Qtl Mapping for Reproductive Maturity in Lowland Switchgrass Populations

Switchgrass (Panicum virgatum L.) has high potential to be a major cellulosic bioenergy crop. Selection for later flowering plants will extend the growing season, likely resulting in larger biomass yields. However, it is little known of the genetic structure and mechanism for reproductive maturity in switchgrass. Accordingly, the major objective of this study was to identify genomic regions for reproductive development. Two lowland switchgrass populations, a hybrid population consisting of 176 progeny derived from a cross between parents NL94 (♀) � SL93 (♂) and a first-generation self-fertilized population of 265 progeny from NL94, were used in this study. Significant genetic variation for reproductive maturity stages was observed within each of the two populations. A total of 178 simple sequence repeat (SSR) markers were genotyped in the hybrid population for the construction of a linkage map while a pre-existing linkage map of 439 SSR markers was used for quantitative trait loci (QTL) analysis between markers and phenotypic data. QTL analysis revealed that reproductive maturity was a complex trait as controlled by multiple genomic regions. The QTL regions between PVGA-1727/1728 and PVGA-1201/1202 on linkage group (LG) 3b, between nfsg-125 and PVE-781/782 on LG 2b, and between PVCAG-2503/2504 and PVAAG-3253/3254 on LG 7a were identified to be associated with reproductive maturity in both populations. Broad sense heritabilities were 0.08 to 0.66 and 0.03 to 0.48 for the selfed and hybrid populations, respectively. Use of the markers linked to the significant QTLs in the populations could accelerate the development of switchgrass varieties having later flowering time as a means in increasing biomass yield in switchgrass.Plant & Soil Scienc

Dissecting key biomass and adaptation traits of Miscanthus through genetic mapping, exploring mechanisms of cold tolerance, and flowering time in Miscanthus and Saccharum

