Conservation genetics of the highly endangered Azorean endemics <Emphasis Type="Italic">Euphrasia azorica</Emphasis> and <Emphasis Type="Italic">Euphrasia grandiflora</Emphasis> using new SSR data

In the Azores Islands, two Euphrasia L. (Orobanchaceae) endemic species are recognized: Euphrasia azorica H.C.Watson, an annual herb, in Flores and Corvo, and Euphrasia grandiflora Hochst. ex Seub., a semi-shrub, in Pico, São Jorge and Terceira. Both species are highly endangered and protected by the Bern Convention and Habitats Directive. A population genetics study was conducted with new microsatellite primer pairs in 159 individuals of E. azorica and E. grandifolia, sampled from populations in Flores, Corvo, Pico and São Jorge. Allele sizing suggested that E. azorica is a diploid while E. grandiflora is a tetraploid. Euphrasia grandiflora revealed higher genetic diversity then E. azorica. The E. grandiflora population of Morro Pelado in São Jorge, displayed higher genetic diversity when compared with all others, while the E. azorica population of Madeira Seca in Corvo, showed the lowest. Private and less common bands were also overall higher in E. grandiflora populations. Population genetic structure analysis confirmed a distinctiveness between the two Azorean endemic Euphrasia, in addition to island-specific genetic patterns in E. azorica. The genetic structure obtained for E. grandiflora was complex with the populations of Cabeço do Mistério in Pico Island and of Pico da Esperança in São Jorge sharing the same genetic group, while a putative spatial barrier to gene flow was still retrieved between both islands. Although some populations of both species might benefit from propagation actions, studies are needed on plant host species and translocations between islands or between some populations of a same island should be avoided, due to the occurrence of putative ESUs. Eradication of invasive species and control of grazing will be fundamental to promote in situ restauration.     

Molecular variation and population structure in endangered <Emphasis Type="BoldItalic">Limonium</Emphasis><Emphasis Type="BoldItalic">bicolor</Emphasis>: genetic diversity of microsatellite markers and amplified fragment length polymorphism analysis

Knowledge and analysis of the genetic structure of an endangered species is important for its conservation and evolutionary process. Simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs) were used in evaluation of the genetic diversity and population differentiation in Limonium bicolor (Plumbaginaceae), an endangered herb with high medicinal and horticulture value. A total of 117 alleles were detected with an average 5.85 alleles per locus using SSR and 222 bands from AFLP were amplified in six populations. It was found that L. bicolor was characterized by high levels of genetic polymorphism (100 and 83.78%), low levels of total genetic diversity (\(H_{\mathrm{t}}=\) 0.2824 and 0.2424), and moderate degrees of genetic differentiation among populations (\(\Phi _{\mathrm{ST}} =\) 0.284 and 0.251). Analysis of molecular variance (AMOVA) revealed that the main variation component existed within populations (71.56%; 74.93%) rather than among populations (28.44%; 25.07%). Four main clusters were displayed in the UPGMA using TFPGA, which was consistent with the result of principal coordinate analysis (PCA) using NTSYS. Mutations or infrequent gene flow among populations can increase the plant slowly, thus in situ conservation policies should be implemented first for effective and sustainable development. At the same time, ex situ measures, such as those individuals with rare alleles, to maintain the relationships between individuals and populations are also proposed.     

<Emphasis Type="Italic">Quinua</Emphasis> and Relatives (<Emphasis Type="Italic">Chenopodium</Emphasis> sect.<Emphasis Type="Italic">Chenopodium</Emphasis> subsect.<Emphasis Type="Italic">Celluloid</Emphasis>)

