUM BICOLOR (POACEAE)

A survey of allozyme variation in cultivated races of sorghum (Sorghum bicolor) was undertaken. Eight plants each of 83 accessions representing the five primary races and five of the intermediate races of sorghum were analyzed for 15 enzyme systems encoded by 27 loci. Low levels of variation were found within accessions, which is typical of self-pollinating species. Little variation was also found among accessions. Compared with other cereals, S. bicolor is depauperate in allozyme variation. We found an average of 1.81 alleles per locus with a mean expected heterozygosity of 0.008 for the accessions and total panmictic heterozygosity of 0.093. Only 9% of the variation present was found within accessions, while 91% was among accessions. Most of the variation present is attributable to differences in geographic origin of the accessions rather than racial differences. Western and eastern Africa have the highest levels of total heterozygosity (0.108 and 0.088, respectively), while southern Africa has the lowest (0.008). Principal component analysis revealed continuous variation among races and geographic regions with the accessions failing to segregate into discrete racial or geographic clusters.     

Impact of gene flow from cultivated beet on genetic diversity of wild sea beet populations

Gene flow and introgression from cultivated plants may have important consequences for the conservation of wild plant populations. Cultivated beets (sugar beet, red beet and Swiss chard: Beta vulgaris ssp. vulgaris) are of particular concern because they are cross-compatible with the wild taxon, sea beet (B.vs. ssp. maritima). Cultivated beet seed production areas are sometimes adjacent to sea beet populations; the numbers of flowering individuals in the former typically outnumber those in the populations of the latter. In such situations, gene flow from cultivated beets has the potential to alter the genetic composition of the nearby wild populations. In this study we measured isozyme allele frequencies of 11 polymorphic loci in 26 accessions of cultivated beet, in 20 sea beet accessions growing near a cultivated beet seed production region in northeastern Italy, and 19 wild beet accessions growing far from seed production areas. We found one allele that is specific to sugar beet, relative to other cultivated types, and a second that has a much higher frequency in Swiss chard and red beet than in sugar beet. Both alleles are typically rare in sea beet populations that are distant from seed production areas, but both are common in those that are near the Italian cultivated beet seed production region, supporting the contention that gene flow from the crop to the wild species can be substantial when both grow in proximity. Interestingly, the introgressed populations have higher genetic diversity than those that are isolated from the crop. The crop-to-wild gene flow rates are unknown, as are the fitness consequences of such alleles in the wild. Thus, we are unable to assess the long-term impact of such introgression. However, it is clear that gene flow from a crop to a wild taxon does not necessarily result in a decrease in the genetic diversity of the native plant.     

Domestication and the distribution of genetic variation in wild and cultivated populations of the Mesoamerican fruit tree Spondias purpurea L. (Anacardiaceae)

Domestication occurs as humans select and cultivate wild plants in agricultural habitats. The amount and structure of variation in contemporary cultivated populations has been shaped, in part, by how genetic material was transferred from one cultivated generation to the next. In some cultivated tree species, domestication involved a shift from sexually reproducing wild populations to vegetatively propagated cultivated populations; however, little is known about how domestication has impacted variation in these species. We employed AFLP data to explore the amount, structure, and distribution of variation in clonally propagated domesticated populations and sexually reproducing wild populations of the Neotropical fruit tree, Spondias purpurea (Anacardiaceae). Cultivated populations from three different agricultural habitats were included: living fences, backyards, and orchards. AFLP data were analysed using measures of genetic diversity (% polymorphic loci, Shannon's diversity index, Nei's gene diversity, panmictic heterozygosity), population structure (F(ST) analogues), and principal components analyses. Levels of genetic variation in cultivated S. purpurea populations are significantly less than variation found in wild populations, although the amount of diversity varies in different agricultural habitats. Cultivated populations have a greater proportion of their genetic variability distributed among populations than wild populations. The genetic structure of backyard populations resembles that of wild populations, but living fence and orchard populations have 1/3 more variability distributed among populations, most likely a reflection of relative levels of vegetative reproduction. Finally, these results suggest that S. purpurea was domesticated in two distinct regions within Mesoamerica.     

Molecular ecology and selection in the drought-related Asr gene polymorphisms in wild and cultivated common bean (Phaseolus vulgaris L.)

