Grass Lineages Research Articles

Genomic and Transcriptomic Insights into the Evolution of C4 Photosynthesis in Grasses.

C4 photosynthesis has independently evolved over 62 times within 19 angiosperm families. The recurrent evolution of C4 photosynthesis appears to contradict the complex anatomical and biochemical modifications required for the transition from C3 to C4 photosynthesis. In this study, we conducted an integrated analysis of genomics and transcriptomics to elucidate the molecular underpinnings of convergent C4 evolution in the grass family. Our genome-wide exploration of C4-related gene families suggests that the expansion of these gene families may have played an important role in facilitating C4 evolution in the grass family. A phylogenomic synteny network analysis uncovered the emergence of C4 genes in various C4 grass lineages from a common ancestral gene pool. Moreover, through a comparison between non-C4 and C4 PEPCs, we pinpointed 14 amino acid sites exhibiting parallel adaptations. These adaptations, occurring post the BEP-PACMAD divergence, shed light on why all C4 origins in grasses are confined to the PACMAD clade. Furthermore, our study revealed that the ancestor of Chloridoideae grasses possessed a more favorable molecular preadaptation for C4 functions compared to the ancestor of Panicoideae grasses. This molecular preadaptation potentially explains why C4 photosynthesis evolved earlier in Chloridoideae than in Panicoideae and why the C3-to-C4 transition occurred once in Chloridoideae but multiple times in Panicoideae. Additionally, we found that C4 genes share similar cis-elements across independent C4 lineages. Notably, NAD-ME subtype grasses may have retained the ancestral regulatory machinery of the C4 NADP-ME gene, while NADP-ME subtype grasses might have undergone unique cis-element modifications.

Interpretable machine learning decodes soil microbiome’s response to drought stress

BackgroundExtreme weather events induced by climate change, particularly droughts, have detrimental consequences for crop yields and food security. Concurrently, these conditions provoke substantial changes in the soil bacterial microbiota and affect plant health. Early recognition of soil affected by drought enables farmers to implement appropriate agricultural management practices. In this context, interpretable machine learning holds immense potential for drought stress classification of soil based on marker taxa.ResultsThis study demonstrates that the 16S rRNA-based metagenomic approach of Differential Abundance Analysis methods and machine learning-based Shapley Additive Explanation values provide similar information. They exhibit their potential as complementary approaches for identifying marker taxa and investigating their enrichment or depletion under drought stress in grass lineages. Additionally, the Random Forest Classifier trained on a diverse range of relative abundance data from the soil bacterial micobiome of various plant species achieves a high accuracy of 92.3 % at the genus rank for drought stress prediction. It demonstrates its generalization capacity for the lineages tested.ConclusionsIn the detection of drought stress in soil bacterial microbiota, this study emphasizes the potential of an optimized and generalized location-based ML classifier. By identifying marker taxa, this approach holds promising implications for microbe-assisted plant breeding programs and contributes to the development of sustainable agriculture practices. These findings are crucial for preserving global food security in the face of climate change.

Convergent and divergent signaling pathways in C3 rice and C4 foxtail millet crops in response to salt stress

Salt stress is a global constraint on agricultural production. Therefore, the development of salt tolerant plants has become a current research hotspot. Salt tolerance evolves more frequently in C4 grass lineages. However, few studies have been carried out to explore the molecular bases underlying salt stress tolerance in C4 crop foxtail millet. In this study, we performed a multi-pronged approach spanning the omics analyses of transcriptomes and physiological analysis of C3 crop rice and C4 model crop foxtail millet in response to salt stress. Our results revealed specifically compared to C3 rice, C4 foxtail millet has upregulated ABA and notably reduced CK biosynthesis and signaling transduction under salt stress. Salt stress in C3 rice plants triggered rapid downregulation of photosynthesis related genes, which was coupled by severely decreased net photosynthetic rates. In the salt-threatened C3 rice and C4 foxtail millet, some stress responsive transcription factors (TFs), such as AP2/ERF, WRKY and MYB underwent strong and distinct transcriptional changes. Based on weighted gene co-expression network analysis (WGCNA), an AP2/ERF transcription factor Rice Starch Regulator1 SiRSR1 (Seita.3G044600) was identified as a key regulator of salt stress response. To confirmed its function, we generated OsRSR1-knockout lines with CRISPR/Cas9 genome editing in rice and its upstream repressor SiMIR172a-overexpressing (172a-OE) transgenic plants in foxtail millet, which increased salt tolerance. Overall, our study not only provided new insights into the convergent regulation of salt stress responses of foxtail millet and rice, but also shed light on the divergent signaling networks between them in response to salt stress.