Traditionally viewed as an Andean grain crop,Chenopodium quinoa Willd. includes domesticated populations that are not Andean, and Andean populations that are not domesticated. Comparative analysis of leaf morphology and allozyme frequencies have demonstrated that Andean populations, both domesticated(quinua) and free-living(ajara), represent an exceptionally homogeneous unit that is well differentiated from allied domesticates of coastal Chile(quingua) and freeliving populations of the Argentine lowlands(C. hircinum). This pattern of relationships indicates that Andean populations represent a monophyletic crop/weed system that has possibly developed through cyclic differentiation (natural vs. human selection) and introgressive hybridization. Relative levels of variation suggest that this complex originated in the southern Andes, possibly from wild types allied withC. hircinum, with subsequent dispersal north to Colombia and south to the Chilean coast. Coastal populations were apparently isolated from post-dispersal differentiation and homogenization that occurred in the Andes. Other data point toward a center of origin in the northern Andes with secondary centers of genetic diversity subsequently developing in the southern Andes and the plains of Argentina. Comparative linkage of South American taxa, all tetraploid, with North American tetraploids of the subsection will eventually clarify this problem. While the possibility of a direct phyletic connection betweenC. quinoa and the Mexican domesticate(C. berlandieri subsp. nuttalliae,) cannot be excluded, available evidence indicates that the latter represents an autonomous lineage that is associated with the basal tetraploid, C. b. subsp.berlandieri, through var.sinuatum, whereas South American taxa show possible affinities to either var. zschackei or var.berlandieri. An extinct domesticate of eastern North America,C. b. subsp.jonesianum, represents either another instance of independent domestication, possibly from subsp. b. var.zschackei, or a northeastern outlier of subsp.nuttalliae.     

Genetic diversity of the African poplar (<Emphasis Type="Italic">Populus ilicifolia</Emphasis>) populations in Kenya

We evaluated the genetic diversity of the African poplar (Populus ilicifolia) populations found in Kenya compared with reference samples of five poplar species from North America and one species introduced in Kenya from India (KEFRI-Kenya). Amplified fragment length polymorphism (AFLP) was used with the objective of providing important information for breeding and in situ/ex situ conservation of this species. Samples collected from three locations along the species’ natural range (Athi, Ewaso Nyiro, and Tana rivers) were compared with four samples of locally planted Populus deltoides stand introduced from India and ten reference samples from North America. Six AFLP primer combinations produced 521 clear bands for analysis. The percentage polymorphic loci were lowest in Tana (20.4 %) and highest in Athi (40.6 %). The average heterozygosity across the studied populations was between 0.07 and 0.3. AMOVA revealed more genetic variation partitioning within population (87 %; P?<?0.01) than among populations (13 %; P?<?0.01) suggesting significant genetic variation between populations. Further, UPGMA delineation showed two clusters of the Tana, Athi, and Ewaso Nyiro populations clustered together compared to the North America and India/KEFRI reference samples. Moreover, the study showed that the Athi population is more diverse than those of Tana and Ewaso Nyiro and may be important for conservation, domestication, and improvement studies. The genetic differentiation (F _ST ?=?0.134) among Kenyan P. ilicifolia populations suggests limited possibility of gene flow between these populations.     

High genetic diversity in an endangered medicinal plant, <Emphasis Type="Italic">Saussurea involucrata</Emphasis> (<Emphasis Type="Italic">Saussurea</Emphasis>, Asteraceae), in western Tianshan Mountains,China

Saussurea involucrata (Asteraceae) is a medicinal and second-degree national priority endangered plant that is mainly distributed in the high latitude region of the western Tianshan Mountains. The population is fragmented and isolated, and extensive human impact merits a suitable and specific conservation strategy, which can be compiled based on the genetic diversity, population structure, and demographic history. Phylogeographic studies were conducted on a total of five natural populations and 150 individuals were sampled. Data from three cpDNA intergenic spacer regions (trnL-F, matK, and ndhF-rpl32) and nrDNA ITS sequences showed that twelve haplotypes in cpDNA and five haplotypes in nrDNA indicated high genetic diversity among populations sampled (H _T?=?0.820 and 0.756) and within populations sampled (H _S?=?0.792 and 0.721). Additionally, the high genetic diversity did not mirror genetic structure in either cpDNA (F _ST?=?0.03153, G _ST?>?N _ST, p?<?0.05) or nrDNA (F _ST?=?0.03666, meaningless G _ST and N _ST). Two groups (north and south) were determined for a SAMOVA analysis. Based on this analysis, the demographic history was conducted with a Bayesian Skyline Plot and Isolation with Migration analysis, which showed sustainable and stable extension without a marked bottleneck. Divergence time was indicated at c. 6.25 Mya (90%HPD: 15.30–0.22 Mya) in the Miocene, which is consistent with the formation of the Kelasu section of Tianshan. The southern populations in the Bayanbulak and Gonglu regions require additional attention and transplanting would be an effective way to restore rare cpDNA haplotypes, increase effective population size, and migration rate. Our results suggested that in situ conservation of S. involucrata in western Tianshan should be the main strategy for protection and recovery of the species.     

Conservation genetics of an ex situ population of <Emphasis Type="Italic">Primula reinii</Emphasis> var. <Emphasis Type="Italic">rhodotricha</Emphasis>, an endangered primrose endemic to Japan on a limestone mountain

Primula reinii var. rhodotricha is a perennial herb endemic to the limestone slope of Mt. Buko, located approximately 50 km northwest of central Tokyo, Japan. In recent years, its natural population size has decreased markedly due to limestone mining, and this species has been assigned to the ‘Critically Endangered (CR)’ category on the latest Japanese Red List. Although a remnant population of this species has been protected by a mining company outside their historical distribution range on Mt. Buko, the ex situ conservation of this endangered plant has been difficult because of insufficient low seed production. The genetic status of ex situ P. reinii var. rhodotricha and related species were investigated to develop an effective conservation plan for this species. Microsatellite analysis indicated that the ex situ population harbors lower genetic diversity than sister taxa, providing molecular evidence for the recent critical status designation of the ex situ population, whereas the presence of rare alleles may imply further potential for seed reproduction by outcrossing. Therefore, an appropriate propagation strategy that considers genetic diversity is needed for restoration and recovery of this critically endangered ex situ primrose population.     

Variation in the <Emphasis Type="Italic">COI</Emphasis> gene of the freshwater pearl mussel <Emphasis Type="Italic">Margaritifera margaritifera</Emphasis> from River Vuokkijoki

The freshwater pearl mussel Margaritifera margaritifera L. is one of the most endangered freshwater mussels in the world. Effective conservation of threatened species requires not only ecological, but also genetic information from the target species and populations. Since low genetic diversity can reduce the ability of a species to adapt to environmental changes, maintaining genetic diversity has been identified as one of the key elements in successful conservation programs. We examined genetic variation of the freshwater pearl mussel from the River Vuokkijoki, Karelia, Russia. We sequenced a fragment of the cytochrome c oxidase subunit I gene (COI) from 22 individuals and compared the data to 32 previously published COI sequences available in GenBank. We identified 10 different COI haplotypes in the sequenced samples, three of which had not been previously reported. Our results show that the River Vuokkijoki has high genetic diversity and suggest that the colonization of this northern freshwater pearl mussel population might have occurred from multiple and even distant refugia. Therefore, the freshwater pearl mussel population of the River Vuokkijoki is valuable for the conservation of the whole species.     

Resistance to herbivory of two populations of <Emphasis Type="Italic">Elodea</Emphasis><Emphasis Type="Italic">canadensis</Emphasis> Michaux and <Emphasis Type="Italic">Elodea nuttallii</Emphasis> Planchon St. John

In this article, we compared the resistance of two introduced populations of Elodea nuttallii and Elodea canadensis to two different herbivores. Samples were collected from the River Rhine and River Rhône in eastern France. The two populations of E. nuttallii differed in their introduction history, whereas E. canadensis was introduced at the same time in the two sites. The Daily Food Consumption (DFC) rates of the two macrophyte populations were evaluated in no-choice experiments using the scraper Lymnaea stagnalis and the shredder Gammarus roeseli. At the same time, we assessed four plant traits: dry matter content (DMC), total nitrogen content, carbon/nitrogen ratio and total phenolic content. The two populations of E. canadensis were consumed at low levels by both the herbivores. L. stagnalis showed a higher DFC on the Rhône population of E. nuttallii than on the Rhine population. No significant difference between the two populations was established with G. roeseli, but the level of DFC was high. This result demonstrates that the assessment of plant palatability should be carried out with several generalist herbivores belonging to various feeding groups (e.g. scrapers or shredders). Although the Rhône population of E. nuttallii had higher levels of phenols than the other populations, it was consistently consumed in greater quantities than E. canadensis. Neither the phenolic contents were not effective against these herbivores, nor the levels of phenolics too low to induce an efficient resistance. The higher DMC and the lower DFC of the two populations of E. canadensis suggest that this introduced plant has co-evolved with indigenous enemies in the introduced range.     

