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Bermudagrass (Cynodon spp.) is one of the drought-resistant warm-season turfgrasses adapted to the southern and transitional zones in the United States. Multiple hybrid varieties have been developed and released for use as a turfgrass and others are in pipeline. Increasing genetic di-versity of commercial varieties is vital to tackle stress tolerance. A DNA profiling study of 21 experimental selections from the Oklahoma State University (OSU) turfgrass breeding program and 11 cultivars was conducted using 51 simple sequence repeat (SSR) primer pairs that spread across the bermudagrass genome. Pairwise genetic relationship analysis among the genotypes using 352 polymorphic bands showed genetic similarity coefficients ranging from 0.59 to 0.89. Cluster analysis using the un-weighted paired group method with arithmetic average (UPGMA) method grouped the entries into six clusters. Correlation analysis identified different levels of pairwise genetic relationship among the entries that largely reflected parental relationship. Di-rectional breeding and selection for cold hardiness or drought resistance created progeny that had distinct genetic diversity in the tested bermudagrasses. It is evident that an increase in genetic diversity of the existing cultivar pool with the release of one or more of the experimental selec-tions for commercial use will strengthen and improve bermudagrass systems.

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a cereal crop vital for food security in West and Central Africa. Its byproducts also serve as fodder for livestock, especially during dry seasons. The objective of this study was to evaluate selected genotypes from West African pearl millet breeding programmes, for dual-purpose (grain and fodder) and elucidate prospects for future breeding. A total of 83 open-pollinated varieties (OPVs), five composites, six landraces, one synthetic and five hybrids were evaluated at 14 environments in Burkina Faso, Mali, Niger and Senegal during the rainy seasons of 2015 and 2016. Combined analysis of data revealed significant differences among genotypes and prevalence of high genotype-by-environment interaction effects. Two stability analyses models consistently indicated that genotypes 10 (SMILBF10), 14 (SMILBF14) and 39 (SMILML5) were widely adaptable across the region. Plant height, panicle length and panicle yield showed significant positive correlations with grain yield; while days to flowering was negatively correlated. Positive correlation between grain and fodder yields indicate possibility for simultaneous improvement involving the two important traits. This result suggests that germplasm exchange and regionally integrated breeding programmes are important for the identification of widely adapted dual-purpose varieties of pearl millet, particularly in West African drylands.

Flowering in perennial species is directed via complex signalling pathways that adjust to developmental regulations and environmental cues. Synchronized flowering in certain environments is a prerequisite to commercial seed production, and so the elucidation of the genetic architecture of flowering time in Miscanthus and switchgrass could aid breeding in these underdeveloped species. In this context, we assessed a mapping population in Miscanthus and two ecologically diverse switchgrass mapping populations over 3 years from planting. Multiple flowering time quantitative trait loci (QTL) were identified in both species. Remarkably, the most significant Miscanthus and switchgrass QTL proved to be syntenic, located on linkage groups 4 and 2, with logarithm of odds scores of 17.05 and 21.8 respectively. These QTL regions contained three flowering time transcription factors: Squamosa Promoter-binding protein-Like, MADS-box SEPELLATA2 and gibberellin-responsive bHLH137. The former is emerging as a key component of the age-related flowering time pathway.

Drought and heat stresses are major challenges for turfgrass management in the desert southwest of the United States where rainfall is insufficient to support managed turfgrass growth. Irrigation water availability and its quality are increasingly strained due to diminishing surface water supplies. Unprecedented drought conditions threaten the reliance on groundwater supplies that are heavily scrutinized for irrigation practices on landscape and recreational turfgrass. Therefore, development of drought tolerant cultivars, lower input turf management strategies that sustains turfgrass appearance and performance with less irrigation water, and tolerance to higher seasonal temperatures will be critically important. Sustainability of acceptable quality turfgrass can be accomplished through harnessing the natural genetic variation, genetic manipulation using modern genomic technology, and optimizing turfgrass management practices for improved drought tolerance. Besides persistent efforts of varietal development and improved turfgrass management for drought tolerance and performance, redefining the quality of irrigated turfgrass for consumers to align with the environmental conditions is envisioned to foster a sustainable golf, sports fields, and landscape turfgrass industry in the region. A comprehensive study encompassing different turfgrass species and enhancing management practices to achieve acceptable performing turfgrass as well as outreach education to improve public perception of realities for a “green” environment will be critically important. The recent developments in turfgrass science and contemporary communication platforms are instrumental in increasing awareness for a sustainable turfgrass paradigm and sustain eco-tourism of the region.

