Genomic resources of broomcorn millet: demonstration and application of a high-throughput BAC mapping pipeline.

BACKGROUND: With high-efficient water-use and drought tolerance, broomcorn millet has emerged as a candidate for food security. To promote its research process for molecular breeding and functional research, a comprehensive genome resource is of great importance. RESULTS: Herein, we constructed a BAC library for broomcorn millet, generated BAC end sequences based on the clone-array pooled shotgun sequencing strategy and Illumina sequencing technology, and integrated BAC clones into genome by a novel pipeline for BAC end profiling. The BAC library consisted of 76,023 clones with an average insert length of 123.48 Kb, covering about 9.9-fold of the 850 Mb genome. Of 9216 clones tested using our pipeline, 8262 clones were mapped on the broomcorn millet cultivar longmi4 genome. These mapped clones covered 308 of the 829 gaps left by the genome. To our knowledge, this is the only BAC resource for broomcorn millet. CONCLUSIONS: We constructed a high-quality BAC libraray for broomcorn millet and designed a novel pipeline for BAC end profiling. BAC clones can be browsed and obtained from our website ( http://eightstarsbio.com/gresource/JBrowse-1.16.5/index.html ). The high-quality BAC clones mapped on genome in this study will provide a powerful genomic resource for genome gap filling, complex segment sequencing, FISH, functional research and genetic engineering of broomcorn millet.

Genotypic identification of Panicum spp. in New South Wales, Australia using DNA barcoding.

Australia has over 30 Panicum spp. (panic grass) including several non-native species that cause crop and pasture loss and hepatogenous photosensitisation in livestock. It is critical to correctly identify them at the species level to facilitate the development of appropriate management strategies for efficacious control of Panicum grasses in crops, fallows and pastures. Currently, identification of Panicum spp. relies on morphological examination of the reproductive structures, but this approach is only useful for flowering specimens and requires significant taxonomic expertise. To overcome this limitation, we used multi-locus DNA barcoding for the identification of ten selected Panicum spp. found in Australia. With the exception of P. buncei, other native Australian Panicum were genetically separated at the species level and distinguished from non-native species. One nuclear (ITS) and two chloroplast regions (matK and trnL intron-trnF) were identified with varying facility for DNA barcode separation of the Panicum species. Concatenation of sequences from ITS, matK and trnL intron-trnF regions provided clear separation of eight regionally collected species, with a maximum intraspecific distance of 0.22% and minimum interspecific distance of 0.33%. Two of three non-native Panicum species exhibited a smaller genome size compared to native species evaluated, and we speculate that this may be associated with biological advantages impacting invasion of non-native Panicum species in novel locations. We conclude that multi-locus DNA barcoding, in combination with traditional taxonomic identification, provides an accurate and cost-effective adjunctive tool for further distinguishing Panicum spp. at the species level.

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

Differential Defense Responses of Upland and Lowland Switchgrass Cultivars to a Cereal Aphid Pest.

Yellow sugarcane aphid (YSA) (Sipha flava, Forbes) is a damaging pest on many grasses. Switchgrass (Panicum virgatum L.), a perennial C4 grass, has been selected as a bioenergy feedstock because of its perceived resilience to abiotic and biotic stresses. Aphid infestation on switchgrass has the potential to reduce the yields and biomass quantity. Here, the global defense response of switchgrass cultivars Summer and Kanlow to YSA feeding was analyzed by RNA-seq and metabolite analysis at 5, 10, and 15 days after infestation. Genes upregulated by infestation were more common in both cultivars compared to downregulated genes. In total, a higher number of differentially expressed genes (DEGs) were found in the YSA susceptible cultivar (Summer), and fewer DEGs were observed in the YSA resistant cultivar (Kanlow). Interestingly, no downregulated genes were found in common between each time point or between the two switchgrass cultivars. Gene co-expression analysis revealed upregulated genes in Kanlow were associated with functions such as flavonoid, oxidation-response to chemical, or wax composition. Downregulated genes for the cultivar Summer were found in co-expression modules with gene functions related to plant defense mechanisms or cell wall composition. Global analysis of defense networks of the two cultivars uncovered differential mechanisms associated with resistance or susceptibility of switchgrass in response to YSA infestation. Several gene co-expression modules and transcription factors correlated with these differential defense responses. Overall, the YSA-resistant Kanlow plants have an enhanced defense even under aphid uninfested conditions.

Phytoremediation potential of switchgrass (Panicum virgatum), two United States native varieties, to remove bisphenol-A (BPA) from aqueous media.

Plastic wastes burdening Earth's water and accumulating on land, releasing toxic leachates, are one of the greatest global threats of our time. Bisphenol-A (BPA), a potent endocrine disrupting compound, is a synthetic ingredient of the polycarbonate plastics and epoxy resins used in food containers, cans, and water bottles. Bisphenol-A's rising concentrations in the environment require a sustainable alternative to current removal practices, which are expensive and/or ecologically unsafe. Switchgrass offers a safe alternative. To investigate its potential for BPA removal, two United States native switchgrass varieties where tested in hydroponic media. Results show minimal hydrolysis and photolysis of BPA over 55 days, confirming its persistence. Both generic and heavy metal switchgrass exhibited statistically significant (p < 0.0001) BPA removal (40% and 46%, respectively) over approximately 3 months, underscoring switchgrass's effectiveness for BPA removal. Significantly higher (p < 0.005) BPA accumulation in roots than shoots and nonsignificant variances in biomass, chlorophyll (p > 0.19), and peroxidase between BPA-treated and untreated plants indicates substantial BPA tolerance in both varieties. Kinetic parameters of BPA removal and translocation factors were also determined, which will inform the design of BPA removal phytotechnologies for a variety of soil conditions, including landfills where BPA accumulation is greatest.

Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars.

The genetics and responses to biotic stressors of tetraploid switchgrass (Panicum virgatum L.) lowland cultivar 'Kanlow' and upland cultivar Summer are distinct and can be exploited for trait improvement. In general, there is a paucity of data on the basal differences in transcription across tissue developmental times for switchgrass cultivars. Here, the changes in basal and temporal expression of genes related to leaf functions were evaluated for greenhouse grown 'Kanlow', and 'Summer' plants. Three biological replicates of the 4th leaf pooled from 15 plants per replicate were harvested at regular intervals beginning from leaf emergence through senescence. Increases and decreases in leaf chlorophyll and N content were similar for both cultivars. Likewise, multidimensional scaling (MDS) analysis indicated both cultivar-independent and cultivar-specific gene expression. Cultivar-independent genes and gene-networks included those associated with leaf function, such as growth/senescence, carbon/nitrogen assimilation, photosynthesis, chlorophyll biosynthesis, and chlorophyll degradation. However, many genes encoding nucleotide-binding leucine rich repeat (NB-LRRs) proteins and wall-bound kinases associated with detecting and responding to environmental signals were differentially expressed. Several of these belonged to unique cultivar-specific gene co-expression networks. Analysis of genomic resequencing data provided several examples of NB-LRRs genes that were not expressed and/or apparently absent in the genomes of Summer plants. It is plausible that cultivar (ecotype)-specific genes and gene-networks could be one of the drivers for the documented differences in responses to leaf-borne pathogens between these two cultivars. Incorporating broad resistance to plant pathogens in elite switchgrass germplasm could improve sustainability of biomass production under low-input conditions.

Investigations into the use of handheld near-infrared spectrometer and novel semi-automated data analysis for the determination of protein content in different cultivars of Panicum miliaceumL.

A set of 42 millet (panicum miliaceum L.) samples was investigated for its protein content using standard Kjeldahl analysis and near-infrared spectroscopy. The performance of three handheld spectrometers was compared to a benchtop instrument. The used spectrometers operate in different regions of the NIR, which gives interesting insights into the applicability of each region. Additionally, semi-automated, consumer-oriented multivariate data analysis was compared to sophisticated data evaluation. The performance of the near-infrared instruments was compared using important statistical parameters of the established cross- and test set validated partial least squares regression (PLS-R) models. Milled and intact samples were analysed, in order to further evaluate the importance of homogeneity. The results showed that the benchtop spectrometer is capable of accurately analysing protein content of millet grains, with root mean square error (RMSEP) values for milled and intact grains of approximately 0.5%. Two PLS-R models of handheld instruments also yielded good results for milled grains with RMSEP values of about 0.6%. The semi-automated multivariate data analysis showed some drawbacks compared to standard data processing software. For intact grains, however, similar results could be achieved.

Diversity in Accessions of Panicum miliaceum L. Based on Agro-Morphological, Antioxidative, and Genetic Traits.

The genetic diversity and antioxidant potential of Panicum miliaceum L. accessions collected from different geo-ecological regions of South Korea were evaluated and compared. Antioxidant potential of seeds was estimated by the 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulfonic acid (ABTS) radical scavenging assays and total phenolic content was determined by the Folin⁻Ciocalteu method. Total phenolic content (TPC) in 80% methanolic extracts ranged from 16.24 ± 0.86 to 58.04 ± 1.00 mg gallic acid equivalent (GAE)/g of the sample extracts and total flavonoid content (TFC) varied from 7.19 ± 1.05 to 52.56 ± 1.50 mg quercetin equivalents (QE) mg/g of the sample extracts. DPPH radical scavenging capacity of the extracts from the 15 accessions of P. miliaceum varied from 206.44 ± 7.72 to 2490.24 ± 4.641 mg GAE/g of the sample extracts and ABTS radical scavenging capacity ranged from 624.85 ± 13.1 to 1087. 77 ± 9.58 mg GAE/g of the sample extracts. A wide range of genetic variation was observed as measured by Shannon's information index (I), number of effective alleles (Ne), number of observed alleles (Na), expected heterozygosity (He), unbiased expected heterozygosity (uHe). The observed variation in the bioactive properties, morphological traits, and genetic diversity among the accessions may provide useful information for breeding programs seeking to improve bioactive properties of P. miliaceum.

The genome of broomcorn millet.

Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 protein-coding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C4 subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C4 biology.

Chromosome conformation capture resolved near complete genome assembly of broomcorn millet.

Broomcorn millet (Panicum miliaceum L.) has strong tolerance to abiotic stresses, and is probably one of the oldest crops, with its earliest cultivation that dated back to ca. ~10,000 years. We report here its genome assembly through a combination of PacBio sequencing, BioNano, and Hi-C (in vivo) mapping. The 18 super scaffolds cover ~95.6% of the estimated genome (~887.8 Mb). There are 63,671 protein-coding genes annotated in this tetraploid genome. About ~86.2% of the syntenic genes in foxtail millet have two homologous copies in broomcorn millet, indicating rare gene loss after tetraploidization in broomcorn millet. Phylogenetic analysis reveals that broomcorn millet and foxtail millet diverged around ~13.1 Million years ago (Mya), while the lineage specific tetraploidization of broomcorn millet may be happened within ~5.91 million years. The genome is not only beneficial for the genome assisted breeding of broomcorn millet, but also an important resource for other Panicum species.

Fall panicum ( Panicum dichotomiflorum) toxicosis in three juvenile goats.

Consumption of certain grasses belonging to the genus Panicum has been found to cause hepatogenous photosensitization and crystal-associated cholangiohepatopathy in small ruminants, and liver disease in horses, in many areas of the world. We describe herein the clinical findings, microscopic lesions, and steroidal saponin analysis of Panicum dichotomiflorum associated with fatal toxicosis in 3 juvenile goats in Nebraska. The disease presentation in our case was fulminant, with anorexia, marked icterus, and death for all affected animals in less than a week. Photosensitization was not observed. The microscopic lesions consisted of severe crystal-associated cholangiohepatopathy and nephropathy, with aggregates of clear or refractile and birefringent, acicular crystals present within bile ducts, macrophages, hepatocytes, and renal tubules. High-performance liquid chromatography-mass spectrometry of the grass samples demonstrated that dichotomin was the major steroidal saponin present (0.89 µg/mg); protodioscin was also present (0.059 µg/mg). The findings were consistent with ingestion of steroidal saponins, and P. dichotomiflorum was identified as the predominant forage available.

The genomic landscape of molecular responses to natural drought stress in Panicum hallii.

Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory networks are more likely to have opposing effects than expected under neutral evolution, supporting a strong influence of compensatory evolution and stabilizing selection. These results implicate trans-regulatory evolution as a driver of drought responses and demonstrate the potential for crop improvement in drought-prone regions through modification of gene regulatory networks.

Phytolith analysis for differentiating between broomcorn millet (Panicum miliaceum) and its weed/feral type (Panicum ruderale).

Domestication of broomcorn millet (Panicum miliaceum) is one of the most significant events in prehistoric East Asia, providing sufficient food supply for the explosive growth of Neolithic populations and the transition into complex societies. However, to date, the process of broomcorn millet domestication is still largely unknown, partly due to the lack of clear diagnostic tools for distinguishing between millet and its related wild grasses in archaeological samples. Here, we examined the percentage of silicified epidermal long-cell undulated patterns in the glume and palea from inflorescence bracts in 21 modern varieties of broomcorn millet and 12 weed/feral-type Panicum ruderale collected across northern China. Our results show that the percentage of ηIII patterns in domesticated broomcorn millet (23.0% ± 5.9%; n = 63) is about 10% higher than in P. ruderale (10.8% ± 5.8%; n = 36), with quartiles of 17.2-28.3% and 5.1-15.5%, respectively. Owing to the increase in ηIII pattern percentage correlates significantly with a decrease in the grain length/width ratio, in the absence of exact wild ancestors of broomcorn millet, the characterization of phytolith differences between P. ruderale and P. miliaceum thus becomes an alternative approach to provide insight into origin of broomcorn millet.

Genome-wide survey of switchgrass NACs family provides new insights into motif and structure arrangements and reveals stress-related and tissue-specific NACs.

NAC proteins comprise of a plant-specific transcription factor (TF) family and play important roles in plant development and stress responses. Switchgrass (Panicum virgatum) is the prime candidate and model bioenergy grass across the world. Excavating agronomically valuable genes is important for switchgrass molecular breeding. In this study, a total of 251 switchgrass NAC (PvNACs) family genes clustered into 19 subgroups were analyzed, and those potentially involved in stress response or tissue-specific expression patterns were pinpointed. Specifically, 27 PvNACs were considered as abiotic stress-related including four membrane-associated ones. Among 40 tissue-specific PvNACs expression patterns eight factors were identified that might be relevant for lignin biosynthesis and/or secondary cell wall formation. Conserved functional domains and motifs were also identified among the PvNACs and potential association between these motifs and their predicted functions were proposed, that might encourage experimental studies to use PvNACs as possible targets to improve biomass production and abiotic stress tolerance.

Rust fungi on Panicum.

Rusts are economically important diseases of switchgrass (Panicum virgatum) and other Paniceae grasses. Phylogenetic analyses based on sequences of the nuc rDNA 5.8S internal transcribed spacer 2 region (ITS2), partial 28S region, and intergenic spacer region (IGS) of nuc rDNA showed that species of rust fungi infecting switchgrass are closely related within Puccinia. Variation among rbcLa sequences for the associated hosts sampled concurred with the original identifications. Five species infecting switchgrass were recognized: Puccinia graminicola (≡ Uromyces graminicola), P. pammelii (= P. panici), and the proposed new species P. amari, P. novopanici, and P. pascua. These species were distinct from P. emaculata, the species previously considered the principal rust pathogen infecting switchgrass but that was found exclusively on witchgrass (Panicum capillare) in this study. Rust fungi on switchgrass previously identified as P. emaculata were identified as the morphologically similar species P. amari, P. novopanici, and P. pammelii. The morphological species Puccinia graminicola was found to comprise three species, P. graminicola and the proposed new species P. pascua on switchgrass and P. cumminsii on Panicum sp.

Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass.

BACKGROUND: Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield. Despite its importance as a prominent bioenergy crop, a genome-wide comprehensive analysis of NB-LRR disease resistance genes has yet to be performed in switchgrass. RESULTS: In this study, we used a homology-based computational approach to identify 1011 potential NB-LRR resistance gene homologs (RGHs) in the switchgrass genome (v 1.1). In addition, we identified 40 RGHs that potentially contain unique domains including major sperm protein domain, jacalin-like binding domain, calmodulin-like binding, and thioredoxin. RNA-sequencing analysis of leaf tissue from 'Alamo', a rust-resistant switchgrass cultivar, and 'Dacotah', a rust-susceptible switchgrass cultivar, identified 2634 high quality variants in the RGHs between the two cultivars. RNA-sequencing data from field-grown cultivar 'Summer' plants indicated that the expression of some of these RGHs was developmentally regulated. CONCLUSIONS: Our results provide useful insight into the molecular structure, distribution, and expression patterns of members of the NB-LRR gene family in switchgrass. These results also provide a foundation for future work aimed at elucidating the molecular mechanisms underlying disease resistance in this important bioenergy crop.

Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.).

BACKGROUND: WRKY genes, as the most pivotal transcription factors in plants, play the indispensable roles in regulating various physiological processes, including plant growth and development as well as in response to stresses. Broomcorn millet is one of the most important crops in drought areas worldwide. However, the WRKY gene family in broomcorn millet remains unknown. RESULTS: A total of 32 PmWRKY genes were identified in this study using computational prediction method. Structural analysis found that PmWRKY proteins contained a highly conserved motif WRKYGQK and two common variant motifs, namely WRKYGKK and WRKYGEK. Phylogenetic analysis of PmWRKYs together with the homologous genes from the representative species could classify them into three groups, with the number of 1, 15, and 16, respectively. Finally, the transcriptional profiles of these 32 PmWRKY genes in various tissues or under different abiotic stresses were systematically investigated using qRT-PCR analysis. Results showed that the expression level of 22 PmWRKY genes varied significantly under one or more abiotic stress treatments, which could be defined as abiotic stress-responsive genes. CONCLUSIONS: This was the first study to identify the organization and transcriptional profiles of PmWRKY genes, which not only facilitates the functional analysis of the PmWRKY genes, and also lays the foundation to reveal the molecular mechanism of stress tolerance in this important crop.