Improving biomass yield is a major goal of Miscanthus breeding. We conducted a study on one interspecific M. sinensis × M. sacchariflorus F1 population and two intraspecific M. sinensis F1 populations, each of which shared a common parent. A field trial was established at Urbana, IL during spring 2011, and phenotypic data was collected in 2012 and 2013 for fourteen yield traits. Six high-density parental genetic maps, as well as a consensus genetic map integrating M. sinensis and M. sacchariflorus, were developed via the pseudo-testcross strategy for non-inbred parents with ≥1,214 single nucleotide polymorphism markers generated from restriction site-associated DNA sequencing. We confirmed for the first time a whole-genome duplication in M. sacchariflorus relative to Sorghum bicolor, similar to that observed previously for M. sinensis. Four quantitative trait locus (QTL) analysis methods for detecting marker-trait associations were compared: 1) individual parental map composite interval mapping (CIM) analysis, 2) individual parental map stepwise analysis, 3) consensus map single-population stepwise analysis and 4) consensus map joint-population stepwise analysis. These four methods detected 288, 264, 133, and 109 total QTLs, which resolved into 157, 136, 106, and 86 meta-QTLs based on QTL congruency, respectively, including a set of 59 meta-QTLs common to all four analysis methods. Composite interval mapping and stepwise analysis co-identified 118 meta-QTLs across six parental maps, suggesting high reliability of stepwise regression in QTL detection. Joint-population stepwise analysis yielded the highest resolution of QTLs compared to the other three methods across all meta-QTLs. Strong, frequently advantageous transgressive segregation in the three populations indicated a promising future for breeding new higher-yielding cultivars of Miscanthus. Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar M. ×giganteus (M×g) ‘1993-1780‘ in regions where average annual minimum temperatures are -26.1 C (USDA hardiness zone 5b) or lower poses a pressing need for developing new cultivars with superior cold tolerance that could be optimized for regions with severe winters. Three complementary studies on the genetics of overwintering ability of Miscanthus were conducted: 1) an interconnected population consisting of three full-sib families each with a parent in common evaluated in the field at Urbana, IL, 2) an M. sinensis germplasm panel consisting of 564 accessions evaluated in field trials at three locations in Asia and two in North America, and 3) comparison of 13 M. ×giganteus genotypes at Urbana, IL, Dixon Springs, IL, and Jonesboro, AR. By using joint population analysis of the three interconnected F1 diploid populations that shared a common parent, we identified 53 quantitative trait loci (QTLs) for nine adaptation traits, including nine overwintering ability QTLs. Negative correlations between overwintering ability and spring regrowth date and autumn dormancy date suggested that the genotypes most likely to survive winters were those that emerged early in spring and/or went dormant early in autumn. From genome-wide association analyses (GWA) of the germplasm panel study, we detected 73 marker-trait associations for overwintering ability. We found that Korea/N China M. sinensis genetic group could be a valuable gene pool for cold tolerance. The M. sinensis Yangtze-Qinling, Southern Japan and Northern Japan genetic groups were also potential sources of cold-tolerance. Comparisons between QTL analyses and GWA analyses, we found two overwintering ability QTLs that corresponded to seven GWA hits. One QTL on Miscanthus LG 8 encompassed five GWA hits and a known cold-responsive gene, COR47. The other overwintering ability QTL on Miscanthus LG 11 contained two GWA hits and two known cold stress related genes, carboxylesterase 13 (CEX13) and WRKY transcription factor (WRKY2). The QTL on LG 11 was also surrounded by one cold shock domain (CDSP1). Many biologically intuitive candidate genes were observed within or near the QTLs and GWA hits detected in this study, suggesting their validity and potential for further study. From the comparison of 13 M×g genotypes at three US locations, we identified several genotypes with superior cold tolerance to the commercial cultivar ‘1993-1780‘, suggesting a promising future for improving adaptation in Miscanthus. Miscanthus is a close relative of Saccharum and a potentially valuable genetic resource for improving sugarcane. Differences in flowering time within and between Miscanthus and Saccharum hinders intra- and interspecific hybridizations. A series of greenhouse experiments were conducted over three years to determine how to synchronize flowering time of Saccharum and Miscanthus genotypes. We found that day length was an important factor influencing when Miscanthus and Saccharum flowered. Sugarcane could be induced to flower in a central Illinois greenhouse using supplemental lighting to reduce the rate at which days shortened during the autumn and winter to 1 min d-1, which allowed us to synchronize the flowering of some sugarcane genotypes with Miscanthus genotypes primarily from low latitudes. In a complementary growth chamber experiment, we evaluated 33 Miscanthus genotypes, including 28 M. sinensis, 2 M. floridulus, and 3 M. ×giganteus collected from 20.91° S to 44.92° N for response to three day lengths (10 h, 12.5 h, and 15 h). High latitude-adapted M. sinensis flowered mainly under 15 h days, but unexpectedly, short days resulted in short, stocky plants that did not flower; in some cases, flag leaves developed under short days but heading did not occur. In contrast, for M. sinensis and M. floridulus from low latitudes, shorter day lengths typically resulted in earlier flowering, and for some low latitude genotypes, 15 h days resulted in no flowering. However, the highest ratio of reproductive shoots to total number of culms was typically observed for 12.5 h or 15 h days. Latitude of origin was significantly associated with culm length, and the shorter the days, the stronger the relationship. Nearly all entries achieved maximal culm length under the 15 h treatment, but the nearer to the equator an accession originated, the less of a difference in culm length between the short-day treatments and the 15 h day treatment. Under short days, short culms for high-latitude accessions was achieved by different physiological mechanisms for M. sinensis genetic groups from the mainland in comparison to those from Japan; for mainland accessions, the mechanism was reduced internode length, whereas for Japanese accessions the phyllochron under short days was greater than under long days. Thus, for M. sinensis, short days typically hastened floral induction, consistent with expectations for a facultative short-day plant. However, for high latitude accessions of M. sinensis, days less than 12.5 h also signaled that plants should prepare for winter by producing many short culms with limited elongation and development; moreover, this response was also epistatic to flowering. Thus, to flower M. sinensis that originates from high latitudes synchronously with sugarcane, the former needs day lengths >12.5 h (perhaps as high as 15 h), whereas the latter needs day lengths <12.5 h

