Response to Waterlogging Stress in Wild and Domesticated Accessions of Timothy (Phleum pratense) and Its Relatives P. alpinum and P. nodosum.

Timothy (Phleum pratense) is a cool-season perennial forage grass widely grown for silage and hay production in northern regions. Climate change scenarios predict an increase in extreme weather events with fluctuating periods of high rainfall, requiring new varieties adapted to waterlogging (WL). Wild accessions could serve as germplasm for breeding, and we evaluated the responses of 11 wild and 8 domesticated accessions of timothy, P. nodosum and P. alpinum from different locations in northern Europe. Young plants at tillering stage were exposed to WL for 21 days in a greenhouse, and responses in growth allocation and root anatomy were studied. All accessions produced adventitious roots and changed allocation of growth between shoot and root as a response to WL, but the magnitude of these responses varied among species and among accessions. P. pratense responded less in these traits in response to WL than the other two species. The ability to form aerenchyma in the root cortex in response to WL was found for all species and also varied among species and among accessions, with the highest induction in P. pratense. Interestingly, some accessions were able to maintain and even increase root growth, producing more leaves and tillers, while others showed a reduction in the root system. Shoot dry weight (SDW) was not significantly affected by WL, but some accessions showed different and significant responses in the rate of production of leaves and tillers. Overall correlations between SDW and aerenchyma and between SDW and adventitious root formation were found. This study identified two wild timothy accessions and one wild P. nodosum accession based on shoot and root system growth, aerenchyma formation and having a root anatomy considered to be favorable for WL tolerance. These accessions are interesting genetic resources and candidates for development of climate-resilient timothy varieties.

Phenotypic Diversity in Domesticated and Wild Timothy Grass, and Closely Related Species for Forage Breeding.

Timothy grass (Phleum pratense L.) is one of the most important forage crops in temperate regions. Forage production, however, faces many challenges, and new cultivars adapted to a changing climate are needed. Wild populations and relatives of timothy may serve as valuable genetic resources in the breeding of improved cultivars. The aim of our study is to provide knowledge about the phenotypic diversity in domesticated (cultivars, breeding lines and landraces) and wild timothy and two closely related species, P. nodosum (lowland species) and P. alpinum, (high altitude species) to identify potential genetic resources. A total of 244 accessions of timothy and the two related species were studied for growth (plant height, fresh and dry weight) and plant development (days to stem elongation, days to booting and days to heading) in the field and in a greenhouse. We found a large diversity in development and growth between the three Phleum species, as well as between the accessions within each species. Timothy showed the highest growth, but no significant difference was found between wild accessions and cultivars of timothy in fresh and dry weight. However, these two groups of accessions showed significant differences in plant development, where timothy cultivars as a group reached flowering earlier than the wild accessions. This suggests that there has not been a strong directional selection towards increased yield during the domestication and breeding of timothy; rather, timothy has been changed for other traits such as earlier heading. Principal component analysis and cluster analysis based on all traits revealed distinct clusters. Accessions falling within the same cluster showed similarities in the development and growth rather than the type of accession. The large diversity found in this study shows the potential of using timothy accessions as genetic resources in crosses with existing cultivars. Also, accessions of P. nodosum with favorable traits can be candidates for the domestication of a novel forage crop, and the high-altitude relative P. alpinum may be a source of genes for the development of more cold and stresstolerant cultivars.

Discussion: Prioritize perennial grain development for sustainable food production and environmental benefits.

Perennial grains have potential to contribute to ecological intensification of food production by enabling the direct harvest of human-edible crops without requiring annual cycles of disturbance and replanting. Studies of prototype perennial grains and other herbaceous perennials point to the ability of agroecosystems including these crops to protect water quality, enhance wildlife habitat, build soil quality, and sequester soil carbon. However, genetic improvement of perennial grain candidates has been hindered by limited investment due to uncertainty about whether the approach is viable. As efforts to develop perennial grain crops have expanded in past decades, critiques of the approach have arisen. With a recent report of perennial rice producing yields equivalent to those of annual rice over eight consecutive harvests, many theoretical concerns have been alleviated. Some valid questions remain over the timeline for new crop development, but we argue these may be mitigated by implementation of recent technological advances in crop breeding and genetics such as low-cost genotyping, genomic selection, and genome editing. With aggressive research investment in the development of new perennial grain crops, they can be developed and deployed to provide atmospheric greenhouse gas reductions.