Simple Sequence Repeat and <Emphasis Type="Italic">S</Emphasis>-locus Genotyping to Explore Genetic Variability in Polyploid <Emphasis Type="Italic">Prunus spinosa</Emphasis> and <Emphasis Type="Italic">P. insititia</Emphasis>

Polyploid Prunus spinosa (2n = 4×) and P. insititia (2n = 6×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programmes. In Hungary, 17 cultivar candidates were selected from wild-growing populations including 10 P. spinosa, 4 P. insititia and three P. spinosa × P. domestica hybrids (2n = 5×). Their taxonomic classification was based on their phenotypic characteristics. Six simple sequence repeats (SSRs) and the multiallelic S-locus genotyping were used to characterize genetic variability and reliable identification of the tested accessions. A total of 98 SSR alleles were identified, which presents 19.5 average allele number per locus, and each of the 17 genotypes could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified. The complete and partial S-genotype was determined for 8 and 9 accessions, respectively. The identification of a cross-incompatible pair of cultivar candidates and several semi-compatible combinations help maximize fruit set in commercial orchards. Our results indicate that the S-allele pools of wild-growing P. spinosa and P. insititia are overlapping in Hungary. A phylogenetic and principal component analysis confirmed the high level of diversity and genetic differentiation present within the analysed genotypes and helped clarify doubtful taxonomic identities. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species. The analysed accessions represent huge genetic potential that can be exploited in commercial cultivation.     

Effective to census population size ratios in two Near Threatened Mediterranean amphibians: <Emphasis Type="Italic">Pleurodeles waltl</Emphasis> and <Emphasis Type="Italic">Pelobates cultripes</Emphasis>

Efforts to mitigate amphibian declines are hindered by a lack of information about basic aspects of their biology and demography. The effective to census population size ratio (N _e /N _c ) is one of the most important parameters for the management of wildlife populations because it combines information on population abundance and genetic diversity and helps predict population viability in the long term. Few studies have calculated this ratio in amphibians, which sometimes show low ratios, associated with a higher extinction risk. Here we integrate field-based (capture-mark-recapture studies, egg string counts) and molecular approaches (estimation of the effective number of breeders (N _b ) and the effective population size (N _e ) based on genotypes from larval cohorts and candidate parents) to produce the first estimates of the N _e /N _c and N _b /N _c ratios in two amphibians, the Iberian ribbed newt Pleurodeles waltl and the western spadefoot Pelobates cultripes. Additionally, we investigate sex-biased dispersal in both species based on direct (field observations) and indirect (genetic) evidence. Both species showed similar ratios, slightly lower in Pleurodeles (0.21–0.24) than in Pelobates (0.25–0.30). Observed displacement rates were low in both species (P. waltl?=?0.51%; P. cultripes?=?1.23%). We found no evidence for sex-biased dispersal in P. cultripes, but both direct and indirect evidences suggest a tendency for female-biased dispersal in P. waltl. We discuss differences in the genetic estimates of N _e and N _b provided by three inference methods and the implications of our findings for the management of these species, characteristic of Mediterranean wetlands in the Iberian Peninsula and listed as Near Threatened.     

Complete chloroplast genome sequence of <Emphasis Type="Italic">Capsicum</Emphasis><Emphasis Type="Italic">baccatum</Emphasis> var. <Emphasis Type="Italic">baccatum</Emphasis>

Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. Complete chloroplast (cp) genome sequences of Capsicum species have been reported. We herein report the complete chloroplast genome sequence of Capsicum baccatum var. baccatum, a wild Capsicum species. The total length of the chloroplast genome is 157,145 bp with 37.7 % overall GC content. One pair of inverted repeats, 25,910 bp in length, was separated by a small single-copy region (17,974 bp) and large single-copy region (87,351 bp). This region contains 86 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 11 genes contain one or two introns. Pair-wise alignments of chloroplast genome were performed for genome-wide comparison. Analysis revealed a total of 134 simple sequence repeat (SSR) motifs and 282 insertions or deletions variants in the C. baccatum var. baccatum cp genome. The types and abundances of repeat units in Capsicum species were relatively conserved, and these loci could be used in future studies to investigate and conserve the genetic diversity of the Capsicum species.     

Genetics and fine mapping of a yellow-green leaf gene (<Emphasis Type="Italic">ygl</Emphasis>-<Emphasis Type="Italic">1</Emphasis>) in cabbage (<Emphasis Type="Italic">Brassica oleracea</Emphasis> var. <Emphasis Type="Italic">capitata</Emphasis> L.)