The sugarcane aphid, Melanaphis sacchari (Zehntner) (Hemiptera: Aphididae) (SCA), has become a major pest of grain sorghum since its appearance in the USA. Several grain sorghum parental lines are moderately resistant to the SCA. However, the molecular and genetic mechanisms underlying this resistance are poorly understood, which has constrained breeding for improved resistance. RNA-Seq was used to conduct transcriptomics analysis on a moderately resistant genotype (TAM428) and a susceptible genotype (Tx2737) to elucidate the molecular mechanisms underlying resistance. Differential expression analysis revealed differences in transcriptomic profile between the two genotypes at multiple time points after infestation by SCA. Six gene clusters had differential expression during SCA infestation. Gene ontology enrichment and cluster analysis of genes differentially expressed after SCA infestation revealed consistent upregulation of genes controlling protein and lipid binding, cellular catabolic processes, transcription initiation, and autophagy in the resistant genotype. Genes regulating responses to external stimuli and stress, cell communication, and transferase activities, were all upregulated in later stages of infestation. On the other hand, expression of genes controlling cell cycle and nuclear division were reduced after SCA infestation in the resistant genotype. These results indicate that different classes of genes, including stress response genes and transcription factors, are responsible for countering the physiological effects of SCA infestation in resistant sorghum plants.

Millets are important cereal crops cultivated in arid and semiarid regions of the world, particularly Africa and southeast Asia. Climate change has triggered multiple abiotic stresses in plants that are the main causes of crop loss worldwide, reducing average yield for most crops by more than 50%. Although millets are tolerant to most abiotic stresses including drought and high temperatures, further improvement is needed to make them more resilient to unprecedented effects of climate change and associated environmental stresses. Incorporation of stress tolerance traits in millets will improve their productivity in marginal environments and will help in overcoming future food shortage due to climate change. Recently, approaches such as application of plant growth-promoting rhizobacteria (PGPRs) have been used to improve growth and development, as well as stress tolerance of crops. Moreover, with the advance of next-generation sequencing technology, genome editing, using the clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system are increasingly used to develop stress tolerant varieties in different crops. In this paper, the innate ability of millets to tolerate abiotic stresses and alternative approaches to boost stress resistance were thoroughly reviewed. Moreover, several stress-resistant genes were identified in related monocots such as rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), and other related species for which orthologs in millets could be manipulated by CRISPR/Cas9 and related genome-editing techniques to improve stress resilience and productivity. These cutting-edge alternative strategies are expected to bring this group of orphan crops at the forefront of scientific research for their potential contribution to global food security.

Background Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distinguished in Senegal: early-flowering Souna and late-flowering Sanio. Phenotypic variabilities related to flowering time play an important role in the adaptation of pearl millet to climate variability. A better understanding of the genetic makeup of these variabilities would make it possible to breed pearl millet to suit regions with different climates. The aim of this study was to characterize the genetic basis of these phenotypic differences. Results We defined a core collection that captures most of the diversity of cultivated pearl millets in Senegal and includes 60 early-flowering Souna and 31 late-flowering Sanio morphotypes. Sixteen agro-morphological traits were evaluated in the panel in the 2016 and 2017 rainy seasons. Phenological and phenotypic traits related with yield, flowering time, and biomass helped differentiate early- and late-flowering morphotypes. Further, using genotyping-by-sequencing (GBS), 21,663 single nucleotide polymorphisms (SNPs) markers with more than 5% of minor allele frequencies were discovered. Sparse non-negative matrix factorization (sNMF) analysis confirmed the genetic structure in two gene pools associated with differences in flowering time. Two chromosomal regions on linkage groups (LG 3) (~ 89.7 Mb) and (LG 6) (~ 68.1 Mb) differentiated two clusters among the early-flowering Souna. A genome-wide association study (GWAS) was used to link phenotypic variation to the SNPs, and 18 genes were linked to flowering time, plant height, tillering, and biomass (P-value < 2.3E-06). Conclusions The diversity of early- and late-flowering pearl millet morphotypes in Senegal was captured using a heuristic approach. Key phenological and phenotypic traits, SNPs, and candidate genes underlying flowering time, tillering, biomass yield and plant height of pearl millet were identified. Chromosome rearrangements in LG3 and LG6 were inferred as a source of variation in early-flowering morphotypes. Using candidate genes underlying these features between pearl millet morphotypes will be of paramount importance in breeding for resilience to climatic variability.

