RFLP-based assay of Sorghum bicolor (L.) Moench genetic diversity

Sixty-two single-copy sorghum DNA clones were used to compare restriction fragment patterns of 53 sorghum accessions from Africa, Asia and the United States. Included were accessions from five morphological races of the cultivated subspecies bicolor, and four races of the wild subspecies verticilliflorum. From two to twelve alleles were detected with each probe. There was greater nuclear diversity in the wild subspecies (255 alleles in ten accessions) than in the domestic accessions (236 alleles in 37 accessions). Overall, 204 of the 340 alleles (60%) that were detected occurred in both subspecies. Phylogenetic analysis using parsimony separated the subspecies into separate clusters, with one group of intermediate accessions. Though exceptions were common, especially for the race bicolor, accessions classified as the same morphological race tended to group together on the basis of RFLP similarities. Selection for traits such as forage quality may have led to accessions genetically more similar to other races being classified as bicolors, which have a loose, small-grained panicle similar to wild races. Population statistics, calculated using four nuclear and four cytoplasmic probes that detect two alleles each, revealed a low but significant amount of heterozygosity, and showed little differentiation in alleles in the wild and cultivated subspecies. Outcrossing with foreign pollen appears to have been more important than migration via seed dispersal as a mechanism for gene flow between the wild and domestic accessions included in this study.     

Population structure and genetic diversity distribution in wild and cultivated populations of the traditional Chinese medicinal plant Magnolia officinalis subsp. biloba (Magnoliaceae)

Magnolia officinalis subsp. biloba, a traditional Chinese medicinal plant, experienced severe declines in the number of populations and the number of individuals in the late 20th century due to the widespread harvest of the subspecies. A large-scale cultivation program was initiated and cultivated populations rapidly recovered the loss in individual plant numbers, but wild populations remained small as a consequence of cutting. In this study, the levels of genetic variation and genetic structure of seven wild populations and five domestic populations of M. officinalis subsp. biloba were estimated employing an AFLP methodology. The plant exhibited a relatively high level of intra-population genetic diversity (h = 0.208 and H _j = 0.268). The cultivated populations maintained approximately 95% of the variation exhibited in wild populations, indicating a slight genetic bottleneck in the cultivated populations. The analysis of genetic differentiation revealed that most of the AFLP diversity resided within populations both for the wild group (78.22%) and the cultivated group (85.92%). Genetic differentiation among populations in the wild group was significant (F _ST = 0.1092, P < 0.005), suggesting wild population level genetic structure. Principal coordinates analysis (PCO) did not discern among wild and cultivated populations, indicating that alleles from the wild population were maintained in the cultivated gene pool. Results from the present study provide important baseline data for effectively conserving the genetic resources of this medicinal subspecies.     

The systematics of autopolyploidy in Epilobium latifolium (Onagraceae)

Diploid (2n = 36) plants ofEpilobium latifolium L. have been found in Alaska and the western Cordillera of North America, and tetraploids in Iceland, western Greenland, and southeastern Quebec. Study of the morphology of these chromosome races revealed a character, the number of pores in the pollen grains, by which they could be distinguished with an average probability of 75%. Tetraploids ofE. latifolium tend to have high percentages of 4-pored pollen, while the diploids usually have only 3-pored pollen. On this basis, the ranges of the races were extrapolated from herbarium material. Detailed comparisons of eight other features of the presumptive diploids and tetraploids showed no significant difference between them. The races appear to form worldwide, allopatric, ecogeographic phases. A high level (57.4%) of quadrivalent formation observed during tetraploid meiosis, and other considerations, indicate that the tetraploids arose by autopolyploidy. The recommendation is made that the races not be given formal taxonomic recognition.     