ABSTRACT: BACKGROUND: The abscisic acid (ABA) pathway plays an important role in the plants' reaction to drought stress and ABA-stress response (Asr) genes are important in controlling this process. In this sense, we accessed nucleotide diversity at two candidate genes for drought tolerance (Asr1 and Asr2), involved in an ABA signaling pathway, in the reference collection of cultivated common bean (Phaseolus vulgaris L.) and a core collection of wild common bean accessions. RESULTS: Our wild population samples covered a range of mesic (semi-arid) to very dry (desert) habitats, while our cultivated samples presented a wide spectrum of drought tolerance. Both genes showed very different patterns of nucleotide variation. Asr1 exhibited very low nucleotide diversity relative to the neutral reference loci that were previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, Asr2 exhibited higher levels of nucleotide diversity, which is indicative of adaptive selection. These patterns were more notable in wild beans than in cultivated common beans indicting that natural selection has played a role over long time periods compared to farmer selection since domestication. CONCLUSIONS: Together these results suggested the importance of Asr1 in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits. Furthermore, one of our major successes was to find that wild common bean is a reservoir of genetic variation and selection signatures at Asr genes, which may be useful for breeding drought tolerance in cultivated common bean.     

A study of the variation in Trifolium burchellianum ssp. johnstonii (Fabaceae)

A study of the variation within the tropical African taxon Trifolium burchellianum ssp. johnstonii , including var. oblongum , is made on the basis of herbarium material and cultivated material. The chromosome numbers 2n = 48 and 2n = 96 were counted in the collections of var. johnstonii and var. oblongum respectively. In most other material, the chromosome number has been estimated from the size of the pollen grains and guard cells. Var. johnstonii was found to have both 2n = 48 and 2n = 96 and var. oblongum was found only to have 2n = 96. Var. oblongum and var. johnstonii with 2n = 96 are found to have complementary distributions, while the distribution of var. johnstonii with 2n = 48 is found sympatric with all the 2n = 96 material. The sterility barriers are persumed to have become weakened at the higher ploidy level, and gene flow is presumed to explain the continuous variation between the two varieties. The origin of var. oblongum is also discussed.     

Genetic Structure of Rhizobium etli biovar phaseoli Associated with Wild and Cultivated Bean Plants (Phaseolus vulgaris and Phaseolus coccineus) in Morelos, Mexico

The genetic structure of Rhizobium etli biovar phaseoli was determined for five populations in three different locations in the state of Morelos, Mexico, by using starch gel electrophoresis for five to nine polymorphic loci. Two populations were sampled during two different years from nodules of cultivated and wild common bean plants (Phaseolus vulgaris). The three other populations were associated with wild runner beans (P. coccineus) and sampled during 1988. The Rhizobium populations differ genetically both among sites and among populations within the same site in different years, as shown by differences in allelic frequencies, genetic differentiation analysis, and differences in electrotypes. The total genetic diversity for the five populations during 1988 was H = 0.487; there were also high levels of genetic variation within each population. We found the highest linkage disequilibrium in a global analysis for all the populations. At a local scale, we also found significant linkage disequilibrium in two populations, although the distribution of the D' suggest some recombination at a local scale. The other three rhizobium populations exhibit low linkage disequilibrium. A cluster analysis (UPGMA) of pairwise genetic distances showed that bacteria isolated from most wild Phaseolus spp. are grouped by population, whereas those obtained from cultivated P. vulgaris are very heterogeneous. The analysis of the genetic structure of Rhizobium strains may allow the identification of strains that are naturally well adapted to a wide range of different environments, which may be useful for agricultural purposes or as a starting point for developing improved Rhizobium strains.     

Genetic differentiation in the Bladder campions, Silene vulgaris and S. uniflora (Caryophyllaceae), in Sweden

Allozyme variation was studied in Swedish populations of Silene vulgaris (a widespread weed), S. uniflora ssp. uniflora (restricted to coastal habitats) and S. uniflora ssp. petraea (endemic to Sweden and confined to open limestone habitats). The taxa are diploid, gynodioecious, perennial herbs and showed high levels of within-taxon and within-population gene diversity at four polymorphic loci. Within-taxon diversity was highest (H_tax=0.52) in S. vulgaris and lowest (H_tax=0.36) in S. uniflora ssp. uniflora. The weedy S. vulgaris has more alleles than either of the other two taxa and 5 out of a total of 27 alleles are unique to S. vulgaris. Most of the gene diversity within each of the taxa is accounted for by within-population diversity. The between-population component of diversity is 10% in S. vulgaris , and 24% and 5%, respectively, in S. uniflora ssp. uniflora and ssp. petraea. Hybrids may occur between S. vulgaris and S. uniflora , but introgression is limited by the species' ecology. Neither allozyme nor distributional data support the suggestion that ssp. petraea is a recent hybrid between S. vulgaris and S. uniflora ssp. uniflora , although an older hybrid origin for ssp. petraea is possible. Patterns of allele frequency variation suggest that there has been some historical gene flow between taxa, outside their present areas of sympatry. It is likely that the two subspecies of S. uniflora , which occur in naturally open habitats, were able to colonize Sweden during the Late Glacial or early post-glacial, whereas S. vulgaris followed the spread of agriculture into Sweden.     