Grass Evolutionary Lineages Can Be Identified Using Hyperspectral Leaf Reflectance

AbstractHyperspectral remote sensing has the potential to map numerous attributes of the Earth’s surface, including spatial patterns of biological diversity. Grasslands are one of the largest biomes on Earth. Accurate mapping of grassland biodiversity relies on spectral discrimination of endmembers of species or plant functional types. We focused on spectral separation of grass lineages that dominate global grassy biomes: Andropogoneae (C4), Chloridoideae (C4), and Pooideae (C3). We examined leaf reflectance spectra (350–2,500 nm) from 43 grass species representing these grass lineages from four representative grassland sites in the Great Plains region of North America. We assessed the utility of leaf reflectance data for classification of grass species into three major lineages and by collection site. Classifications had very high accuracy (94%) that were robust to site differences in species and environment. We also show an information loss using multispectral sensors, that is, classification accuracy of grass lineages using spectral bands provided by current multispectral satellites is much lower (accuracy of 85.2% and 61.3% using Sentinel 2 and Landsat 8 bands, respectively). Our results suggest that hyperspectral data have an exciting potential for mapping grass functional types as informed by phylogeny. Leaf‐level hyperspectral separability of grass lineages is consistent with the potential increase in biodiversity and functional information content from the next generation of satellite‐based spectrometers.

Biochemical and Structural Diversification of C4 Photosynthesis in Tribe Zoysieae (Poaceae).

C4 photosynthesis has evolved independently multiple times in grass lineages with nine anatomical and three biochemical subtypes. Chloridoideae represents one of the separate events and contains species of two biochemical subtypes, NAD-ME and PEP-CK. Assessment of C4 photosynthesis diversification is limited by species sampling. In this study, the biochemical subtypes together with anatomical leaf traits were analyzed in 19 species to reveal the evolutionary scenario for diversification of C4 photosynthesis in tribe Zoysieae (Chloridoideae). The effect of habitat on anatomical and biochemical diversification was also evaluated. The results for the 19 species studied indicate that 11 species have only NAD-ME as a decarboxylating enzyme, while eight species belong to the PEP-CK subtype. Leaf anatomy corresponds to the biochemical subtype. Analysis of Zoysieae phylogeny indicates multiple switches between PEP-CK and NAD-ME photosynthetic subtypes, with PEP-CK most likely as the ancestral subtype, and with multiple independent PEP-CK decarboxylase losses and its secondary acquisition. A strong correlation was detected between C4 biochemical subtypes studied and habitat annual precipitation wherein NAD-ME species are confined to drier habitats, while PEP-CK species prefer humid areas. Structural adaptations to arid climate include increases in leaf thickness and interveinal distance. Our analysis suggests that multiple loss of PEP-CK decarboxylase could have been driven by climate aridization followed by continued adaptive changes in leaf anatomy.

Allometries of cell and tissue anatomy and photosynthetic rate across leaves of C3 and C4 grasses.

Allometric relationships among the dimensions of leaves and their cells hold across diverse eudicotyledons, but have remained untested in the leaves of grasses. We hypothesised that geometric (proportional) allometries of cell sizes across tissues and of leaf dimensions would arise due to the coordination of cell development and that of cell functions such as water, nutrient and energy transport, and that cell sizes across tissues would be associated with light-saturated photosynthetic rate. We tested predictions across 27 globally distributed C3 and C4 grass species grown in a common garden. We found positive relationships among average cell sizes within and across tissues, and of cell sizes with leaf dimensions. Grass leaf anatomical allometries were similar to those of eudicots, with exceptions consistent with the fewer cell layers and narrower form of grass leaves, and the specialised roles of epidermis and bundle sheath in storage and leaf movement. Across species, mean cell sizes in each tissue were associated with light-saturated photosynthetic rate per leaf mass, supporting the functional coordination of cell sizes. These findings highlight the generality of evolutionary allometries within the grass lineage and their interlinkage with coordinated development and function.

Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage.

Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses. We detect 168 laterally acquired genes in the five reference genomes (32-100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6-28 per Ma) and subsequent losses (11-24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02-0.8% per Ma). This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.

Carbon isotope values for grasses in Madagascar's Central Highlands establish baselines for historical and paleoecological research

Societal Impact StatementGrasses are significant drivers of fires and are the primary food source for cattle in Madagascar's Central Highlands. However, their extent and importance to animals and people in the past remain poorly understood. Clarifying the history of Malagasy grasslands is necessary for building climate resilient food systems and supporting carbon stores that also conserve biodiversity. We generated chemical data for grasses that grow in open habitats in central Madagascar, which will help improve our understanding of the ecological and economic importance of modern grassy ecosystems, reconstruct the regional history of grasses, and anticipate how vegetation may respond to changing climate and rising atmospheric carbon dioxide levels.Summary Stable carbon isotope (δ13C) data for Malagasy grasses are needed to establish expected values for C3 and C4 grasses from particular regions in Madagascar, and possible differences among different grass lineages, or species with different distributions or adaptations. These data, in turn, may help inform how widespread grasses were in the past, and the importance of grasses to endemic and domesticated animals as well as people over time. We analysed both δ13C and weight %C:N from 63 Poaceae species that grow in open grassy biomes in Madagascar's Central Highlands and explored how these values relate to multiple variables, including encounter frequency, distribution, lineage, adaptations to grazing and fire and the typical floral assemblage in which each species occurs. Of the species sampled, 56 are C4 and seven are C3. There are no differences in δ13C or weight %C:N among either C3 or C4 species with different distributions or adaptations, from different assemblages, or that are frequently or infrequently encountered. However, there are differences in both δ13C and weight %C:N among C4 lineages, and the single C3 arundinoid (Styppeiochloa hitchcockii) has larger weight %C:N than C3 Paniceae. Our results provide a foundation for evaluating reliance on C4 resources by people, as well as domesticated and endemic animals both today and in the past. We encourage gathering additional comparative data for co‐occurring individual plants from the same open grassy biome localities, as well as other species, habitats and regions in Madagascar.

Structural diversity in salt excreting glands and salinity tolerance in Oryza coarctata, Sporobolus anglicus and Urochondra setulosa

Unlike the bicellular glands characteristic of all known excreting grasses, unique single-celled salt glands were discovered in the only salt tolerant species of the genus Oryza, Oryza coarctata. Salt tolerance has evolved frequently in a large number of grass lineages with distinct difference in mechanisms. Mechanisms of salt tolerance were studied in three species of grasses characterized by salt excretion: C3 wild rice species Oryza coarctata, and C4 species Sporobolus anglicus and Urochondra setulosa. The leaf anatomy and ultrastructure of salt glands, pattern of salt excretion, gas exchange, accumulation of key photosynthetic enzymes, leaf water content and osmolality, and levels of some osmolytes, were compared when grown without salt, with 200mM NaCl versus 200mM KCl. Under salt treatments, there was little effect on the capacity for CO2 assimilation, while stomatal conductance decreased with a reduction in water loss by transpiration and an increase in water use efficiency. All three species accumulate compatible solutes but with drastic differences in osmolyte composition. Having high capacity for salt excretion, they have distinct structural differences in the salt excreting machinery. S. anglicus and U. setulosa have bicellular glands while O. coarctata has unique single-celled salt glands with a partitioning membrane system that are responsible for salt excretion rather than multiple hairs as previously suggested. The features of physiological responses and salt excretion indicate similar mechanisms are involved in providing tolerance and excretion of Na+ and K+.

Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass.

SUMMARYMomilactone A, an important plant labdane‐related diterpenoid, functions as a phytoalexin against pathogens and an allelochemical against neighboring plants. The genes involved in the biosynthesis of momilactone A are found in clusters, i.e., momilactone A biosynthetic gene clusters (MABGCs), in the rice and barnyardgrass genomes. In addition, we know little about the origin and evolution of MABGCs. Here, we integrated results from comprehensive phylogeny and comparative genomic analyses of the core genes of MABGC‐like clusters and MABGCs in 40 monocot plant genomes, providing convincing evidence for the birth and evolution of MABGCs in grass species. The MABGCs found in the PACMAD clade of the core grass lineage (including Panicoideae and Chloridoideae) originated from a MABGC‐like cluster in Triticeae (BOP clade) via lateral gene transfer (LGT) and followed by recruitment of MAS1/2 and CYP76L1 genes. The MABGCs in Oryzoideae originated from PACMAD through another LGT event and lost CYP76L1 afterwards. The Oryza MABGC and another Oryza diterpenoid cluster c2BGC are two distinct clusters, with the latter originating from gene duplication and relocation within Oryzoideae. Further comparison of the expression patterns of the MABGC genes between rice and barnyardgrass in response to pathogen infection and allelopathy provides novel insights into the functional innovation of MABGCs in plants. Our results demonstrate LGT‐mediated origination of MABGCs in grass and shed lights into the evolutionary innovation and optimization of plant biosynthetic pathways.

Mechanism for the genomic and functional evolution of the MIR2118 family in the grass lineage.

The MIR2118 family has undergone tremendous expansion in the grass lineage, in which the miRNA targets numerous noncoding PHAS loci to produce 21-nt phased small interfering RNAs (phasiRNAs) involved in male fertility. However, the evolutionary trajectory of the grass MIR2118 genes and the functions of phasiRNAs have not yet been fully elucidated. We conducted comparative genomic, molecular evolution, expression and parallel analysis of RNA ends (PARE) analyses of MIR2118 and the miR2118-mediated regulatory pathway in grasses, focusing on Oryza sativa. In total, 617 MIR2118 and eight MIR1859 novel members were identified. Phylogenetic analyses showed that grass MIR2118 genes form a distinct clade from the MIR482/2118 genes of nongrass species. We reconstructed hypothetical evolutionary histories of the grass MIR2118 clusters and its MIR1859 variants, and examined the polycistronic composition and the differential expression of the osa-MIR2118 clusters. PARE data showed that osa-miR2118 might also direct the cleavage of some protein-coding gene transcripts. Importantly, we found that PARE analysis is inherently prone to false-positive target predictions when a large number of small RNAs, such as phasiRNAs, are analysed. Our results revealed the evolution and diversification of the MIR2118 family, and provide new insights into the functions of phasiRNAs in the grasses.

New Genes Interacted With Recent Whole-Genome Duplicates in the Fast Stem Growth of Bamboos.

As drivers of evolutionary innovations, new genes allow organisms to explore new niches. However, clear examples of this process remain scarce. Bamboos, the unique grass lineage diversifying into the forest, have evolved with a key innovation of fast growth of woody stem, reaching up to 1 m/day. Here, we identify 1,622 bamboo-specific orphan genes that appeared in recent 46 million years, and 19 of them evolved from noncoding ancestral sequences with entire de novo origination process reconstructed. The new genes evolved gradually in exon−intron structure, protein length, expression specificity, and evolutionary constraint. These new genes, whether or not from de novo origination, are dominantly expressed in the rapidly developing shoots, and make transcriptomes of shoots the youngest among various bamboo tissues, rather than reproductive tissue in other plants. Additionally, the particularity of bamboo shoots has also been shaped by recent whole-genome duplicates (WGDs), which evolved divergent expression patterns from ancestral states. New genes and WGDs have been evolutionarily recruited into coexpression networks to underline fast-growing trait of bamboo shoot. Our study highlights the importance of interactions between new genes and genome duplicates in generating morphological innovation.

Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae).

