Dataset Information

Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia.

ABSTRACT: Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites. Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43·6°N) and on southern Sakhalin Island (46·6°N). Miscanthus sacchariflorus was found inland at latitudes as high as 49·3°N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0·007 among diploid groups) but high genetic diversity (expected heterozygosity = 0·14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits. Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.

SUBMITTER: Clark LV

PROVIDER: S-EPMC5055818 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia.

Clark Lindsay V LV Dzyubenko Elena E Dzyubenko Nikolay N Bagmet Larisa L Sabitov Andrey A Chebukin Pavel P Johnson Douglas A DA Kjeldsen Jens Bonderup JB Petersen Karen Koefoed KK Jørgensen Uffe U Yoo Ji Hye JH Heo Kweon K Yu Chang Yeon CY Zhao Hua H Jin Xiaoli X Peng Junhua J Yamada Toshihiko T Sacks Erik J EJ

Annals of botany 20161001 5

Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanth ...[more]

PMID: 27451985

Similar Datasets

Project description:Extensive restoration and translocation efforts beginning in the mid-20th century helped to reestablish eastern wild turkeys (Meleagris gallopavo silvestris) throughout their ancestral range. The adaptability of wild turkeys resulted in further population expansion in regions that were considered unfavorable during initial reintroductions across the northern United States. Identification and understanding of species distributions and contemporary habitat associations are important for guiding effective conservation and management strategies across different ecological landscapes. To investigate differences in wild turkey distribution across two contrasting regions, heavily forested northern Wisconsin, USA, and predominately agricultural southeast Wisconsin, we conducted 3050 gobbling call-count surveys from March to May of 2014-2018 and used multiseason correlated-replicate occupancy models to evaluate occupancy-habitat associations and distributions of wild turkeys in each study region. Detection probabilities varied widely and were influenced by sampling period, time of day, and wind speed. Spatial autocorrelation between successive stations was prevalent along survey routes but was stronger in our northern study area. In heavily forested northern Wisconsin, turkeys were more likely to occupy areas characterized by moderate availability of open land cover. Conversely, large agricultural fields decreased the likelihood of turkey occupancy in southeast Wisconsin, but occupancy probability increased as upland hardwood forest cover became more aggregated on the landscape. Turkeys in northern Wisconsin were more likely to occupy landscapes with less snow cover and a higher percentage of row crops planted in corn. However, we were unable to find supporting evidence in either study area that the abandonment of turkeys from survey routes was associated with snow depth or with the percentage of agricultural cover. Spatially, model-predicted estimates of patch-specific occupancy indicated turkey distribution was nonuniform across northern and southeast Wisconsin. Our findings demonstrated that the environmental constraints of turkey occupancy varied across the latitudinal gradient of the state with open cover, snow, and row crops being influential in the north, and agricultural areas and hardwood forest cover important in the southeast. These forces contribute to nonstationarity in wild turkey-environment relationships. Key habitat-occupancy associations identified in our results can be used to prioritize and strategically target management efforts and resources in areas that are more likely to harbor sustainable turkey populations.

Project description:Sugarcane (Saccharum spp.) has a complex genome with variable ploidy and frequent aneuploidy, which hampers the understanding of phenotype and genotype relations. Despite this complexity, genome-wide association studies (GWAS) may be used to identify favorable alleles for target traits in core collections and then assist breeders in better managing crosses and selecting superior genotypes in breeding populations. Therefore, in the present study, we used a diversity panel of sugarcane, called the Brazilian Panel of Sugarcane Genotypes (BPSG), with the following objectives: (i) estimate, through a mixed model, the adjusted means and genetic parameters of the five yield traits evaluated over two harvest years; (ii) detect population structure, linkage disequilibrium (LD) and genetic diversity using simple sequence repeat (SSR) markers; (iii) perform GWAS analysis to identify marker-trait associations (MTAs); and iv) annotate the sequences giving rise to SSR markers that had fragments associated with target traits to search for putative candidate genes. The phenotypic data analysis showed that the broad-sense heritability values were above 0.48 and 0.49 for the first and second harvests, respectively. The set of 100 SSR markers produced 1,483 fragments, of which 99.5% were polymorphic. These SSR fragments were useful to estimate the most likely number of subpopulations, found to be four, and the LD in BPSG, which was stronger in the first 15 cM and present to a large extension (65 cM). Genetic diversity analysis showed that, in general, the clustering of accessions within the subpopulations was in accordance with the pedigree information. GWAS performed through a multilocus mixed model revealed 23 MTAs, six, three, seven, four and three for soluble solid content, stalk height, stalk number, stalk weight and cane yield traits, respectively. These MTAs may be validated in other populations to support sugarcane breeding programs with introgression of favorable alleles and marker-assisted selection.