Abundant Microsatellite Diversity and Oil Content in Wild Arachis Species

The peanut (Arachis hypogaea) is an important oil crop. Breeding for high oil content is becoming increasingly important. Wild Arachis species have been reported to harbor genes for many valuable traits that may enable the improvement of cultivated Arachis hypogaea, such as resistance to pests and disease. However, only limited information is available on variation in oil content. In the present study, a collection of 72 wild Arachis accessions representing 19 species and 3 cultivated peanut accessions were genotyped using 136 genome-wide SSR markers and phenotyped for oil content over three growing seasons. The wild Arachis accessions showed abundant diversity across the 19 species. A. duranensis exhibited the highest diversity, with a Shannon-Weaver diversity index of 0.35. A total of 129 unique alleles were detected in the species studied. A. rigonii exhibited the largest number of unique alleles (75), indicating that this species is highly differentiated. AMOVA and genetic distance analyses confirmed the genetic differentiation between the wild Arachis species. The majority of SSR alleles were detected exclusively in the wild species and not in A. hypogaea, indicating that directional selection or the hitchhiking effect has played an important role in the domestication of the cultivated peanut. The 75 accessions were grouped into three clusters based on population structure and phylogenic analysis, consistent with their taxonomic sections, species and genome types. A. villosa and A. batizocoi were grouped with A. hypogaea, suggesting the close relationship between these two diploid wild species and the cultivated peanut. Considerable phenotypic variation in oil content was observed among different sections and species. Nine alleles were identified as associated with oil content based on association analysis, of these, three alleles were associated with higher oil content but were absent in the cultivated peanut. The results demonstrated that there is great potential to increase the oil content in A. hypogaea by using the wild Arachis germplasm.     

Islands and streams: clusters and gene flow in wild barley populations from the Levant

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter‐mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analysing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication.     

Determination of Seed Storage Proteins and Total Isoflavones in Wild and Cultivated Soybeans

Two soybean components namely, storage proteins and isoflavone content in a wild and three cultivated soybean genotypes were characterized and compared. The storage proteins, β-conglycinin and glycinin were separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and two major storage proteins and their subunits were characterized using mass spectrometry. The three isoflavones, aglycon and the nine conjugated forms were separated by HPLC (high performance liquid chromatography) and identified by comparison of retention time, ultraviolet and mass spectral analyses. Comparison between the number of 2D-PAGE protein spots of the storage protein subunits and HPLC area of twelve isoflavones was also evaluated. The analysis of proteins and isoflavones from the wild genotype and the three cultivated genotypes suggested possible interactions between proteins and isoflavones. The same wild genotype, which showed significant statistical differences in β-conglycinin and glycinin protein profiles also revealed considerable reduction in total isoflavones (> 55%) content.     

QTL clusters reflect character associations in wild and cultivated rice

The genetic basis of character association related to differentiation found in the primary gene pool of rice was investigated based on the genomic distribution of quantitative trait loci (QTLs). Major evolutionary trends in cultivated rice of Asiatic origin (Oryza sativa) and its wild progenitor (O. rufipogon) are: (1) differentiation from wild to domesticated types (domestication), (2) ecotype differentiation between the perennial and annual types in wild races, and (3) the Indica versus Japonica type differentiation in cultivated races. Using 125 recombinant inbred lines (RILs) derived from a cross between an Indica cultivar of O. sativa and a strain of O. rufipogon carrying some Japonica-like characteristics, we mapped 147 markers, mostly RFLPs, on 12 chromosomes. Thirty-seven morphological and physiological quantitative traits were evaluated, and QTLs for 24 traits were detected. The mapped loci showed a tendency to form clusters that are composed of QTLs of the domestication-related traits as well as Indica/Japonica diagnostic traits. QTLs for perennial/annual type differences did not cluster. This cluster phenomenon could be considered "multifactorial linkages" followed by natural selection favoring co-adapted traits. Further, it is possible that the clustering phenomenon is partly due to pleiotropy of some unknown key factor(s) controlling various traits through diverse metabolic pathways. Chromosomal regions where QTL clusters were found coincided with the regions harboring genes or gene blocks where the frequency of cultivar-derived alleles in RILs is higher than expected. This distortion may be partly due to unconscious selection favoring cultivated plant type during the establishment of RILs.     

Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation

The research objectives were to determine aspects of the population dynamics relevant to effective monitoring of gene flow in the soybean crop complex in Japan. Using 20 microsatellite primers, 616 individuals from 77 wild soybean (Glycine soja) populations were analysed. All samples were of small seed size (< 0.03 g), were directly collected in the field and came from all parts of Japan where wild soybeans grow, except Hokkaido. Japanese wild soybean showed significant reduction in observed heterozygosity, low outcrossing rate (mean 3.4%) and strong genetic differentiation among populations. However, the individual assignment test revealed evidence of rare long-distance seed dispersal (> 10 km) events among populations, and spatial autocorrelation analysis revealed that populations within a radius of 100 km showed a close genetic relationship to one another. When analysis of graphical ordination was applied to compare the microsatellite variation of wild soybean with that of 53 widely grown Japanese varieties of cultivated soybean (Glycine max), the primary factor of genetic differentiation was based on differences between wild and cultivated soybeans and the secondary factor was geographical differentiation of wild soybean populations. Admixture analysis revealed that 6.8% of individuals appear to show introgression from cultivated soybeans. These results indicated that population genetic structure of Japanese wild soybean is (i) strongly affected by the founder effect due to seed dispersal and inbreeding strategy, (ii) generally well differentiated from cultivated soybean, but (iii) introgression from cultivated soybean occurs. The implications of the results for the release of transgenic soybeans where wild soybeans grow are discussed.     

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.     

不同繁殖模式下甘草药用成分含量积累速度差异研究

目的:系统比较野生甘草无性繁殖的甘草根和人工甘草种子有性繁殖的甘草根中药用成分的积累速度差异情况,为进一步研究影响甘草药用成分积累的基因机制奠定理论基础。方法:本研究基于HPLC和UV等分析方法,比较野生甘草和人工甘草在甘草酸、甘草苷和甘草总黄酮以及其他类成分的含量差异。基于HPLC指纹图谱技术,全面分析不同繁殖模式下甘草根的化学信息和内在质量的差异情况。结果:除甘草素和异甘草素外,野生甘草不定根中其他三种药用成分和总黄酮的含量均高于人工甘草实生根,经SPSS分析,除异甘草素外,其他成分在两组之间均存在显著差异;根据HPLC指纹图谱,两种甘草药用成分之间差异显著,相似度为0.647。结论:野生无性繁殖的甘草根和人工有性繁殖的甘草根中主要药用成分含量之间存在显著差异,野生甘草具有快速积累药用成分的功能。本研究结果对于今后人工调控生产优质甘草药材,实现甘草资源的可持续利用具有重要的理论和实践意义。     

On the Dispersal of Bottle Gourd [<Emphasis Type="Italic">Lagenaria siceraria</Emphasis> (Mol.) Standl.] Out of Africa: a Contribution from the Analysis of Nuclear Ribosomal DNA Haplotypes,Divergent Paralogs and Variants of 5.8S Protein Sequences

Bottle gourd (Lagenaria siceraria), a multipurpose crop, is among the first domesticates of humans. This study analyses nuclear ribosomal DNA (nrDNA) of the two cultivated subspecies to improve our understanding on the African origin and the dispersal to Asia. A total of 146 nrDNA sequences representing 79 individuals from African cultivars and 67 individuals from Asian cultivars were compared; the resulting nrDNA sequences were composed of 35 and 16 haplotypes specific to Africa and Asia, respectively, and two additional haplotypes shared by both continents. When all the rDNA haplotypes were bulked, the genetic differentiation (F _ST ) was significant between the subspecies (P?<?0.001), within Africa (P?<?0.001) and within Asia (P?<?0.05), and the nucleotide diversity was 2.5-fold higher in Africa. Sorting the haplotypes by classes of paralogs revealed more classes in Africa, and in classes where African and Asian cultivars were represented, the diversity was higher in Africa, in general. The 5.8S-coding regions showed two to four amino acid differences resulting to nine protein sequence variants, one of which encompassed all the Asian cultivars. The nucleotide diversity at that shared variant was 1.43-fold higher in Africa than in Asia. Analyses of phylogenetic networks revealed major shared haplotypes containing 23.91 % of the cultivars and having founder locations. We suggest that African cultivars reached Asia. The study tags for the first time nrDNA haplotypes capable of discriminating between and within the subspecies. Thirty single nucleotide polymorphisms (SNPs) and five insertion-deletions (Indels) derived from the haplotypes and registered in GenBank are provided.     

Changes in growth,hormones levels and essential oil content of Ammi visnaga L. plants treated with some bioregulators

The effects of foliar application of different concentrations of amino acids (tyrosine and phenylalanine) and phenolic acids (trans-cinnamic acid, benzoic acid and salicylic acid) on growth, pigment content, hormones levels and essential oil content of Ammi visnaga L were carried out during two successive seasons. It is clear that foliar application of either amino acids or phenolics significantly promoted the growth parameters in terms of shoot height, fresh and dry biomass, number of branches and number of umbels per plant. The increment of growth parameter was associated with elevated levels of growth promoters (IAA, GA3, total cytokinins) and low level of ABA. The greatest increase in the previously mentioned parameters was measured in plants exposed to different concentrations of phenols particularly in benzoic acid-treated plants. Such effect was concentration dependent. All treatments led to significant increments in yield seeds and oil content. Moreover, gas liquid chromatographic analysis revealed that the main identified components of essential oil were 2,2-dimethyl butanoic acid, isobutyl isobutyrate, α-isophorone, thymol, fenchyl acetate and linalool. Phenolics and amino acid treatments resulted in qualitative differences in these components of essential oil.     

Genetic Signature of Rice Domestication Shown by a Variety of Genes

Cultivated rice was domesticated from common wild rice. However, little is known about genetic adaptation under domestication. We investigated the nucleotide variation of both cultivated rice and its wild progenitors at 22 R-gene and 10 non–R-gene loci. A significant regression was observed between wild rice and rice cultivars in their polymorphic levels, particularly in their nonsynonymous substitutions (θ _a ). Our data also showed that a similar proportion (approximately 60%) of nucleotide variation in wild rice was retained in cultivated rice in both R-genes and non–R-genes. Interestingly, the slope always was >1 and the intercept always >0 in linear regressions when a cultivar’s polymorphism was x-axis. The slope and intercept values can provide a basis by which to estimate the founder effect and the strength of artificial direct selection. A larger founder effect than previously reported and a strong direct-selection effect were shown in rice genes. In addition, two-directional selection was commonly found in differentiated genes between indica and japonica rice subspecies. This kind of selection may explain the mosaic origins of indica and japonica rice subspecies. Furthermore, in most R-genes, no significant differentiation between cultivated and wild rice was detected. We found evidence for genetic introgression from wild rice, which may have played an important role during the domestication of rice R-genes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Yuanli Zhang and Jiao Wang contributed equally to this work.     

Assessment of the Genetic Diversity of Different Job's Tears (Coix lacryma-jobi L.) Accessions and the Active Composition and Anticancer Effect of Its Seed Oil

Job’s tears (Coix lachryma-jobi L.) is an important crop used as food and herbal medicine in Asian countries. A drug made of Job’s tears seed oil has been clinically applied to treat multiple cancers. In this study, the genetic diversity of Job’s tears accessions and the fatty acid composition, triglyceride composition, and anti-proliferative effect of Job’s tears seed oil were analyzed using morphological characteristics and ISSR markers, GC-MS, HPLC-ELSD, and the MTT method. ISSR analysis demonstrated low genetic diversity of Job’s tears at the species level (h = 0.21, I = 0.33) and the accession level (h = 0.07, I = 0.10), and strong genetic differentiation (G_ST = 0.6702) among all accessions. It also clustered the 11 accessions into three cultivated clades corresponding with geographical locations and two evidently divergent wild clades. The grouping patterns based on morphological characteristics and chemical profiles were in accordance with those clustered by ISSR analysis. Significant differences in morphological characteristics, fatty acid composition, triglyceride composition, and inhibition rates of seed oil were detected among different accessions, which showed a highly significant positive correlation with genetic variation. These results suggest that the seed morphological characteristics, fatty acid composition, and triglyceride composition may be mainly attributed to genetic factors. The proportion of palmitic acid and linoleic acid to oleic acid displayed a highly significant positive correlation with the inhibition rates of Job’s tears seed oil for T24 cells, and thus can be an important indicator for quality control for Job’s tears.     

Nucleotide diversity and Pleistocene population expansion in Atlantic and Mediterranean scallops (Pecten maximus and P. jacobaeus) as revealed by the mitochondrial 16S ribosomal RNA gene

Atlantic (Pecten maximus) and Mediterranean (Pecten jacobaeus) scallops have been traditionally considered as distinct species, but recent genetic studies have shown that they are races or subspecies separated by the Almeria-Oran oceanographic front in SE Spain. We have scored the nucleotide polymorphism of a 511 base pairs long fragment of the mitochondrial 16S ribosomal RNA gene in 85 individuals from 4 populations of P. maximus and 3 of P. jacobaeus. The populations were characterized by sharing the 2 most common haplotypes. We found no significant differences in haplotype frequencies among populations or species. However, slight, significant differentiation between taxa appeared when haplotypes were pooled in two groups according to their phylogenetic relationships and after analysis of molecular variance, in agreement with previous allozyme studies. Levels of within-population nucleotide diversity were similar in all populations except in P. jacobaeus from the northern Adriatic Sea, suggesting a smaller effective population size in that area which could be due to variable recruitment. Finally, populations showed an excess of rare haplotypes. The mismatch distribution and several population genetic statistics indicate that the excess of rare variants is due to a population expansion which occurred in the second half of the Pleistocene period, less than 0.9 my before present, and probably well after the origin of the two scallop races.     