Perennials as Future Grain Crops: Opportunities and Challenges.

Perennial grain crops could make a valuable addition to sustainable agriculture, potentially even as an alternative to their annual counterparts. The ability of perennials to grow year after year significantly reduces the number of agricultural inputs required, in terms of both planting and weed control, while reduced tillage improves soil health and on-farm biodiversity. Presently, perennial grain crops are not grown at large scale, mainly due to their early stages of domestication and current low yields. Narrowing the yield gap between perennial and annual grain crops will depend on characterizing differences in their life cycles, resource allocation, and reproductive strategies and understanding the trade-offs between annualism, perennialism, and yield. The genetic and biochemical pathways controlling plant growth, physiology, and senescence should be analyzed in perennial crop plants. This information could then be used to facilitate tailored genetic improvement of selected perennial grain crops to improve agronomic traits and enhance yield, while maintaining the benefits associated with perennialism.

Evidence for magnesium-phosphorus synergism and co-limitation of grain yield in wheat agriculture.

Modern crop production is characterized by high nitrogen (N) application rates, which can influence the co-limitation of harvested yield by other nutrients. Using a multidimensional niche volume concept and scaling exponents frequently applied in plant ecological research, we report that increased N and phosphorus (P) uptake in a growing wheat crop along with enhanced grain biomass is associated with more than proportional increase of other nutrients. Furthermore, N conversion efficiency and grain yield are strongly affected by the magnesium (Mg) to P ratio in the growing crop. We analyzed a field trial in Central Sweden including nine wheat varieties grown during two years with contrasting weather, and found evidence for Mg co-limitation at lower grain yields and P co-limitation at higher yields. We argue that critical concentrations of single nutrients, which are often applied in agronomy, should be replaced by nutrient ratios. In addition, links between plant P and Mg contents and root traits were found; high root number enhanced the P:N ratio, whilst steep root angle, indicating deep roots, increased the Mg:N ratio. The results have significant implications on the management and breeding targets of agriculturally grown wheat, which is one of the most important food crops worldwide.

Variation in susceptibility to Wheat dwarf virus among wild and domesticated wheat.

We investigated the variation in plant response in host-pathogen interactions between wild (Aegilops spp., Triticum spp.) and domesticated wheat (Triticum spp.) and Wheat dwarf virus (WDV). The distribution of WDV and its wild host species overlaps in Western Asia in the Fertile Crescent, suggesting a coevolutionary relationship. Bread wheat originates from a natural hybridization between wild emmer wheat (carrying the A and B genomes) and the wild D genome donor Aegilops tauschii, followed by polyploidization and domestication. We studied whether the strong selection during these evolutionary processes, leading to genetic bottlenecks, may have resulted in a loss of resistance in domesticated wheat. In addition, we investigated whether putative fluctuations in intensity of selection imposed on the host-pathogen interactions have resulted in a variation in susceptibility to WDV. To test our hypotheses we evaluated eighteen wild and domesticated wheat taxa, directly or indirectly involved in wheat evolution, for traits associated with WDV disease such as leaf chlorosis, different growth traits and WDV content. The plants were exposed to viruliferous leafhoppers (Psammotettix alienus) in a greenhouse trial and evaluated at two time points. We found three different plant response patterns: i) continuous reduction in growth over time, ii) weak response at an early stage of plant development but a much stronger response at a later stage, and iii) remission of symptoms over time. Variation in susceptibility may be explained by differences in the intensity of natural selection, shaping the coevolutionary interaction between WDV and the wild relatives. However, genetic bottlenecks during wheat evolution have not had a strong impact on WDV resistance. Further, this study indicates that the variation in susceptibility may be associated with the genome type and that the ancestor Ae. tauschii may be useful as genetic resource for the improvement of WDV resistance in wheat.

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

BACKGROUND: Wild 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. RESULTS: Two 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. CONCLUSIONS: The 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.