Comparative analysis reveals chromosome number reductions in the evolution of African bermudagrass (Cynodon transvaalensis Burtt-Davy)

African bermudagrass (Cynodon transvaalensis Burtt-Davy) (2n = 2x = 18) belongs to the genus Cynodon, tribe Cynodonteae, subfamily Chloridoideae in the grass family Poaceae. The species is frequently crossed with common bermudagrass (Cynodon dactylon Pers.) in developing high-quality hybrid turf cultivars. Molecular resources for C. transvaalensis are scarce; thus, its genomic evolution is unknown. Recently, a linkage map consisting of 1278 markers provided a powerful tool for African bermudagrass genomic research. The objective of this study was to investigate chromosome number reduction events that resulted in the nine haploid chromosomes in this species. Tag sequences of mapped single nucleotide polymorphism markers in C. transvaalensis were compared against genome sequences of Oropetium thomaeum (L.f.) Trin. (2n = 2x = 20), a genomic model in the Cynodonteae tribe. The comparative genomic analyses revealed broad collinearity between the genomes of these two species. The analyses further revealed that two major interchromosomal rearrangements of the paleochromosome ρ12 (ρ1– ρ12–ρ1 and ρ6–ρ12–ρ6) resulted in nine chromosomes in the genome of C. transvaalensis. The findings provide novel information regarding the formation of the initial diploid species in the Cynodon genus.Horticulture and Landscape ArchitecturePlant and Soil Science

Genetic and QTL mapping in African bermudagrass

Cynodon transvaalensis Burtt-Davy is frequently used to cross with C. dactylon Pers. in the creation of F1 hybrid cultivars that are some of the most widely used in the worldwide turf industry. However, molecular resource development in this species is limited. Accordingly, the objectives of this study were to construct a high-density genetic map, and to identify genomic regions associated with establishment rate. In this study, we constructed the first high-density linkage map for African bermudagrass using a genotyping by sequencing approach based on 109 S1 progenies. A total of 1,246 single nucleotide polymorphisms and 32 simple sequence repeat markers were integrated in the linkage map. The total length of nine linkage groups was 882.3 cM, with an average distance of 0.69 cM per interval. Four genomic regions were identified to be associated with sod establishment rate. The results provide important genetic resources towards understanding the genome as well as marker-assisted selection for improving the establishment rate in bermudagrass breeding.Horticulture and Landscape ArchitecturePlant and Soil Science

Genetic diversity and population structure of bermudagrass (Cynodon spp.) revealed by genotyping-by-sequencing

Bermudagrass (Cynodon spp.) breeding and cultivar development is hampered by limited information regarding its genetic and phenotypic diversity. To explore diversity in bermudagrass, a total of 206 Cynodon accessions consisting of 193 common bermudagrass (C. dactylon var. dactylon) and 13 African bermudagrass (C. transvaalensis) accessions of worldwide origin were assembled for genetic characterization. Genotyping-by-sequencing (GBS) was employed for genetic marker development. With a minor allele frequency of 0.05 and a minimum call rate of 0.5, a total of 37,496 raw single nucleotide polymorphisms (SNPs) were called de novo and were used in the genetic diversity characterization. Population structure analysis using ADMIXTURE revealed four subpopulations in this germplasm panel, which was consistent with principal component analysis (PCA) and phylogenetic analysis results. The first three principal components explained 15.6%, 10.1%, and 3.8% of the variance in the germplasm panel, respectively. The first subpopulation consisted of C. dactylon accessions from various continents; the second subpopulation was comprised mainly of C. transvaalensis accessions; the third subpopulation contained C. dactylon accessions primarily of African origin; and the fourth subpopulation represented C. dactylon accessions obtained from the Oklahoma State University bermudagrass breeding program. Genetic diversity parameters including Nei’s genetic distance, inbreeding coefficient, and Fst statistic revealed substantial genetic variation in the Cynodon accessions, demonstrating the potential of this germplasm panel for further genetic studies and cultivar development in breeding programs