Insights into genome differentiation: pheromone-binding protein variation and population history in the European corn borer (Ostrinia nubilalis)

Examination of sequence variation at nuclear loci can give insights into population history and gene flow that cannot be derived from other commonly used molecular markers, such as allozymes. Here, we report on sequence variation at a single nuclear locus, the pheromone-binding protein (PBP) locus, in the European corn borer (Ostrinia nubilalis). The European corn borer has been divided into three races in New York State on the basis of differences in pheromone communication and life history. Previous allozyme data have suggested that there is a small but significant amount of genetic differentiation between these races. The PBP does not appear to be involved in the pheromone differences between these races. Examination of variation at the PBP locus in the three races reveals no fixed differences between races despite high levels of polymorphism. There also appears to have been considerable recombination in the history of the pheromone-binding protein alleles. Observation of both recombination between alleles and lack of significant nucleotide or insertion/deletion divergence between races leads us to suggest that these populations are either recently diverged or have continued to exchange genetic material subsequent to divergence in pheromone communication and life history.     

Distribution and Differentiation of Wild,Feral, and Cultivated Populations of Perennial Upland Cotton (Gossypium hirsutum L.) in Mesoamerica and the Caribbean

Perennial forms of Gossypium hirsutum are classified under seven races. Five Mesoamerican races would have been derived from the wild race ‘yucatanense’ from northern Yucatán. ‘Marie-Galante’, the main race in the Caribbean, would have developed from introgression with G. barbadense. The racial status of coastal populations from the Caribbean has not been clearly defined. We combined Ecological Niche Modeling with an analysis of SSR marker diversity, to elucidate the relationships among cultivated, feral and wild populations of perennial cottons. Out of 954 records of occurrence in Mesoamerica and the Caribbean, 630 were classified into four categories cultivated, feral (disturbed and secondary habitats), wild/feral (protected habitats), and truly wild cotton (TWC) populations. The widely distributed three first categories cannot be differentiated on ecological grounds, indicating they mostly belong to the domesticated pool. In contrast, TWC are restricted to the driest and hottest littoral habitats, in northern Yucatán and in the Caribbean (from Venezuela to Florida), as confirmed by their climatic envelope in the factorial analysis. Extrapolating this TWC climatic model to South America and the Pacific Ocean points towards places where other wild representatives of tetraploid Gossypium species have been encountered. The genetic analysis sample comprised 42 TWC accessions from 12 sites and 68 feral accessions from 18 sites; at nine sites, wild and feral accessions were collected in close vicinity. Principal coordinate analysis, neighbor joining, and STRUCTURE consistently showed a primary divergence between TWC and feral cottons, and a secondary divergence separating ‘Marie-Galante’ from all other feral accessions. This strong genetic structure contrasts strikingly with the absence of geographic differentiation. Our results show that TWC populations of Mesoamerica and the Caribbean constitute a homogenous gene pool. Furthermore, the relatively low genetic divergence between the Mesoamerican and Caribbean domesticated pools supports the hypothesis of domestication of G. hirsutum in northern Yucatán.     

The Population Genetics of Cultivation: Domestication of a Traditional Chinese Medicine,Scrophularia ningpoensis Hemsl. (Scrophulariaceae)

Background

Domestic cultivation of medicinal plants is an important strategy for protecting these species from over harvesting. Some species of medicinal plants have been brought into cultivation for more than hundreds years. Concerns about severe loss of genetic diversity and sustainable cultivation can potentially limit future use of these valuable plants. Genetic studies with comprehensive sampling of multiple medicinal species by molecular markers will allow for assessment and management of these species. Here we examine the population genetic consequences of cultivation and domestication in Scrophularia ningpoensis Hemsl. We used chloroplast DNA and genomic AFLP markers to clarify not only the effects of domestication on genetic diversity, but also determine the geographic origins of cultivars and their genetic divergence from native populations. These results will allow both better management of cultivated populations, but also provide insights for crop improvement.