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.

Quantitative trait loci controlling cyanogenic glucoside and dry matter content in cassava (Manihot esculenta Crantz) roots.

Cassava (Manihot esculenta Crantz) is a starchy root crop grown in the tropics mainly by small-scale farmers even though agro-industrial processing is rapidly increasing. For this processing market improved varieties with high dry matter root content (DMC) is required. Potentially toxic cyanogenic glucosides are synthesized in the leaves and translocated to the roots. Selection for varieties with low cyanogenic glucoside potential (CNP) and high DMC is among the principal objectives in cassava breeding programs. However, these traits are highly influenced by the environmental conditions and the genetic control of these traits is not well understood. An S(1) population derived from a cross between two bred cassava varieties (MCOL 1684 and Rayong 1) that differ in CNP and DMC was used to study the heritability and genetic basis of these traits. A broad-sense heritability of 0.43 and 0.42 was found for CNP and DMC, respectively. The moderate heritabilities for DMC and CNP indicate that the phenotypic variation of these traits is explained by a genetic component. We found two quantitative trait loci (QTL) on two different linkage groups controlling CNP and six QTL on four different linkage groups controlling DMC. One QTL for CNP and one QTL for DMC mapped near each other, suggesting pleiotrophy and/or linkage of QTL. The two QTL for CNP showed additive effects while the six QTL for DMC showed additive effect, dominance or overdominance. This study is a first step towards developing molecular marker tools for efficient breeding of CNP and DMC in cassava.

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.

Electrophoretic evidence for disomic inheritance and allopolyploid origin of the octoploid Cerastium alpinum (Caryophyllaceae).

The mode of inheritance of six enzyme markers in the octoploid alpine plant Cerastium alpinum was analyzed. Offspring from crosses between heterozygotes showed fixed heterozygosity at malate dehydrogenase-2, phosphoglucoisomerase-2, triosephosphate isomerase-2, and triosephosphate isomerase-3. Phosphoglucomutase-1 also showed fixed heterozygosity except in offspring from one cross. Fixed heterozygosity in five enzyme systems suggests that C. alpinum has originated through at least some allopolyploidization. Offspring from plants heterozygous for two alleles at the menadione reductase-1 (Mr-1) locus did not deviate significantly from a 1:2:1 ratio. The large proportion of homozygotes suggests disomic inheritance because any kind of polysomic inheritance would result in a substantially increased proportion of heterozygotes relative to disomic inheritance. Assuming a diploid model for Mr-1, this locus was used to analyze the population genetic structure within C. alpinum populations. Inbreeding was found in many alpine populations. This may help explain the large genetic distances found among alpine populations in a previous study. The analysis is only based on one segregating locus, and the results should therefore be treated with caution. However, by establishing the mode of inheritance through crosses, we have been able to use a codominant marker in population genetic analysis of an octoploid plant.

The inheritance and evolution of leaf pigmentation and pubescence in teosinte.

To investigate the genetic mechanisms that underlie morphological evolution in natural populations, we employed QTL mapping to dissect the inheritance of leaf sheath characters that distinguish Chalco from Balsas teosinte. Abundant macrohairs (trichomes) and intense anthocyanin accumulation are found in Chalco teosinte sheaths whereas Balsas teosinte leaf sheaths are green and glabrous. These character states may represent adaptations to the cooler highland (Chalco) vs. warmer middle-elevation (Balsas) climates. QTL mapping in multiple populations revealed a mix of major- and minor-effect QTL affecting both sheath color (anthocyanin) and macrohair abundance. The major QTL for macrohairs accounts for 52% of the parental difference. Epistatic interactions were detected between the major-effect QTL and multiple other QTL for both traits, accounting for substantial portions of phenotypic variance. Developmental analyses suggest that regulatory program changes underlie the phenotypic differences. Sheath anthocyanin QTL are clearly associated with b1 and a3, both of which are regulators of anthocyanin biosynthesis. Our findings suggest that changes in a small number of QTL can lead to morphological evolution by modulating existing developmental programs.

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.

Morphological traits defining species differences in wild relatives of maize are controlled by multiple quantitative trait loci.

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.

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.