Flowering in perennial species is directed via complex signalling pathways that adjust to developmental regulations and environmental cues. Synchronized flowering in certain environments is a prerequisite to commercial seed production, and so the elucidation of the genetic architecture of flowering time in Miscanthus and switchgrass could aid breeding in these underdeveloped species. In this context, we assessed a mapping population in Miscanthus and two ecologically diverse switchgrass mapping populations over 3 years from planting. Multiple flowering time quantitative trait loci (QTL) were identified in both species. Remarkably, the most significant Miscanthus and switchgrass QTL proved to be syntenic, located on linkage groups 4 and 2, with logarithm of odds scores of 17.05 and 21.8 respectively. These QTL regions contained three flowering time transcription factors: Squamosa Promoter‐binding protein‐Like, MADS‐box SEPELLATA2 and gibberellin‐responsive bHLH137. The former is emerging as a key component of the age‐related flowering time pathway., Genetic factors control flowering in the bioenergy species Miscanthus and switchgrass are poorly understood, yet commercial seed production to upscale sustainable bioenergy requires flowering synchronization. Using populations (of both species) with diverse flowering times, we identified a region that was strikingly conserved, not only between Miscanthus and switchgrass, but also with Sorghum, another bioenergy grass. The region contained DNA sequences encoding genes known to be involved in flowering time control in other species, and appears highly important for flowering time regulation. This provides a potential tool to synchronize flowering in these crops to speed up the breeding of new varieties.

Additional file 1: Table S1. List of accessions from the Senegalese pearl millet core collection. Table S2. Representativeness statistics of early-flowering Souna morphotype and late-flowering Sanio morphotypes within the core collection. %MD = Percentage of mean difference, %VD = Percentage of variance difference, %CR = Coincidence rate, and %VR = Variable rate. Table S3. Means, P-values and correlation with axis from the discriminant analysis (DA) of early- and late- flowering millets. Table S4. Significantly associated SNPs from GWAS, mapped in the pearl millet genome and associated with phenotypic traits. Figure S1. Genetic structure of Senegalese pearl millet landraces core collection at chromosome level (a-g) from chromosome 1 to chromosome 7, respectively. Figure S2. Discriminant analysis of (a) early-flowering (Axis1 = 98.49, Axis2 = 1.51) and (b) late-flowering morphotypes (Axis1 = 95.59, Axis2 = 4.41), from phenotypic traits of landraces from the core collection. Boxplots of (c) grain yield, (d) panicle yield, (e) spike thickness, (f) nodal tillering and (g) flag leaf length according to different subsets of early-flowering morphotype. Boxplots of (h) panicle yield, (i) grain yield and (j) nodal tillering according to different subsets of late-flowering morphotype.

Pearl millet [Pennisetum glaucum (L.) R. Br.; Syn. Cenchrus americanus (L.) Morrone] is the sixth most important cereal in the world. Today, pearl millet is grown on more than 30 million ha mainly in West and Central Africa and the Indian sub-continent as a staple food for more than 90 million people in agriculturally marginal areas. It is rich in proteins and minerals and has numerous health benefits such as being gluten-free and having slow-digesting starch. It is grown as a forage crop in temperate areas. It is drought and heat tolerant, and a climate-smart crop that can withstand unpredictable variability in climate. However, research on pearl millet improvement is lagging behind other major cereals mainly due to limited investment in terms of man and money power. So far breeding achievements include the development of cytoplasmic male sterility (CMS), maintenance counterparts (rf) system and nuclear fertility restoration genes (Rf) for hybrid breeding, dwarfing genes for reduced height, improved input responsiveness, photoperiod neutrality for short growing season, and resistance to important diseases. Further improvement of pearl millet for genetic yield potential, stress tolerance, and nutritional quality traits would enhance food and nutrition security for people living in agriculturally dissolute environments. Application of molecular technology in the pearl millet breeding program has a promise in enhancing the selection efficiency while shortening the lengthy phenotypic selection process ultimately improving the rate of genetic gains. Linkage analysis and genome-wide association studies based on different marker systems in detecting quantitative trait loci (QTLs) for important agronomic traits are well demonstrated. Genetic resources including wild relatives have been categorized into primary, secondary and tertiary gene pools based on the level of genetic barriers and ease of gene introgression into pearl millet. A draft on pearl millet whole genome sequence was recently published with an estimated 38,579 genes annotated to establish genomic-assisted breeding. Resequencing a large number of germplasm lines and several population genomic studies provided a valuable insight into population structure, genetic diversity and domestication history of the crop. Successful improvement in combination with modern genomic/genetic resources, tools and technologies and adoption of pearl millet will not only improve the resilience of global food system through on-farm diversification but also dietary intake which depends on diminishingly fewer crops.