Results

Twenty-one cpDNA haplotypes of S. ningpoensis were identified. Wild populations contain all haplotypes, whereas only three haplotypes were found in cultivated populations with wild populations having twice the haplotype diversity of cultivated populations. Genetic differentiation between cultivated populations and wild populations was significant. Genomic AFLP markers revealed similar genetic diversity patterns. Furthermore, Structure analysis grouped all wild populations into two gene pools; two of which shared the same gene pool with cultivated S. ningpoensis. The result of Neighbor-Joining analysis was consistent with the structure analysis. In principal coordinate analysis, three cultivated populations from Zhejiang Province grouped together and were separated from other cultivated populations.

Conclusions

These results suggest that cultivated S. ningpoensis has experienced dramatic loss of genetic diversity under anthropogenic influence. We postulate that strong artificial selection for medicinal quality has resulted in genetic differentiation between cultivated and wild populations. Furthermore, it appears that wild populations in Jiangxi-Hunan area were involved in the origin of cultivated S. ningpoensis.     

Origins and Domestication of Cultivated Banana Inferred from Chloroplast and Nuclear Genes

Background

Cultivated bananas are large, vegetatively-propagated members of the genus Musa. More than 1,000 cultivars are grown worldwide and they are major economic and food resources in numerous developing countries. It has been suggested that cultivated bananas originated from the islands of Southeast Asia (ISEA) and have been developed through complex geodomestication pathways. However, the maternal and parental donors of most cultivars are unknown, and the pattern of nucleotide diversity in domesticated banana has not been fully resolved.

Methodology/Principal Findings

We studied the genetics of 16 cultivated and 18 wild Musa accessions using two single-copy nuclear (granule-bound starch synthase I, GBSS I, also known as Waxy, and alcohol dehydrogenase 1, Adh1) and two chloroplast (maturase K, matK, and the trnL-F gene cluster) genes. The results of phylogenetic analyses showed that all A-genome haplotypes of cultivated bananas were grouped together with those of ISEA subspecies of M. acuminata (A-genome). Similarly, the B- and S-genome haplotypes of cultivated bananas clustered with the wild species M. balbisiana (B-genome) and M. schizocarpa (S-genome), respectively. Notably, it has been shown that distinct haplotypes of each cultivar (A-genome group) were nested together to different ISEA subspecies M. acuminata. Analyses of nucleotide polymorphism in the Waxy and Adh1 genes revealed that, in comparison to the wild relatives, cultivated banana exhibited slightly lower nucleotide diversity both across all sites and specifically at silent sites. However, dramatically reduced nucleotide diversity was found at nonsynonymous sites for cultivated bananas.

Conclusions/Significance

Our study not only confirmed the origin of cultivated banana as arising from multiple intra- and inter-specific hybridization events, but also showed that cultivated banana may have not suffered a severe genetic bottleneck during the domestication process. Importantly, our findings suggested that multiple maternal origins and a reduction in nucleotide diversity at nonsynonymous sites are general attributes of cultivated bananas.     

Assessment of the domestication state of ackee (Blighia sapida K.D. Koenig) in Benin based on AFLP and microsatellite markers

Ackee (Blighia sapida) is a native multipurpose species important for the livelihoods of the rural populations in Benin. Trees are found in natural forests or are managed by farmers in different traditional agroforestry systems. Genetic variation at amplified fragment length polymorphism (AFLP) markers, four nuclear microsatellites (nSSRs) and one chloroplast microsatellite (cpSSR) were investigated in 279 individuals from six wild and eight cultivated populations from Benin. The AFLP data revealed moderate levels of diversity of ackee in Benin (mean diversity values are proportion of polymorphic loci = 52.8% and Nei??s gene diversity = 0.157, for 375 AFLP fragments). The mean diversity values based on nSSR-markers are expected heterozygosity = 0.286, allelic richness = 2.77. Genetic variation of wild and cultivated populations did not differ markedly. AMOVA revealed that only 7.3 and 5.2% of the variation was partitioned among populations for nSSR- and AFLP-markers, respectively. A Mantel test based on these both marker-types revealed significant correlations between population pairwise geographic distance and genetic differentiation. Differentiation among cultivated populations was higher than among wild populations. The only polymorphic chloroplast microsatellite marker (ccmp7) showed three haplotypes. Cultivated populations from northeastern Benin were fixed on one haplotype which was not observed elsewhere indicating a different origin of these populations possibly from neighboring Nigeria. Farmer-led domestication had an impact on the spatial distribution of genetic variation but did not result in significant losses of diversity within populations. Measures to conserve genetic resources of ackee in each of the three main bioclimatic zones in Benin are proposed.