Genetic Diversity and Population Structure of Broomcorn Millet (Panicum miliaceum L.) Cultivars and Landraces in China Based on Microsatellite Markers.

Broomcorn millet (Panicum miliaceum L.), one of the first domesticated crops, has been grown in Northern China for at least 10,000 years. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, we analyzed the genetic diversity of 88 accessions of broomcorn millet collected from various provinces of China. Amplification with 67 simple sequence repeat (SSR) primers revealed moderate levels of diversity in the investigated accessions. A total of 179 alleles were detected, with an average of 2.7 alleles per locus. Polymorphism information content and expected heterozygosity ranged from 0.043 to 0.729 (mean = 0.376) and 0.045 to 0.771 (mean = 0.445), respectively. Cluster analysis based on the unweighted pair group method of mathematical averages separated the 88 accessions into four groups at a genetic similarity level of 0.633. A genetic structure assay indicated a close correlation between geographical regions and genetic diversity. The uncovered information will be valuable for defining gene pools and developing breeding programs for broomcorn millet. Furthermore, the millet-specific SSR markers developed in this study should serve as useful tools for assessment of genetic diversity and elucidation of population structure in broomcorn millet.

Salvia officinalis L. coverage on plants development / Cobertura de Salvia officinalis L. no desenvolvimento de plantas

ABSTRACT Medicinal plants with essential oils in their composition havetypicallybeen shown to be promising in plant control. Sage (Salvia officinalis L.) is cited for its allelopathic effects. This study evaluated the allelopathic potential of dried sage leaves in vegetation, soil and the development of Lycopersicon esculentum Mill. (tomato), Panicum maximum Jacq. (guinea grass) and Salvia hispanica L. (chia) plants. Three seedlings were transplanted seven days after germination in 1 kg plastic containers with soil, in a greenhouse. The grinded dry mass of sage was placed at rates of 3.75; 7.5 15 t ha-1, and a control (no mass). After 30 days, the chlorophyll index of tomato and guinea grass plants were inhibited with 7.5 and 15 t ha-1 sage cover crops. Tomato shoot length was inhibited in all tested rates, and guinea grass plants showed some reduction in growth when using the highest rate of sage mass (15 t ha-1). The dry mass of tomato and guinea grass plants was reduced when using the15 t ha-1, and 7.5 and 15 t ha-1 of sage cover crops, respectively. It can be concluded that there was some effect of sage coverage on the soil in tomato and guinea grass, but no effect was observed on chia plants.

RESUMO As plantas medicinais que apresentam óleos essenciais em sua composição normalmente têm se mostrado promissoras no controle de plantas. A sálvia (Salvia officinalis L.) é citada por seus efeitos alelopáticos. Assim, esse estudo avaliou o potencial alelopático das folhas secas de sálvia na cobertura vegetal, no solo, sobre o desenvolvimento das plantas de Lycopersicon esculentum Mill. (tomate), Panicum maximum Jacq. (capim mombaça) e Salvia hispanica L. (chia). Três plântulas foram transplantadas, sete dias após germinação, em vasos plásticos de 1 kg, com terra, em casa de vegetação. Sobre elas foi disposta a massa seca triturada de sálvia nas proporções 3,75; 7,5 e 15 t ha-1, além da testemunha (sem massa). Após 30 dias, o teor de clorofila das plantas de tomate e capim mombaça foi inibido com 7,5 e 15 t ha-1 de sálvia em cobertura. O comprimento da parte aérea do tomate foi inibido em todas as proporções testadas e as plantas de capim mombaça apresentaram redução do crescimento quando se utilizou 15 t ha-1 de sálvia como cobertura. A massa seca das plantas de tomate e capim mombaça reduziu com o uso de 15 t ha-1 e, 7,5 e 15 t ha-1 de sálvia como cobertura, respectivamente. Finalmente, pode-se concluir que houve efeito da sálvia em cobertura sobre o solo em tomate e capim mombaça, mas não houve efeito da mesma sobre as plantas de chia.

Diversity and population structure of northern switchgrass as revealed through exome capture sequencing.

Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.