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a warm-season, C4 annual cereal primarily grown in Africa and India for food and fodder. It is also grown in the United States, mainly as a forage crop on a limited area. It is the sixth most important cereal crop in the world. More than 90 million people around the world rely on it as a food grain. It is known for its drought and heat tolerance to reliably produce crops in arid environments. This review is meant to assess the current status of pearl millet breeding and its future prospects globally, with major emphasis on breeding efforts in the United States and India. The topics discussed relate to improvements in plant stature, maturity, photoperiod insensitivity, discovery of cytoplasmic male sterility (CMS), and transfer of apomixis from wild relatives. These improvements have led to increased grain and forage yields, nutritional quality, and enhanced disease resistance. Hybrids developed using CMS reportedly have an average of 50% higher grain yield than openpollinated cultivars. We discuss important genetic and breeding achievements in pearl millet for different traits and their implications for further improvement as a potential crop. Additional research is needed to enhance its productivity, early stand establishment, drought tolerance, and nutritional quality for growing it as a grain crop in moisture-limited areas. The application of advanced genomics and markerassisted selection tools is needed to accelerate pearl millet breeding and accomplish targeted breeding goals.

Natural genetic variation for reduced recalcitrance can be used to improve switchgrass for biofuel production. A full-sib switchgrass mapping population developed by crossing a lowland genotype, AP13, and upland genotype, VS16, was evaluated at three locations (Ardmore and Burneyville, OK and Watkinsville, GA). Biomass harvested after senescence in 2009 and 2010 was evaluated at the National Renewable Energy Laboratory (NREL) for sugar release using enzymatic hydrolysis and for lignin content and syringyl/guaiacyl lignin monomer (S/G) ratio using pyrolysis molecular beam mass spectrometry (py-MBMS). Glucose and xylose release ranged from 120 to 313 and 123 to 263 mg g−1, respectively, while lignin content ranged from 19 to 27 % of the dry biomass. Statistically significant differences were observed among the genotypes and the environments for the cell wall composition traits. Regression analysis showed that a unit increase in lignin content reduced total sugar release by an average of 10 mg g−1. Quantitative trait loci (QTL) analysis detected 9 genomic regions underlying sugar release and 14 for lignin content. The phenotypic variation explained by the individual QTL identified for sugar release ranged from 4.5 to 9.4 and for lignin content from 3.8 to 11.1 %. Mapping of the QTL regions to the switchgrass genome sequence (v1.1) found that some of the QTL colocalized with genes involved in carbohydrate processing and metabolism, plant development, defense systems, and transcription factors. The markers associated with QTL can be implemented in breeding programs to efficiently develop improved switchgrass cultivars for biofuel production.

Switchgrass (Panicum virgatum L.), a warm season, C4, perennial grass, is one of the predominant grass species of the North American tall grass prairies. It is viewed as a high-potential bioenergy feedstock species because it can produce large amounts of lignocellulosic material with relatively few inputs. The objectives of this project were to develop an advanced switchgrass population and use it for the construction of genetic linkage maps and trait characterization. A three-generation, four-founder population was created and a total of 182 progeny of this advanced population were genotyped, including a mixture of self-pollinated and hybrid individuals. The female map integrated both subpopulations and covered 1629 cM of the switchgrass genome, with an average map length of 91 cM per linkage group. The male map of the hybrid progeny covered 1462 cM, with an average map length of 81 cM per linkage group. Average marker density of the female and male maps was 3.9 and 3.5 cM per marker interval, respectively. Based on the parental maps, the genome length of switchgrass was estimated to be 1776 cM and 1596 cM for the female map and male map, respectively. The proportion of the genome within 5 cM of a mapped locus was estimated to be 92% and 93% for the female map and male map, respectively. Thus, the linkage maps have covered most of the switchgrass genome. The assessment of marker transmission ratio distortion found that 26% of the genotyped markers were distorted from either 1:1 or 3:1 ratios expected for segregation of single dose markers in one or both parents, respectively. Several regions affected by transmission ratio distortion were found, with linkage groups Ib-m and VIIIa-f most affected.