The bamboos (Bambusoideae, Poaceae) comprise a major grass lineage with a complex evolutionary history involving ancient hybridization and allopolyploidy. About 1700 described species are classified into three tribes, Olyreae (herbaceous bamboos), Bambuseae (tropical woody bamboos), and Arundinarieae (temperate woody bamboos). Nuclear analyses strongly support monophyly of the woody tribes, whereas plastome analyses strongly support paraphyly, with Bambuseae sister to Olyreae. Our objectives were to clarify the origin(s) of the woody bamboo tribes and resolve the nuclear vs. plastid conflict using genomic tools. For the first time, plastid and nuclear genomic information from the same bamboo species were combined in a single study. We sampled 51 species of bamboos representing the three tribes, estimated their genome sizes and generated low-depth sample sequence data, from which plastomes were assembled and nuclear repeats were analyzed. The distribution of repeat families was found to agree with nuclear gene phylogenies, but also provides novel insights into nuclear evolutionary history. We infer two early, independent hybridization events, one between an Olyreae ancestor and a woody ancestor giving rise to the two Bambuseae lineages, and another between two woody ancestors giving rise to the Arundinarieae. Retention of the Olyreae plastome associated with differential dominance of nuclear genomes and subsequent diploidization in some lineages explains the paraphyly observed in plastome phylogenetic estimations. We confirm ancient hybridization and allopolyploidy in the origins of the extant woody bamboo lineages and propose biased fractionation and diploidization as important factors in their evolution.

The Genetic Control of Stomatal Development in Barley: New Solutions for Enhanced Water-Use Efficiency in Drought-Prone Environments

Increased drought frequency due to climate change is limiting the agronomic performance of cereal crops globally, where cultivars often experience negative impacts on yield. Stomata are the living interface responsible for >90% of plant water loss through transpiration. Thus, stomata are a prospective target for improving drought tolerance by enhancing water-use efficiency (WUE) in economically important cereals. Reducing stomatal density through molecular approaches has been shown to improve WUE in many plant species, including the commercial cereals barley, rice, wheat and maize. Rice with reduced stomatal density exhibit yields 27% higher than controls under drought conditions, reflecting the amenability of grasses to stomatal density modification. This review presents a comprehensive overview of stomatal development, with a specific emphasis on the genetic improvement of WUE in the grass lineage. Improved understanding of the genetic regulation of stomatal development in the grasses, provides significant promise to improve cereal adaptivity in drought-prone environments whilst maximising yield potential. Rapid advances in gene-editing and ‘omics’ technologies may allow for accelerated adaption of future commercial varieties to water restriction. This may be achieved through a combination of genomic sequencing data and CRISPR-Cas9-directed genetic modification approaches.

International Association for Plant Taxonomy 2021 Stebbins Medal

Luke T. Dunning, Jill K. Olofsson, Christian Parisod, Rimjhim R. Choudhury, Jose J. Moreno-Villena, Yang Yang, Jacqueline Dionora, W. Paul Quick, Minkyu Park, Jeffrey L. Bennetzen, Guillaume Besnard, Patrik Nosil, Colin P. Osborne & Pascal-Antoine Christin. 2019. Lateral transfers of large DNA fragments spread functional genes among grasses. Proc. Natl. Acad. Sci. U.S.A. 116(10): 4416–4425. https://www.pnas.org/content/116/10/4416.short The Stebbins Medal was first awarded in 2003 in honour of the American botanist and geneticist George Ledyard Stebbins (1906–2000), one of the world's leading plant evolutionary biologists of the 20th century. The medal is awarded biennially by IAPT for an outstanding paper in phylogenetic systematics and evolution of plants. The 2021 award considered papers published in 2018 and 2019. In their paper, Dunning & al. presented the most thorough and far-reaching study to date that convincingly demonstrates extensive lateral gene transfer (LGT) in plants. By comparing genomes of many grasses, they showed that large blocks of DNA containing functional genes are laterally passed among species that are distantly related across the grass phylogeny. Through stringent phylogenomic analyses, they discovered 59 LGTs clustered on 23 laterally acquired genomic fragments that are up to 170 kb long in the genome of the grass Alloteropsis semialata (R.Br.) Hitchc., involving at least nine different donor species. They also showed that some of these laterally transferred genes have added functions to the recipient species genomes. This suggests that LGT represents a potent evolutionary force capable of spreading functional genes among distantly related lineages of grasses. Luke Dunning (Fig. 1), the first author of the 2021 Stebbins Medal paper, studied for his Bachelor's Degree at Cardiff University, Wales, United Kingdom and his Ph.D. at the University of Auckland in New Zealand. Since October 2020, he holds a Natural Environment Research Council (NERC) Independent Research Fellowship in the Department of Animal and Plant Sciences at the University of Sheffield, U.K. Previously, he worked as a postdoctoral researcher with Pascal-Antoine Christin, the senior author of the winning paper, also at the University of Sheffield. Luke's work focuses on the genomics of rapid adaptation in grasses and combines cutting-edge genomic techniques, comparative analyses and experimental approaches to understand how organisms adapt to their environment (https://dunning-lab.group.shef.ac.uk). Many congratulations to Luke Dunning and colleagues! The Stebbins Award committee comprises Paula Rudall (U.K.), Loren Rieseberg (Canada) and Colin Hughes, Chair (Switzerland). The IAPT Council is grateful to the committee for their hard work in making this outstanding selection.

Seeing the forest for the trees-and the grasses: revisiting the evidence for grazer-maintained grasslands in Madagascar's Central Highlands.

Seeing the forest for the trees-and the grasses: revisiting the evidence for grazer-maintained grasslands in Madagascar's Central Highlands.

Evolutionary dynamics of transposable elements and satellite DNAs in polyploid Spartina species

Repeated sequences and polyploidy play a central role in plant genome dynamics. Here, we analyze the evolutionary dynamics of repeats in tetraploid and hexaploid Spartina species that diverged during the last 10 million years within the Chloridoideae, one of the poorest investigated grass lineages. From high-throughput genome sequencing, we annotated Spartina repeats and determined what sequence types account for the genome size variation among species. We examined whether differential genome size evolution correlated with ploidy levels and phylogenetic relationships. We also examined the tempo of repeat sequence dynamics associated with allopatric speciation over the last 3–6 million years between hexaploid species that diverged on the American and European Atlantic coasts and tetraploid species from North and South America. The tetraploid S. spartinae, whose phylogenetic placement has been debated, exhibits a similar repeat content as hexaploid species, suggesting common ancestry. Genome expansion or contraction resulting from repeat dynamics seems to be explained mostly by the contrasting divergence times between species, rather than by genome changes triggered by ploidy level change per se. One 370 bp satellite may be exhibiting ‘meiotic drive’ and driving chromosome evolution in S. alterniflora. Our results provide crucial insights for investigating the genetic and epigenetic consequences of such differential repeat dynamics on the ecology and distribution of the meso- and neopolyploid Spartina species.

Biosynthesis and Emission of Stress-Induced Volatile Terpenes in Roots and Leaves of Switchgrass (Panicum virgatum L.).

Switchgrass (Panicum virgatum L.), a perennial C4 grass, represents an important species in natural and anthropogenic grasslands of North America. Its resilience to abiotic and biotic stress has made switchgrass a preferred bioenergy crop. However, little is known about the mechanisms of resistance of switchgrass against pathogens and herbivores. Volatile compounds such as terpenes have important activities in plant direct and indirect defense. Here, we show that switchgrass leaves emit blends of monoterpenes and sesquiterpenes upon feeding by the generalist insect herbivore Spodoptera frugiperda (fall armyworm) and in a systemic response to the treatment of roots with defense hormones. Belowground application of methyl jasmonate also induced the release of volatile terpenes from roots. To correlate the emission of terpenes with the expression and activity of their corresponding biosynthetic genes, we identified a gene family of 44 monoterpene and sesquiterpene synthases (mono- and sesqui-TPSs) of the type-a, type-b, type-g, and type-e subfamilies, of which 32 TPSs were found to be functionally active in vitro. The TPS genes are distributed over the K and N subgenomes with clusters occurring on several chromosomes. Synteny analysis revealed syntenic networks for approximately 30–40% of the switchgrass TPS genes in the genomes of Panicum hallii, Setaria italica, and Sorghum bicolor, suggesting shared TPS ancestry in the common progenitor of these grass lineages. Eighteen switchgrass TPS genes were substantially induced upon insect and hormone treatment and the enzymatic products of nine of these genes correlated with compounds of the induced volatile blends. In accordance with the emission of volatiles, TPS gene expression was induced systemically in response to belowground treatment, whereas this response was not observed upon aboveground feeding of S. frugiperda. Our results demonstrate complex above and belowground responses of induced volatile terpene metabolism in switchgrass and provide a framework for more detailed investigations of the function of terpenes in stress resistance in this monocot crop.

Molecular Dissection of Quantitative Variation in Bermudagrass Hybrids (Cynodon dactylon x transvaalensis): Morphological Traits.

Bermudagrass (Cynodon (L.)) is the most important warm-season grass grown for forage or turf. It shows extensive variation in morphological characteristics and growth attributes, but the genetic basis of this variation is little understood. Detection and tagging of quantitative trait loci (QTL) affecting above-ground morphology with diagnostic DNA markers would provide a foundation for genetic and molecular breeding applications in bermudagrass. Here, we report early findings regarding genetic architecture of foliage (canopy height, HT), stolon (stolon internode length, ILEN and length of the longest stolon LLS), and leaf traits (leaf blade length, LLEN and leaf blade width, LW) in 110 F1 individuals derived from a cross between Cynodon dactylon (T89) and C. transvaalensis (T574). Separate and joint environment analyses were performed on trait data collected across two to five environments (locations, and/or years, or time), finding significant differences (P < 0.001) among the hybrid progeny for all traits. Analysis of marker-trait associations detected 74 QTL and 135 epistatic interactions. Composite interval mapping (CIM) and mixed-model CIM (MCIM) identified 32 main effect QTL (M-QTL) and 13 interacting QTL (int-QTL). Colocalization of QTL for plant morphology partially explained significant correlations among traits. M-QTL qILEN-3-2 (for ILEN; R2 = 11–19%), qLLS-7-1 (for LLS; R2 = 13–27%), qLEN-1-1 (for LLEN; R2 = 10–11%), and qLW-3-2 (for LW; R2 = 10–12%) were ‘stable’ across multiple environments, representing candidates for fine mapping and applied breeding applications. QTL correspondence between bermudagrass and divergent grass lineages suggests opportunities to accelerate progress by predictive breeding of bermudagrass.

Grass habitat analysis and phytolith-based quantitative reconstruction of Asian monsoon climate change in the sand-loess transitional zone, northern China

AbstractWe investigated climate niches of grasses at regional scales and quantitatively reconstruct Asian monsoon precipitation at the sand-loess transitional zone in northern China. Our results provide direct evidence that certain grass lineages have been specialized in specific habitats: Pooideae grasses stand out and occupy a much cooler environment than all other subfamilies; Pooideae, Aristidoideae, and Chloridoieae occupy dry environments. Pooideae grasses occupy the coldest and driest environments compared to all other subfamilies, with a mean annual temperature (MAT) and precipitation (MAP) of ~13.6 to ~15.3°C and 224 to ~1674 mm, respectively, at a regional scale. We built a database for grasses and their corresponding climate parameters. Based on this database, past climate parameters at the margin of the Asian summer monsoon since ~70 ka were quantitatively reconstructed by phytolith assemblages. They show that this area was dominated by cold- and dry-adapted grasses since ~70 ka with a MAT and MAP of ~3.3 to ~11.0 °C and ~442 to ~900 mm, respectively, generally consistent with the results of phytolith-based transfer function reconstructions and with the results of previous nearby pollen-based quantitative reconstructions. With the improvement of the species-climate and ecosystem dataset, our database-based method is a promising quantitative reconstruction approach to past climatic change in the monsoon region.