Atrial Fibrillation Follow-up Investigation to Recover Memory and Learning Trial (AFFIRMING): Rationale and Design of a Multi-center, Double-blind, Randomized Controlled Trial

Background: People with atrial fibrillation (AF) have elevated risk of developing cognitive impairment. At present, there is a dearth of randomized controlled trials investigating cognitive impairment management in patients with AF. The Atrial Fibrillation Follow-up Investigation to Recover Memory and learning (AFFIRMING) study is aimed at evaluating the potential for computerized cognitive training to improve cognitive function in patients with AF. Methods: The study is a multi-center, double-blind, randomized controlled study using a 1:1 parallel design. A total of 200 patients with AF and mild cognitive decline without dementia are planned to be recruited. The intervention group will use the adaptive training software with changes in difficulty, whereas the positive control group will use basic training software with minimal or no variation in difficulty level. At the end of 12 weeks, the participants will be unblinded, and the positive control group will stop training. The intervention group will be rerandomized 1:1 to stop training or continue training. All participants will be followed up until 24 weeks. The primary endpoint is the proportion of the improvement of the global cognitive function at week 12 compared with baseline, using the Basic Cognitive Ability Test (BCAT)

Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. x giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses

Monitoring the Methyl Eugenol Response and Non-Responsiveness Mechanisms in Oriental Fruit Fly Bactrocera dorsalis in China

Bactrocera dorsalis is a notorious polyphagous pest in China, and its management strategies largely depend on methyl eugenol (ME), which has been widely used as an attractant to monitor and eradicate B. dorsalis populations for seven decades. However, the non-responsiveness levels in field B. dorsalis populations to ME is unknown. In this study, we monitored the response to ME in field populations from the four most heavily infested provinces in China, and the results showed that the populations had lower sensitivity to ME relative to GZS susceptible strain. The percent responsiveness of the lowest sensitivity population was 5.88-, 3.47-, and 1.47-fold lower relative to the susceptible strain at doses of 1, 10, and 100 &micro;L of ME, respectively. Gene expression analysis and inhibitor assays further revealed that odorant binding protein (BdorOBP2, BdorOBP83b) and the P450 enzyme system may be associated with the lower response to ME. To our knowledge, this work is the first to report that the P450 enzyme system confers a lower responsiveness to lure insects. These findings provided valuable insights for exploiting ME non-responsiveness to protect sterile males from ME-based control strategies and the use of lures combined with insecticides

The effect of the additional load on the ground support on the settlement of the surrounding ground

Based on the existing engineering examples, this paper uses numerical simulation combined with the actual monitoring values on site to study the effect of the additional load on the support and the settlement of the surrounding ground, and the following conclusions are drawn: (1) When the enclosure structure is good, the settlement curve generally assumes a “spoon shape”. As the distance from the foundation pit increases, the surface settlement curve first increases and then decreases. The distance between the location of the maximum surface settlement and the foundation pit is generally half of the maximum excavation depth of the foundation pit. (2) The existence of additional load accelerates the rate of change of surface settlement, making the soil settlement from the excavation of the first layer of soil as a whole smaller than the unacted additional load to the excavation to the bottom layer as a whole larger than the unapplied load. (3) There will be a certain gap between the numerical simulation and the actual monitoring value. This gap will become larger and larger as the excavation of the foundation pit continues, but the law of change between the two is the same