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.     

Evidence for gene flow via seed dispersal from crop to wild relatives in Beta vulgaris (Chenopodiaceae): consequences for the release of genetically modified crop species with weedy lineages

Gene flow and introgression from cultivated to wild plant populations have important evolutionary and ecological consequences and require detailed investigations for risk assessments of transgene escape into natural ecosystems. Sugar beets (Beta vulgaris ssp. vulgaris) are of particular concern because: (i) they are cross-compatible with their wild relatives (the sea beet, B. vulgaris ssp. maritima); (ii) crop-to-wild gene flow is likely to occur via weedy lineages resulting from hybridization events and locally infesting fields. Using a chloroplastic marker and a set of nuclear microsatellite loci, the occurrence of crop-to-wild gene flow was investigated in the French sugar beet production area within a 'contact-zone' in between coastal wild populations and sugar beet fields. The results did not reveal large pollen dispersal from weed to wild beets. However, several pieces of evidence clearly show an escape of weedy lineages from fields via seed flow. Since most studies involving the assessment of transgene escape from crops to wild outcrossing relatives generally focused only on pollen dispersal, this last result was unexpected: it points out the key role of a long-lived seed bank and highlights support for transgene escape via man-mediated long-distance dispersal events.     

Variable populations within variable populations: quantifying mitochondrial heteroplasmy in natural populations of the gynodioecious plant Silene vulgaris

Populations of mitochondria reside within individuals. Among angiosperms, these populations are rarely considered as genetically variable entities and typically are not found to be heteroplasmic in nature, leading to the widespread assumption that plant mitochondrial populations are homoplasmic. However, empirical studies of mitochondrial variation in angiosperms are relatively uncommon due to a paucity of sequence variation. Recent greenhouse studies of Silene vulgaris suggested that heteroplasmy might occur in this species at a level that it is biologically relevant. Here, we use established qualitative methods and a novel quantitative PCR method to study the intraindividual population genetics of mitochondria across two generations in natural populations of S. vulgaris. We show incidences of heteroplasmy for mitochondrial atpA and patterns of inheritance that are suggestive of more widespread heteroplasmy at both atpA and cox1. Further, our results demonstrate that quantitative levels of mitochondrial variation within individuals are high, constituting 26% of the total in one population. These findings are most consistent with a biparental model of mitochondrial inheritance. However, selection within individuals may be instrumental in the maintenance of variation because S. vulgaris is gynodioecious. Male sterility is, in part, regulated by the mitochondrial genome, and strong selection pressures appear to influence the frequency of females in these populations.     

Phylogeography of two European newt species--discordance between mtDNA and morphology

The newts Triturus vulgaris and Triturus montandoni are sister species that exhibit contrasting levels of intraspecific morphological variation. Triturus vulgaris has a broad Eurasiatic distribution encompassing both formerly glaciated and unglaciated areas and shows substantial morphological differentiation in the southern part of its range, while T. montandoni, confined to the Carpathians, is morphologically uniform. We analysed sequence variation of two mtDNA fragments of the total length of c. 1850 bp in 285 individuals of both species collected from 103 localities. Phylogenetic analysis of 200 unique haplotypes defined 12 major clades, their age estimated at c. 4.5-1.0 million years (Myr). Most of the older clades were found in the southern part of the range, and also in central Europe, mainly in Romania. The distribution of mtDNA clades points to the existence of several glacial refugia, located in the Caucasus region, Anatolia, the Balkan Peninsula, Italy, and more to the north in central Europe. The concordance between mtDNA based phylogeny and the distribution of T. vulgaris subspecies was weak. Triturus montandoni haplotypes did not form a monophyletic group. Instead they were found in six clades, in five of them mixed with T. vulgaris haplotypes, most likely as a result of past or ongoing hybridization and multiple introgression of mtDNA from T. vulgaris to T. montandoni. Patterns of sequence variation within clades suggested long-term demographic stability in the southern groups, moderate and relatively old demographic growth in the populations inhabiting central Europe, and high growth in some of the groups that colonized northern parts of Europe after the last glacial maximum.     

Variability of traits associated with phosphorus efficiency in wild and cultivated genotypes of common bean

Genetic variation in plant growth under limited phosphorus (P) supply is necessary to obtain more productive cultivars on low P-available soils. Two pot experiments were conducted to evaluate the variability of some traits associated with efficiency of P absorption and utilization in wild and cultivated genotypes of common bean (Phaseolus vulgaris L.) under biological N2 fixation. At two P levels (20 and 80 mg P kg-1 soil, P1 and P2, respectively), 20 wild and 6 cultivated genotypes were grown in Experiment 1, and 4 wild and 27 cultivated genotypes were grown in Experiment 2. Plants were harvested at flowering, but in Experiment 1 wild accessions that did not flower were harvested at the beginning of leaf senescence. In Experiment 1, part of the genotypic variability of wild accessions was attributed to a less homogeneous ontogenetic stage at harvest, whereas in Experiment 2 some variation in biomass production was due to distinct phenologies of cultivated genotypes. Wild lines did not seem more tolerant to low P conditions, but the genotypic variation observed suggests these materials as a source of genetic diversity. Part of the variation in the root area and root efficiency ratio (total P content:root area) was compensatory, resulting in narrow genotypic differences in the total P content. The total P content and root efficiency ratio presented a wider amplitude of variation at P2 than at P1, and P uptake was more influenced by P supply than root production. Since the genotype × P level interaction was not significant for shoot biomass and shoot P concentration in Experiment 2, P utilization efficiency may be a useful selection criterion for cultivars between limited and adequate P supply. Within the sample of genetic diversity evaluated herein, there was large genotypic variability for traits related to P efficiency among wild and cultivated genotypes of common bean.     

Diversity of common beans (Phaseolus vulgaris,Fabaceae) and conditions of production in Aguascalientes,Mexico

This study analyzes the regional diversity of common beans (Phaseolus vulgaris, Fabaceae) in Aguascalientes, Mexico, in relation to local physical, biological, cultural, and socioeconomic factors. A close direct relationship between bean diversity and the physical and biological factors and a close inverse relationship between bean diversity and the cultural and socioeconomic factors was found. Greater bean diversity was found in areas under rainfed conditions with low-input traditional agriculture where farmers with low income cultivate a great number of local heterogeneous landraces to insure some production for home use in spite of environmental stress conditions. Reduced bean diversity is cultivated under irrigated conditions with high-input modern agriculture where farmers with high income grow a few uniform improved cultivars to obtain high yields for commercial purposes. A previous study showed greater morphological variation in the seed collected in the 1940s compared to that collected in 1984. The bean variants of 1984 showed significantly earlier maturation. These findings suggest the necessity of periodic studies for a better understanding of the dynamic process of evolution of beans under continuous ecological, cultural, and socioeconomic change.     

SNP deserts of Asian cultivated rice: genomic regions under domestication

When performing a genome‐wide comparison between indica (93‐11) and japonica (Nipponbare), we find 8% of the genome, which have an extremely low SNP rate (< 1 SNP/kb). Inside these ‘SNP deserts’, experimentally confirmed genes show increased K_a/K_s that indicate adaptive selection. To further elucidate this connection, we survey the level and pattern of genetic variation in both cultivated and wild rice groups, using 155 noncoding regions located within SNP deserts. The results suggest that cultivated rice has greatly reduced genetic variation within SNP deserts as compared to either the nondesert or corresponding genomic regions in wild rice. Consistent with this reduction in genetic variation, we find a biased distribution of derived allele frequency in the cultivated group, indicative of positive selection. Furthermore, over half of the confirmed, domestication‐related genes are found within SNP deserts, also suggesting that SNP deserts are strongly related to domestication, and might be the key sites in the process of domestication.     

半连续及连续培养小球藻减排沼液及CO2

采用半连续或连续模式培养小球藻,考察小球藻减排沼液和CO2的能力。结果表明:在半连续培养模式中,当更新率为30%时,沼液中的N、P质量浓度可分别稳定在16～18和0.4～0.6 mg/L,达到污水二级排放标准;提高更新率到40%以上,3 d后微藻生物量及其对沼液中N、P的吸收达到动态平衡,但N、P去除率未达到污水直接排放标准;在连续培养模式中,分别选用20%及30%的日更新率,7 L规模12 d后沼液中的总氮(TN)仍高达55.64 mg/L。说明大规模培养条件下的光限制是微藻法减排沼液的主要制约因素。     

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.