Core Ideas Mapping of GBS reads of 398 accessions to the draft genome sequence identified 82,112 SNPs Model‐based clustering analysis revealed a hierarchical genetic structure of six subgroups Greater LD decay in the west‐African subpopulation is likely due to long history of recombination Genetic differentiation analysis among subpopulations revealed variation in selection signatures Pearl millet [Cenchrus americanus (L.) Morrone syn. Pennisetum glaucum (L.) R. Br.] is one of the most extensively cultivated cereals in the world, after wheat (Triticum aestivum L.), maize (Zea mays L.), rice (Oryza sativa L.), barley (Hordeum vulgare L.), and sorghum [Sorghum bicolor (L.) Moench]. It is the main component of traditional farming systems and a staple food in the arid and semiarid regions of Africa and southern Asia. However, its genetic improvement is lagging behind other major cereals and the yield is still low. Genotyping‐by‐sequencing (GBS)‐based single‐nucleotide polymorphism (SNP) markers were screened on a total of 398 accessions from different geographic regions to assess genetic diversity, population structure, and linkage disequilibrium (LD). By mapping the GBS reads to the reference genome sequence, 82,112 genome‐wide SNPs were discovered. The telomeric regions of the chromosomes have the higher SNP density than in pericentromeric regions. Model‐based clustering analysis of the population revealed a hierarchical genetic structure of six subgroups that mostly overlap with the geographic origins or sources of the genotypes but with differing levels of admixtures. A neighbor‐joining phylogeny analysis revealed that germplasm from western Africa rooted the dendrogram with much diversity within each subgroup. Greater LD decay was observed in the west‐African subpopulation than in the other subpopulations, indicating a long history of recombination among landraces. Also, genome scan of genetic differentiatation detected different selection histories among subpopulations. These results have potential application in the development of genomic‐assisted breeding in pearl millet and heterotic grouping of the lines for improved hybrid performance.

Switchgrass (Panicum virgatum L.) is a native perennial warm season (C4) grass that has been identified as a promising species for bioenergy research and production. Consequently, biomass yield and feedstock quality improvements are high priorities for switchgrass research. The objective of this study was to develop a switchgrass genetic linkage map using a full-sib pseudo-testcross mapping population derived from a cross between two heterozygous genotypes selected from the lowland cultivar ‘Alamo’ (AP13) and the upland cultivar ‘Summer’ (VS16). The female parent (AP13) map consists of 515 loci in 18 linkage groups (LGs) and spans 1,733 cM. The male parent (VS16) map arranges 363 loci in 17 LGs and spans 1,508 cM. No obvious cause for the lack of one LG in VS16 could be identified. Comparative analyses between the AP13 and VS16 maps showed that the two major ecotypic classes of switchgrass have highly colinear maps with similar recombination rates, suggesting that chromosomal exchange between the two ecotypes should be able to occur freely. The AP13 and VS16 maps are also highly similar with respect to marker orders and recombination levels to previously published switchgrass maps. The genetic maps will be used to identify quantitative trait loci associated with biomass and quality traits. The AP13 genotype was used for the whole genome-sequencing project and the map will thus also provide a tool for the anchoring of the switchgrass genome assembly.

Pearl millet (Penisetum glaucum (L) R. Br.) is a hardy cereal crop grown in the arid and semiarid tropics where other cereals are likely to fail to produce economic yields due to drought and heat stresses. Adaptive evolution, a form of natural selection shaped the crop to grow and yield satisfactorily with limited moisture supply or under periodic water deficits in the soil. Drought tolerance is a complex polygenic trait that various morphological and physiological responses are controlled by hundreds of genes and significantly influenced by the environment. The development of genomic tools will have enormous potential to improve the efficiency and precision of conventional breeding. The apparent independent domestication events, highly outcrossing nature and traditional cultivation in stressful environments maintained tremendous amount of polymorphism in pearl millet. This high polymorphism of the crop has been revealed by genome mapping that in turn stimulated the mapping and tagging of genomic regions controlling important traits such as drought tolerance. Mapping of a major QTL for terminal drought tolerance in independent populations envisaged the prospect for the development of molecular breeding in pearl millet. To accelerate genetic gains for drought tolerance targeted novel approaches such as establishment of marker-trait associations, genomic selection tools, genome sequence and genotyping-by-sequencing are still limited. Development and application of high throughput genomic tools need to be intensified to improve the breeding efficiency of pearl millet to minimize the impact of climate change on its production.

Hybridization and selection has been one of the methods used to generate turfgrass cultivars in buffalograss improvement. Three half-sib populations were developed by crossing three buffalograss female genotypes, NE 3296, NE 2768, and NE 2769, with NE 2871, a male genotype, to 1) investigate the pattern of genetic variability generated for turfgrass characteristics through hybridization; 2) assess the effect of parental change on the level of genetic variability generated in a buffalograss diploid population; and 3) predict the performance of a progeny generated from two heterozygous parents for turfgrass performance. The four parents and 20 random F1 progeny selected from each population were established in 2006 at the John Seaton Anderson Turfgrass Research Facility located near Mead, NE. A randomized complete block design (RCBD) was used with the progeny nested in the crosses. A visual rating scale of 1–9 was used to evaluate the population. Mean population lateral spread, genetic color, density, and turfgrass quality from early summer to fall ranged from 3.5 to 4.5, 7.1 to 7.9, 6.9 to 8.1, and 5.2 and 6.8, respectively. There were significant differences among the crosses and the parents for all the traits studied except quality in June and August. The progeny nested within crosses differed for turfgrass genetic color and quality. Best linear unbiased prediction (BLUP) indicated a high improvement potential for turfgrass lateral spread and spring density in NE 2768 × NE 2871 and for turfgrass genetic color in NE 3296 × NE 2871. From these findings, it can be concluded that hybridization breeding is a worthwhile approach for generating and identifying transgressive segregants for specific buffalograss traits.

Switchgrass rust caused by Puccinia emaculata is a major limiting factor for switchgrass (Panicum virgatum L.) production, especially in monoculture. Natural populations of switchgrass displayed diverse reactions to P. emaculata when evaluated in an Ardmore, OK, field. To identify the differentially expressed genes during the rust infection process and the mechanisms of switchgrass rust resistance, transcriptome analysis using RNA-Seq was conducted in two pseudo-F1 parents ('PV281' and 'NFGA472'), and three moderately resistant and three susceptible progenies selected from a three-generation, four-founder switchgrass population (K5 × A4) × (AP13 × VS16). On average, 23.5 million reads per sample (leaf tissue was collected at 0, 24, and 60 h post-inoculation (hpi)) were obtained from paired-end (2 × 100 bp) sequencing on the Illumina HiSeq2000 platform. Mapping of the RNA-Seq reads to the switchgrass reference genome (AP13 ver. 1.1 assembly) constructed a total of 84,209 transcripts from 98,007 gene loci among all of the samples. Further analysis revealed that host defense-related genes, including the nucleotide binding site-leucine-rich repeat domain containing disease resistance gene analogs, play an important role in resistance to rust infection. Rust-induced gene (RIG) transcripts inherited across generations were identified. The rust-resistant gene transcripts can be a valuable resource for developing molecular markers for rust resistance. Furthermore, the rust-resistant genotypes and gene transcripts identified in this study can expedite rust-resistant cultivar development in switchgrass.

Buffalograss [Buchloe dactyloides (Nutt.) Engelm.] use as a fairway turfgrass is limited in northern portions of its adaptation zone by its extended winter dormancy and tan coloration in early spring and late fall. Cool-season grasses mixed with buffalograss could enhance turfgrass appearance and performance in fall and early spring. Research was conducted near Mead, NE, with eight buffalograss genotypes maintained under fairway conditions to determine the effect of blue fescue (Festuca ovina L. var. glauca Lam.) overseeding rate on turfgrass performance. Interactions were nonsignificant in most cases so main effects are emphasized. Differences were observed between seeding rates and genotypes for most traits studied. Overseeding blue fescue enhanced spring green-up, fall color retention, stand density, and turfgrass quality. These effects were most pronounced in late fall and early spring, when buffalograss plants were entering or exiting winter dormancy. The 5 g·m−2 blue fescue overseeding rate improved all performance traits studied when compared with the nonoverseeded buffalograss control and was not different from the 10 g·m−2 seeding rate treatment. Thus, the 5 g·m−2 blue fescue overseeding rate appeared to be near optimum for overall turfgrass performance, offering reduced seed cost and decreased potential for species interference. The ‘Legacy’ buffalograss and ‘SR-3200’ blue fescue mixture had the best performance of the genotypes studied as a result of their visual compatibility in terms of color similarity.

Fifteen buffalograss, Buchloe dactyloides (Nutt.) Engelm, genotypes and 94 diploid full-sib progeny were evaluated for western chinch bug, Blissus occiduus Barber (Hemiptera: Lygaeidae), resistance in two separate studies. The experimental design for each study was a completely randomized design. Adult chinch bugs were introduced onto caged single clone genotypes and progeny in the greenhouse. Chinch bug damage was assessed using a 1-5 visual damage rating scale with 1 =or = 10%; 2 = 11-30%; 3 = 31-50%; 4 = 51-70%; and 5 =or = 70% of the buffalograss leaf area with severe discoloration, or dead tissue. Highly significant differences were found among the genotypes and progeny for chinch bug damage. Among the genotypes, Legacy, Prestige, 184, 196, Bowie, NE 3297, NE 2769, and NE 2768 were moderately resistant with damage ratings of1, but3, while NE 2990, NE 2838, and 1-57-19 were moderately susceptible with damage ratings ofor = 3, but4. Among the progeny, one progeny (MP45) was highly resistant with a chinch bug damage rating of 1.0, 78 progeny (83%) had moderate resistance, with damage ratings of1.0 and3.0, 13 progeny (14%) were moderately susceptible with damage ratings ranging from 3.0 to 3.9, while only two were highly susceptible with damage ratings ofor = 4.0. The significant variability among genotypes and progeny for chinch bug resistance indicates the ability to improve buffalograss resistance to chinch bugs through selection or hybridization of selected genotypes.

A switchgrass (Panicum virgatum L.) consensus map was developed that combined data from two mapping populations and integrated recombination data from both parents of this largely obligate outcrossing species. The consensus map consisted of 1,321 loci and spanned 2,122 cM. An analysis of the distribution of genic and genomic markers across the length of a linkage group showed that genic markers were relatively overrepresented in distal regions, while genomic markers were relatively overrepresented in pericentromeric regions. Furthermore, genic markers located in distal and pericentromeric regions identified orthologs in the genome of the closely related species foxtail millet (Setaria italica (L.) P. Beauv.) at a similar rate, but fewer orthologs were found for genomic markers that mapped to pericentromeric regions compared to distal regions. Because cross-species sequence conservation is largely limited to genes, our data suggest that genomic markers that map to distal regions are more likely to be derived from genic regions than those that map to pericentromeric regions. A comparative analysis between loci on the switchgrass consensus map and their orthologs in the foxtail millet genome showed that the two species varied by at least nine inversions and one reciprocal translocation. Extending the comparative analysis to sorghum demonstrated that the majority of the rearrangements occurred in the foxtail millet genome in the past 13 million years. The reduction in chromosome number from 10 in the Andropogoneae to 9 in the Paniceae was achieved through a complex set of rearrangements involving three ancestral chromosomes orthologous to sorghum chromosomes 6, 8, and 9 and chromosomes III and VII in the lineage leading to switchgrass and foxtail millet. Upon insertion of ancestral chromosome 9 into ancestral chromosome 8, the centromere of the recipient chromosome was lost, and this was accompanied by a loss of repetitive DNA. The switchgrass–foxtail millet comparative map provides a guide of the rearrangements that need to be taken into account when using foxtail millet as a surrogate for switchgrass in genetic analyses.

Several fungal pathogens have been identified on ornamental and native stands of switchgrass (Panicum virgatum L.). Diseases of switchgrass, particularly rust, have been largely neglected and are likely to become the major limiting factor to biomass yield and quality, especially when monocultured over a large acreage. Based on teliospore morphology and internal transcribed spacer-based diagnostic primers, the rust pathogen collected from switchgrass research fields in Oklahoma was identified as Puccinia emaculata. Furthermore, to identify genetically diverse source(s) of rust resistance, several switchgrass genotypes from both upland (cv. ‘Summer’ and ‘Cave-in-Rock’) and lowland (cv. ‘Alamo’ and ‘Kanlow’) ecotypes were evaluated in Ardmore, Oklahoma during 2008 and 2009 and in growth chamber assays. Field and growth chamber evaluations revealed a high degree of genetic variation within and among switchgrass cultivars. In general, Alamo and Kanlow showed moderate resistance to P. emaculata, while Summer was highly susceptible. Distinct ecotypic variations for reactions to rust were also prevalent with the lowlands maintaining a high level of resistance. These results suggest the potential for improvement of rust resistance via the selection of resistant individuals from currently available cultivars. Further, the selection pressure on the pathogen would also be reduced by employing several rust resistant cultivars in production-scale situations.

Switchgrass (Panicum virgatum L.) biomass yield and feedstock quality improvement are priority research areas for bioenergy feedstock development. Identification of quantitative trait loci (QTL) underlying these traits and of trait-linked markers for application in marker-assisted selection (MAS) is of paramount importance in facilitating switchgrass breeding. Detection of QTL for biomass yield and plant height was conducted on parental linkage maps constructed using a heterozygous pseudo-F1 population derived from a cross between lowland Alamo genotype AP13 and upland Summer genotype VS16. QTL analysis was performed with composite interval mapping. Four QTL for biomass yield and five QTL for plant height were identified using best linear unbiased predictors across ten and eight environments, respectively. The phenotypic variability explained (PVE) by QTL detected in the across environments analysis ranged from 4.9 to 12.4 % for biomass yield and 5.1 to 12.0 % for plant height. A total of 34 and 38 main effect QTL were detected for biomass yield and plant height, respectively, when data from each environment were analyzed separately. The PVE by individual environment QTL ranged from 3.3 to 15.3 % for biomass yield and from 4.3 to 17.4 % for plant height. In addition, 60 and 51 epistatic QTL were detected for biomass yield and plant height, respectively. Significant QTL by environment interactions were detected for QTL mapped in eight genomic regions for each of the two traits. Seven QTL affected both traits and may represent pleiotropic loci. Overall, 11 genomic regions were identified that were important in controlling biomass yield and/or plant height in switchgrass. The markers linked to the main effect and epistatic QTL may be used in MAS to maximize selection gain in switchgrass breeding, leading to a faster development of better biofuel cultivars.

Background Switchgrass, a warm-season perennial grass studied as a potential dedicated biofuel feedstock, is classified into two main taxa – lowland and upland ecotypes – that differ in morphology and habitat of adaptation. But there is limited information on their inherent molecular variations. Results Transcriptome analysis by RNA-sequencing (RNA-Seq) was conducted for lowland and upland ecotypes to document their gene expression variations. Mapping of transcriptome to the reference genome (Panicum virgatum v1.1) revealed that the lowland and upland ecotypes differ substantially in sets of genes transcribed as well as levels of expression. Differential gene expression analysis exhibited that transcripts related to photosynthesis efficiency and development and photosystem reaction center subunits were upregulated in lowlands compared to upland genotype. On the other hand, catalase isozymes, helix-loop-helix, late embryogenesis abundant group I, photosulfokinases, and S-adenosyl methionine synthase gene transcripts were upregulated in the upland compared to the lowlands. At ≥100x coverage and ≥5% minor allele frequency, a total of 25,894 and 16,979 single nucleotide polymorphism (SNP) markers were discovered for VS16 (upland ecotype) and K5 (lowland ecotype) against the reference genome. The allele combination of the SNPs revealed that the transition mutations are more prevalent than the transversion mutations. Conclusions The gene ontology (GO) analysis of the transcriptome indicated lowland ecotype had significantly higher representation for cellular components associated with photosynthesis machinery controlling carbon fixation. In addition, using the transcriptome data, SNP markers were detected, which were distributed throughout the genome. The differentially expressed genes and SNP markers detected in this study would be useful resources for traits mapping and gene transfer across ecotypes in switchgrass breeding for increased biomass yield for biofuel conversion. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3377-8) contains supplementary material, which is available to authorized users.