Cabbage (Brassica oleracea var. capitata L.) is one of the most popular cultivated vegetables worldwide. Cabbage has rich phenotypic diversity, including plant height, head shape, head color, leaf shape and leaf color. Leaf color plays an important role in cabbage growth and development. At present, there are few reports on fine mapping of leaf color mutants in B. oleracea. In this study, a naturally occurring yellow-green leaf cabbage mutant (YL-1), derived from the self-pollinated progenies of the hybrid ‘Hosom’, was used for inheritance analysis and gene mapping. Segregation populations including F₂ and BC₁ were generated from the cross of two inbred lines, YL-1 and 01–20. Genetic analysis with the F₂ and BC₁ populations demonstrated that the yellow-green leaf color was controlled by a single recessive nuclear gene, ygl-1. Insertion–deletion (InDel) markers, designed based on the parental re-sequencing data, were used for the preliminary mapping with BSA (bulked segregant analysis) method. A genetic map constructed with 15 InDels indicated that ygl-1 was located on chromosome C01. The ygl-1 gene is flanked by InDel markers ID2 and M8, with genetic distances of 0.4 cM and 0.35 cM, respectively. The interval distance between two markers is 167 kb. Thus, it enables us to locate the ygl-1 gene for the first time in B. oleracea. This study lays the foundation for candidate gene prediction and ygl-1gene cloning.     

Genetic structure of populations and natural hybridization between <Emphasis Type="Italic">Dactylorhiza salina</Emphasis> and <Emphasis Type="Italic">D. incarnata</Emphasis> (Orchidaceae)

The results of studying the polymorphism and genetic structure of populations of D. salina and D. incarnata growing in Zabaykalsky krai and Buryatia are represented according to the data of allozyme analysis of eight genetic loci (PGI, NADHD, SKDH, GDH, PGM, DIA, ADH, and IDH). The specificity of the allelic structure of loci SKDH, PGM, and IDH is established, for which D. salina and D. incarnata reliably differ from each other. It is shown that interspecies introgressive hybrid complexes with different genetic structures were formed in Transbaikalia. Places of mass growth of D. incarnata were observed to have single plants of D. salina, the interspecies hybrids of the first and subsequent generations. Places of mass growth of D. salina were observed to contain only the hybrids that are not hybrids of the first generation. They were heterozygous not for three loci with differentiating alleles of both parents, SKDH, PGM, and IDH, but for only one of them. The degree of genetic differentiation among five populations of D. salina was on average 7.5% and that of D. incarnata was 7.1%, which in accordance with Wright’s estimation relates to mean values. The average value of FST for all studied populations of the two related species of the genus Dactylorhiza was 0.478, indicating a very high degree of genetic differentiation between D. salina and D. incarnata growing in Transbaikalia. The greatest differences between the species are for the allelic structure of loci SKDH, PGM, and IDH (FST was equal to 0.705, 0.976, and 0.762, respectively). Analysis of molecular variance (AMOVA) showed that populations of D. salina and D. incarnata in the zone where their ranges in Zabaykalsky krai and Buryatya overlap have essential differences both for the variation of alleles frequencies of eight loci (71%, d.f. = 9) and for the variability of genotypes (61%, d.f. = 9). Despite the fact that D. salina and D. incarnata explicitly share a gene flow as a result of interspecies hybridization, the genetic differentiation of populations of these related species remains at a high level.     

Isolation and Characterization of Microsatellite Markers for <Emphasis Type="Italic">Viola websteri</Emphasis> (Violaceae) and Cross-Species Amplification within the Genus <Emphasis Type="Italic">Viola</Emphasis>

We isolated and characterized microsatellite loci in Viola websteri (Violaceae), an endangered species from Korea and endemic to Northeast Asia. A total of 27 microsatellite loci were developed and tested in Korean and Chinese populations. The number of alleles per locus varied from two to eight. The observed and expected heterozygosities within two populations were 0.000 to 1.000 and 0.080 to 0.816, respectively. Korean and Chinese populations were clearly distinguished by the private alleles from 16 loci. A total of 21 loci out of the 27 developed loci were successfully cross-amplified in 39 other Viola species. We believe that these microsatellite loci will be useful for future studies on genetic diversity and population structure of V. websteri, as well as other Viola species.     

Local and Temporal Variation at the MHC I-<Emphasis Type="Italic">A1</Emphasis> Locus in Pink Salmon <Emphasis Type="Italic">Oncorhynchus gorbuscha</Emphasis> of Southern Sakhalin

In order to test the MHC I-A1 locus of the main histocompatiblity complex as an effective molecular marker for identification of populations of Far Eastern pink salmon, Oncorhynchus gorbuscha, the comparison of the allelic and genotypic frequencies between two neighboring populations of the Lyutoga and Taranay rivers (Aniva Bay, Sakhalin Island), as well as within the populations: within generation, between adjacent and distant generations, have been performed. It was revealed that temporal variation at MHC I-A1 is statistically insignificant in comparison between the samples of the juveniles sampled at different times during the downstream migration. It is also insignificant between the samples of juvenile and adult fish of the same generation, and between samples divided by a single and seven generations. At the same time, the samples of neighboring populations differ significantly. The possibility of differentiation of the populations on the local scale and temporal stability of the allele frequencies indicate the MHC I-A1 as valuable marker for the development of the population data bases. Inclusion of the MHC I-A1 into the panel of other markers (microsatellites, in particular) allows for considerable increase in the resolution power for identification as to which population an individual in the mixed sea catch belongs.     

The <Emphasis Type="Italic">Adh</Emphasis> locus and adaptation of <Emphasis Type="Italic">cn</Emphasis> and <Emphasis Type="Italic">vg</Emphasis> mutants in experimental populations of <Emphasis Type="Italic">Drosophila melanogaster MEIG</Emphasis>

A complex study on the adaptation of cn and vn mutants and the allozymes of alcoholdehydrogenase (ADH) was carried out in initially pure lines, and their panmixia populations during exchange of the mutant genotype with that of wild-type flies (C-S) and D) through saturating crossings. The relative adaptation of the genotypes was estimated by their effect on reproductive efficiency in the experimentally obtained population. Fecundity, lifespan, and the resistance of the studied genotypes to hyperthermia were investigated individually. It was shown that the high level of adaptation of the cn mutants and the low level of adaptation of the vg mutants was correlated with the presence of different ADH allozymes. In the studied population, the F-allozyme of ADH accompanied the vg mutation, while the S-allozyme of the enzyme was detected in cn mutants. Saturating crossings of C-S(Adh ^S)×vg(Adh ^F) and D(Adh ^F) × cn(Adh ^S), along with the parallel determination of the allele composition of the Adh locus, demonstrated that the complete substitution of the F-allozyme of ADH in the vg mutants by the S-allozyme in D flies, as well as the substitution of the S-allozyme of ADH in the cn mutants by the F-allozyme in D flies was realized only after the 15th–20th backcrosses. These results favor the coadaptation of cn and vg marker genes with alleles of the Adh locus and indicate the important role of the latter in the adaptation of genotypes. In the studied population, selection acted primarily against the vg mutants, which were inferior to the cn mutants, and heterozygote genotypes in indices of the main adaptation components.     

Landscape genetic structure of <Emphasis Type="Italic">Olea europaea</Emphasis> subsp. <Emphasis Type="Italic">cuspidata</Emphasis> in Ethiopian highland forest fragments

Understanding patterns of genetic diversity at the landscape scale will enhance conservation and management of natural populations. Here we analyzed the genetic diversity, population connectivity, and spatial genetic structure among subpopulations and age groups of Olea europaea subsp. cuspidata, a cornerstone species of the Afromontane highlands. The study was conducted at the landscape level within a radius of approximately 4 km, as well as on a fine scale (intensive study plot) of less than 300 m radius. In total 542 samples from four natural subpopulations in northwestern Ethiopia were analyzed using ten nuclear microsatellite markers. Inbreeding was higher in smaller populations. No genetic difference was detected among cohorts of different tree sizes in the intensive studied plot. Average population differentiation was low but significant (F _ST ?=?0.016). Landscape genetic analysis inferred two groups: the most distant subpopulation WE located less than 4 kms from the other three subpopulations formed a separate group. Sixty-four percent of the total migrants were shared among the three latter subpopulations, which are spatially clustered. Immigrants were non-randomly distributed inside of the intensive study plot. Significant spatial genetic structure (SGS) was found both at the landscape scale and in the intensive study plot, and adults showed stronger SGS than young trees. An indirect estimate of 220 m as mean gene dispersal distance was obtained. We conclude that even under fragmentation migration is not disrupted in wild olive trees and that large protected populations at church forests are very important to conserve genetic resources. However, the higher level of inbreeding and evidence for population bottlenecks in the small populations, as well as the persisting heavy pressure on most remaining populations, warrants quick action to maintain genetic diversity of wild olive in the Ethiopian highlands.     

Identification of <Emphasis Type="Italic">Pm58</Emphasis> from <Emphasis Type="Italic">Aegilops tauschii</Emphasis>

Key message

A novel powdery mildew-resistance gene, designated Pm58, was introgressed directly from Aegilops tauschii to hexaploid wheat, mapped to chromosome 2DS, and confirmed to be effective under field conditions. Selectable KASP? markers were developed for MAS.

Abstract

Powdery mildew caused by Blumeria graminis (DC.) f. sp. tritici (Bgt) remains a significant threat to wheat (Triticum aestivum L.) production. The rapid breakdown of race-specific resistance to Bgt reinforces the need to identify novel sources of resistance. The d-genome species, Aegilops tauschii, is an excellent source of disease resistance that is transferrable to T. aestivum. The powdery mildew-resistant Ae. tauschii accession TA1662 (2n?=?2x?=?DD) was crossed directly with the susceptible hard white wheat line KS05HW14 (2n?=?6x?=?AABBDD) followed by backcrossing to develop a population of 96 BC₂F₄ introgression lines (ILs). Genotyping-by-sequencing was used to develop a genome-wide genetic map that was anchored to the Ae. tauschii reference genome. A detached-leaf Bgt assay was used to screen BC₂F_4:6 ILs, and resistance was found to segregate as a single locus (χ?=?2.0, P value?=?0.157). The resistance gene, referred to as Pm58, mapped to chromosome 2DS. Pm58 was evaluated under field conditions in replicated trials in 2015 and 2016. In both years, a single QTL spanning the Pm58 locus was identified that reduced powdery mildew severity and explained 21% of field variation (P value?<?0.01). KASP? assays were developed from closely linked GBS-SNP markers, a refined genetic map was developed, and four markers that cosegregate with Pm58 were identified. This novel source of powdery mildew-resistance and closely linked genetic markers will support efforts to develop wheat varieties with powdery mildew resistance.

     

Linkages of <Emphasis Type="Italic">Firmicutes</Emphasis> and <Emphasis Type="Italic">Bacteroidetes</Emphasis> populations to methanogenic process performance

To identify potential linkages between specific bacterial populations and process performance in anaerobic digestion, the dynamics of bacterial community structure was monitored with high-throughput sequencing in triplicate anaerobic digesters treating animal waste. Firmicutes and Bacteroidetes were found as the two most abundant populations, however, with contrasting population dynamics in response to organic overloading. Firmicutes dominated the bacterial community during stable process performance at low organic loading rate, representing over 50 % of the bacterial abundance. In contrast, the onset of organic overloading raised the relative abundance of Bacteroidetes from 20 ± 2.6 to 44 ± 3.1 %. In addition to the significant negative correlation between the relative abundance of Firmicutes and Bacteroidetes, populations of Firmicutes and Bacteroidetes were found to be linked to process parameters including organic loading rate, volatile fatty acids concentration, and methane production. Therefore, the population abundance ratio of Firmicutes to Bacteroidetes (F/B ratio) was suggested as a potential indicator for process performance. The interactions between Firmicutes and Bacteroidetes populations could be exploited to develop strategies for the prevention of performance perturbation in anaerobic digestion processes.     

Genetic variability of the banded murex (<Emphasis Type="Italic">Hexaplex trunculus</Emphasis>) revealed by <Emphasis Type="Italic">ND2</Emphasis> and <Emphasis Type="Italic">ITS2</Emphasis> sequences

The gastropod Hexaplex trunculus is widely distributed in a relatively large range of habitats, but has no dispersal stage. We investigated its genetic structure across its distribution range, from Mediterranean Sea to adjacent Atlantic coasts, by sequencing mitochondrial DNA portions of the NADH dehydrogenase gene ND2 (420 pb) and the internal transcribed spacer ITS2 (450 pb). Our results suggested a significant genetic variability of ND2 (π = 0.009 and Hd = 0.629) and low variability of the ITS2 sequences. A strong phylogeographic break, separated the Aegean populations from those of Western/Eastern Mediterranean and the Atlantic ones, was founded. The tow lineages may have been separated by vicariance events due to the Peloponnese break that separates the Aegean populations from other populations and was maintained until now by the quasi-circular anticyclonic front associated to the straits of Cretan Arc of the Peloponnesian Peninsula. Tunisian coasts appear particularly diverse since the two divergent lineages co-occured. These results may have management consequences since H. trunculus is a high commercial value harvested species.