Anna Westerbergh

The effect of serpentine on the population structure of Silene dioica (Caryophyllaceae)

Serpentine soils are rich in heavy metals and have a distinctive flora. Silene dioica is a member of the Scandinavian serpentine plant community but is also widespread outside serpentine soils. To study the population genetic consequences of serpentine stress and the origin and evolution of serpentine populations we analyzed the isozyme genetic structure of S. dioica. Seventeen populations located in the mountains of Västerbotten and Jämtland, central Sweden, were investigated by starch gel enzyme electrophoresis. About one half of the populations grow in serpentine soils and the rest on adjacent non‐serpentine sites. Analyses of allele frequencies show that both serpentine and non‐serpentine populations in the northern part of the studied area (Västerbotten) are genetically similar. Evidently serpentine does not exert strong selection acting upon isozyme loci. In the south (Jämtland), however, the serpentine populations exhibit genetic differentiation. This allozyme divergence is probably not due to direct selection but rather represents the effects of isolation and genetic drift. The results suggest that S. dioica has colonized serpentine repeatedly and that the tolerant populations have a multiple origin.

Gene Flow and Pollinator Behaviour in Silene dioica Populations

Silene dioica (L.) Clairv. (Caryophyllaceae) is an insect pollinated and obligately cross-fertilising herb commonly found on serpentine, i.e. soils rich in heavy metals, and on cultivated meadows. Groups of Silene populations were studied in two areas in the Scandinavian mountains. In a northern area Silene populations grow in an open pine and birch forest while in the south, populations are surrounded by a continuous and dense spruce forest. Gene flow, estimated on the basis of allele frequencies, is highly restricted in the south in comparison to the north. This has led to an extensive genetic differentiation among populations. The pollinator guilds (Thricops flies, syrphid flies and bumblebees) are similar in the northern and southern populations and can therefore not account for the difference in gene flow. The flowering in nearby populations overlaps broadly and is also not the reason for the genetic differentiation in the south. The differentiation is more likely due to vegetation that limits pollinator movement. The level of gene flow differs in the two habitats both in the north and in the south. The gene flow is restricted among serpentine populations but common among meadow populations. Pollen dispersal, and in particular, anthropogenic seed dispersal mediate gene flow among meadows. Serpentine populations are unaffected by human activity. Pollinators are therefore the main agent of gene flow on serpentine. This study shows the importance of the surrounding vegetation in influencing gene flow patterns among populations as well as that habitat fragmentation affects the genetic properties of plant populations. In addition, we have also observed a restricted gene flow within populations. Enzyme allele frequencies show an excess of homozygotes within most of the populations. This can be explained through limited pollen dispersal and differences in male and female flowering density.

MORPHOLOGICAL TRAITS DEFINING SPECIES DIFFERENCES IN WILD RELATIVES OF MAIZE ARE CONTROLLED BY MULTIPLE QUANTITATIVE TRAIT LOCI

Abstract We analyzed the genetic basis of morphological differences between two wild species of teosinte (Zea diploperennis and Z. mays ssp. parviglumis), which are relatives of maize. These two species differ in a number of taxonomically important traits including the structure of the tassel (male inflorescence), which is the focus of this report. To investigate the genetic inheritance of six tassel traits, quantitative trait locus (QTL) mapping with 95 RFLP markers was employed on a population of 425 F2 plants. Each trait was analyzed by interval mapping (IM) and composite interval mapping (CIM) to identify and characterize the QTL controlling the differences in tassel morphology. We detected two to eight QTL for each trait. In total, 30 QTL with IM and 33 QTL with CIM were found for tassel morphology. QTL for several of the traits mapped near each other, suggesting pleiotropy and/or linkage of QTL. The QTL showed small to moderate magnitudes of effect. No QTL of exceptionally large effect were found as seen under domestication and in the case of some other natural species. Thus, the model involving major QTL of large effect seems not to apply to the traits and species analyzed. A mixture of QTL with positive and negative allelic effects was found for most tassel traits and may suggest a history of periodic changes in the direction of selection during the divergence of Z. diploperennis and Z. mays ssp. parviglumis or fixation of QTL alleles by random genetic drift rather than selection.

Genetic diversity and variety composition of cassava on small-scale farms in Uganda: an interdisciplinary study using genetic markers and farmer interviews.

Cassava is a tropical crop and grown for its tuberous starchy roots. In Africa it is mainly cultivated by small-scale farmers who observe, select and name their cassava varieties based on morphology, food, social and economic interest. Here we have used an interdisciplinary approach involving farmer interviews, genetic markers and morphological descriptors to study the composition of cassava varieties on small-scale farms in 11 villages located in three districts in Uganda, the genetic structure within and between these varieties and their morphology. The composition of local, newly introduced and improved varieties differed widely between villages and districts. The Ugandan farmers in our study seemed to adopt improved varieties to a greater extent when there was a nearby market, prevalence of disease epidemics and good extension service. We found considerable genetic variation both within and between cassava varieties though the variation was larger between varieties. However, most local and improved varieties showed predominating genotypes at many loci. Accessions of commonly grown varieties meeting farmers’ preferences could therefore be selected and implemented in future breeding programmes involving development, dissemination and adoption. The like-named varieties in different villages were genetically similar, demonstrating farmers’ ability to differentiate and maintain the same variety over large areas. However, some varieties with different names in different villages showed both genetic and morphological similarity, suggesting that farmers may rename plants when they are introduced into their fields. The large differences found in variety and genetic composition between villages and districts in Uganda may be a result of the diverse needs and growing conditions characteristic for traditional farming system. This suggests that efforts to conserve and increase the genetic diversity in farmers’ fields will require policies tailored to each area.

Selective grazing of hairless Silene dioica plants by land gastropods

Silene dioica (Caryophyllaceae) has evolved different morphotypes that vary in hairiness in different habitats in the Swedish mountains. A hairy form, var. serpentinicola and a hairless (glabrous) form, var. smithii grow on serpentine, i.e. a dry soil rich in heavy metals. Var. lapponica is a densely hairy morphotype on subalpine meadows. Crosses between these varieties showed that glabrousness has a simple Mendelian inheritance and that glabrousness is determined by a recessive allele. The crosses further suggested that the recessive allele has been present in the original population that invaded the mountain area. Glabrous plants have, however, never been found on subalpine meadows, even though an earlier study has shown that gene flow is relatively common among serpentine and nearby meadow populations. In addition to the genetic background of glabrousness, we studied the grazing on glabrous smithii and hairy serpentinicola and lapponica plants by the slugs Arion fasciatus and Arion subfuscus and the snail Arianta arbustorum in greenhouse and in nature. Arion slugs, abundant on subalpine meadows, preferred glabrous plants and, in particular, A. fasciatus consumed high amounts of S. dioica. Arianta snails, however, consumed irrespective of morphotype. The selective behaviour was seen both at the seedling stage and the adult plant stage. Arion slugs were more choosy when they were given a choice of glabrous smithii and densely hairy lapponica plants then when they were served smithii and the less hairy variety serpentinicola. This study implies that the Arion slugs are important agents of selection on subalpine meadows. The selective grazing seems to counteract the flow of the recessive allele that determines glabrousness, from serpentine into meadow populations. Gastropods are rare in the dry serpentine habitat. The evolution of a distinct glabrous morphotype on serpentine is therefore rather due to relaxation of selection than to adaptation to serpentine stress.

Quantitative trait loci controlling phenotypes related to the perennial versus annual habit in wild relatives of maize

We used quantitative trait locus/loci (QTL) mapping to study the inheritance of traits associated with perennialism in a cross between an annual (Zea mays ssp. parviglumis) and a perennial (Z. diploperennis) species of teosinte. The most striking difference between these species is that Z. diploperennis forms rhizomes, whereas Z. mays ssp. parviglumis lacks these over-wintering underground stems. An F2 population of 425 individuals was genotyped at 95 restriction fragment length polymorphism marker loci and the association between phenotype and genotype was analyzed by composite interval mapping. We detected a total of 38 QTL for eight traits. The number of QTL found for each trait ranged from two for rhizome formation to nine for tillering. QTL for six of the traits mapped near each other on chromosome 2, and QTL for four traits mapped near each other on chromosome 6, suggesting that these regions play an important role in the evolution of the perennial habit in teosinte. Most of the 38 QTL had small effects, and no single QTL showed a strikingly large effect. The map positions that we determined for rhizome formation and other traits in teosinte may help to locate corresponding QTL in pasture and turf grasses used as forage for cattle and for erosion control in agro-ecosystems.

Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts

BackgroundWild barley is adapted to highly diverse environments throughout its geographical distribution range. Transcriptome sequencing of differentially adapted wild barley ecotypes from contrasting environments contributes to the identification of genes and genetic variation involved in abiotic stress tolerance and adaptation.ResultsTwo differentially adapted wild barley ecotypes from desert (B1K2) and Mediterranean (B1K30) environments were analyzed for drought stress response under controlled conditions. The desert ecotype lost more water under both irrigation and drought, but exhibited higher relative water content (RWC) and better water use efficiency (WUE) than the coastal ecotype. We sequenced normalized cDNA libraries from drought-stressed leaves of both ecotypes with the 454 platform to identify drought-related transcripts. Over half million reads per ecotype were de novo assembled into 20,439 putative unique transcripts (PUTs) for B1K2, 21,494 for B1K30 and 28,720 for the joint assembly. Over 50% of PUTs of each ecotype were not shared with the other ecotype. Furthermore, 16% (3,245) of B1K2 and 17% (3,674) of B1K30 transcripts did not show orthologous sequence hits in the other wild barley ecotype and cultivated barley, and are candidates of ecotype-specific transcripts. Over 800 unique transcripts from each ecotype homologous to over 30 different stress-related genes were identified. We extracted 1,017 high quality SNPs that differentiated the two ecotypes. The genetic distance between the desert ecotype and cultivated barley was 1.9-fold higher than between the Mediterranean ecotype and cultivated barley. Moreover, the desert ecotype harbored a larger proportion of non-synonymous SNPs than the Mediterranean ecotype suggesting different demographic histories of these ecotypes.ConclusionsThe results indicate a strong physiological and genomic differentiation between the desert and Mediterranean wild barley ecotypes and a closer relationship of the Mediterranean to cultivated barley. A significant number of novel transcripts specific to wild barley were identified. The higher SNP density and larger proportion of SNPs with functional effects in the desert ecotype suggest different demographic histories and effects of natural selection in Mediterranean and desert wild barley. The data are a valuable genomic resource for an improved genome annotation, transcriptome studies of drought adaptation and a source of new genetic markers for future barley improvement.

The effect of cassava mosaic disease on the genetic diversity of cassava in Uganda

SummaryCassava (Manihot esculenta) is a tropical crop that is grown in Africa, Latin America and Southeast Asia. Cassava was introduced from Latin America into West and East Africa at two independent events. In Uganda a serious threat to cassavas survival is the cassava mosaic disease (CMD). Uganda has had two notable CMD epidemics since the introduction of cassava in the 1850s causing severe losses. SSR markers were used to study the effect of CMD on the genetic diversity in five agroecologies in Uganda with high and low incidence of CMD. Surprisingly, high gene diversity was detected. Most of the diversity was found within populations, while the diversity was very small among agroecological zones and the high and low CMD incidence areas. The high genetic diversity suggests a mechanism by which diversity is maintained by the active involvement of the Ugandan farmer in continuously testing and adopting new genotypes that will serve their diverse needs. However, in spite of the high genetic diversity we found a loss of rare alleles in areas with high CMD incidence. To study the effect of the introgression history on the gene pool the genetic differentiation between East and West Africa was also studied. Genetic similarities were found between the varieties in Uganda and Tanzania in East Africa and Ghana in West Africa. Thus, there is no evidence for a differentiation of the cassava gene pool into a western and an eastern genetic lineage. However, a possible difference in the genetic constitution of the introduced cassava into East and West Africa may have been diminished by germplasm movement.

Swedish Spring Wheat Varieties with the Rare High Grain Protein Allele of NAM-B1 Differ in Leaf Senescence and Grain Mineral Content

Some Swedish spring wheat varieties have recently been shown to carry a rare wildtype (wt) allele of the gene NAM-B1, known to affect leaf senescence and nutrient retranslocation to the grain. The wt allele is believed to increase grain protein concentration and has attracted interest from breeders since it could contribute to higher grain quality and more nitrogen-efficient varieties. This study investigated whether Swedish varieties with the wt allele differ from varieties with one of the more common, non-functional alleles in order to examine the effect of the gene in a wide genetic background, and possibly explain why the allele has been retained in Swedish varieties. Forty varieties of spring wheat differing in NAM-B1 allele type were cultivated under controlled conditions. Senescence was monitored and grains were harvested and analyzed for mineral nutrient concentration. Varieties with the wt allele reached anthesis earlier and completed senescence faster than varieties with the non-functional allele. The wt varieties also had more ears, lighter grains and higher yields of P and K. Contrary to previous information on effects of the wt allele, our wt varieties did not have increased grain N concentration or grain N yield. In addition, temporal studies showed that straw length has decreased but grain N yield has remained unaffected over a century of Swedish spring wheat breeding. The faster development of wt varieties supports the hypothesis of NAM-B1 being preserved in Fennoscandia, with its short growing season, because of accelerated development conferred by the NAM-B1 wt allele. Although the possible effects of other gene actions were impossible to distinguish, the genetic resource of Fennoscandian spring wheats with the wt NAM-B1 allele is interesting to investigate further for breeding purposes.

Role of nutrient-efficient plants for improving crop yields: bridging plant ecology, physiology, and molecular biology

The efficient use of nutrients underpins food security and reduces losses of nutrients to the environment. Different approaches have been applied to improve and evaluate the nutrient use efficiency (NUE) of plants, depending on the purpose to which the concept has been put. The various approaches differ greatly in the scale and target for NUE improvement and assessment. In this chapter, various approaches and conceptions for improving and evaluating NUE across different scales are discussed: (1) the investigation of the physiology and genetics of NUE at single tissue, cell and molecular scales, targeting understanding and improvement of NUE-related traits through, for example, plant breeding; and (2) the assessment of NUE and nutrient balances at whole plant, field, and regional scales for evaluating crops with NUE-improved traits. Appropriate methodologies are available to link the processes acting at molecular, individual plant, farm, and regional scales, but require increased collaborative efforts between the different disciplines.