Project description:A panel of 60 genotypes comprising New Plant Types (NPTs) along with indica, tropical and temperate japonica genotypes was phenotypically evaluated for four seasons in irrigated situation for grain yield per se and component traits. Twenty NPT genotypes were found promising with an average grain yield varying from 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to identify QTLs associated with grain yield per se and related traits. Sixty-six (77.65%) markers were found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 8% within genotypes, 68% among the genotypes within the population and 24% among the populations were observed (AMOVA). This information may help in identification of potential parents for development of transgressive segregants with very high yield. The association analysis using GLM and MLM models led to the identification of 30 and 10 SSR markers associated with 70 and 16 QTLs, respectively. Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely tiller number (qTL-6.1, qTL-11.1, qTL-4.1), panicle length (qPL-1.1, qPL-5.1, qPL-7.1, qPL-8.1), flag leaf length (qFLL-8.1, qFLL-9.1), flag leaf width (qFLW-6.2, qFLW-5.1, qFLW-8.1, qFLW-7.1), total no. of grains (qTG-2.2, qTG-a7.1), thousand-grain weight (qTGW-a1.1, qTGW-a9.2, qTGW-5.1, qTGW-8.1), fertile grains (qFG-7.1), seed length-breadth ratio (qSlb-3.1), plant height (qPHT-6.1, qPHT-9.1), days to 50% flowering (qFD-1.1) and grain yield per se (qYLD-5.1, qYLD-6.1a, qYLD-11.1).Some of the SSRs were co-localized with more than two traits. The highest co-localization was identified with RM5709 linked to nine traits, followed by RM297 with five traits. Similarly, RM5575, RM204, RM168, RM112, RM26499 and RM22899 were also recorded to be co-localized with more than one trait and could be rated as important for marker-assisted backcross breeding programs, for pyramiding of these QTLs for important yield traits, to produce new-generation rice for prospective increment in yield potentiality and breaking yield ceiling.

Project description:background:Predicting the evolutionary potential of natural tree populations requires the estimation of heritability and genetic correlations among traits on which selection acts, as differences in evolutionary success between species may rely on differences for these genetic parameters. In situ estimates are expected to be more accurate than measures done under controlled conditions which do not reflect the natural environmental variance. aims:The aim of the current study was to estimate three genetic parameters (i.e. heritability, evolvability and genetic correlations) in a natural mixed oak stand composed of Quercus petraea and Quercus robur about 100 years old, for 58 traits of ecological and functional relevance (growth, reproduction, phenology, physiology, resilience, structure, morphology and defence). methods:First we estimated genetic parameters directly in situ using realized genomic relatedness of adult trees and parentage relationships over two generations to estimate the traits additive variance. Secondly, we benefited from existing ex situ experiments (progeny tests and conservation collection) installed with the same populations, thus allowing comparisons of in situ heritability estimates with more traditional methods. results:Heritability and evolvability estimates obtained with different methods varied substantially and showed large confidence intervals, however we found that in situ were less precise than ex situ estimates, and assessments over two generations (with deeper relatedness) improved estimates of heritability while large sampling sizes are needed for accurate estimations. At the biological level, heritability values varied moderately across different ecological and functional categories of traits, and genetic correlations among traits were conserved over the two species. conclusion:We identified limits for using realized genomic relatedness in natural stands to estimate the genetic variance, given the overall low variance of genetic relatedness and the rather low sampling sizes of currently used long term genetic plots in forestry. These limits can be overcome if larger sample sizes are considered, or if the approach is extended over the next generation.

Dataset Information

Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia.

Publications

Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets