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Methyl jasmonate (MeJA) induces various defence responses in seed plants, but for early plant lineages, information on the potential of jasmonates to elicit stress signalling and trigger physiological modifications is limited. The spikemoss Selaginella martensii was exposed to a range of MeJA concentrations (0, 10, 25, and 50 mM), and biogenic volatile organic compound (BVOC) emissions, photosynthetic rate (A), and stomatal conductance (gs) were continuously measured. In addition, changes in phytohormone concentrations and gene expression were studied. Enhancement of methanol, lipoxygenase pathway volatiles and linalool emissions, and reductions in A and gs, were MeJA dose-dependent. Before MeJA treatment, the concentration of 12-oxo-phytodienoic acid (OPDA) was 7-fold higher than jasmonic acid (JA). MeJA treatment rapidly increased OPDA and JA concentrations (within 30 min), with the latter more responsive. Some genes involved in BVOC biosynthesis and OPDA-specific response were up-regulated at 30 min after MeJA spraying, whereas those in the JA signalling pathway were not affected. Although JA was synthesized in S. martensii, OPDA was prioritized as a signalling molecule upon MeJA application. MeJA inhibited primary and enhanced secondary metabolism; we propose that fast-emitted linalool could serve as a marker of elicitation of stress-induced metabolism in lycophytes.

Adjustable stomatal pores in leaves control the balance between CO2entry for photosynthesis and water loss via transpiration. The drought and low humidity-induced phytohormone abscisic acid (ABA) is the major regulator of active stomatal closure responses in angiosperms. Whether the ABA signalling pathway for stomatal closure functions similarly in older land plant groups, such as lycophytes and ferns, is still unclear: some studies find no stomatal ABA response in ferns, others find that ABA response is present or triggered by specific environmental conditions. Here we analysed steady-state gas-exchange, stomatal density and stomatal response to exogenously applied ABA in nine fern species grown from spores under controlled growth conditions. We find that ABA responses in ferns are species-specific: stomata in four out of nine species closed in response to ABA. The ABA-sensitive species mostly had slow responses of low magnitude, suggesting reduced ABA-sensitivity of ABA signalling pathway in ferns. Species with larger stomatal conductance tended to close stomata in response to ABA, whereas a relatively strong response of ~35% was also found inCyrtomium falcatum, a fern with low stomatal conductance. Our results show that ferns constitute a diverse group with varying degree of stomatal ABA-sensitivity. Further characterisation of ABA signalling pathway components in diverse fern species is needed to understand the genetic basis for the variable ABA-sensitivity in ferns.

The NAC (NAM, ATAF1/2, and CUC2) family is a group of plant-specific transcription factors that have vital roles in the growth and development of plants, and especially in fruit and kernel development. This study aimed to identify members of the NAC gene (PsNACs) family and investigate their functions in siberian apricot (Prunus sibirica). A total of 102 predicted PsNAC proteins (PsNACs) were divided into 14 clades and the genes were mapped to the eight chromosomes in siberian apricot. The PsNACs of the same clade had similar structures. A synteny analysis showed that the PsNACs had close relationships with the NAC genes of japanese apricot (Prunus mume). An expression pattern analysis of the PsNACs revealed many differences in various tissues and at different stages of fruit and kernel development. All eight PsNACs in clade XI have crucial roles in fruit and kernel development. Seven PsNACs (PsNACs 18, 64, 23, 33, 9, 4, and 50) in clades I, III, VI, VII, and XIII are related to fruit development. Eight PsNACs (PsNACs 6, 13, 46, 51, 41, 67, 37, and 59) in clades I, II, V, VIII, and XIII are involved in fruit ripening. Five PsNACs (PsNACs 6, 94, 41, 32, and 17) in clades I, IV, V, VII, and XI regulated the rapid growth of the kernel. Four PsNACs (PsNACs 50, 4, 67, and 84) in clades I, III, V, and XIII affected the hardening of the kernel. Four PsNACs (PsNACs 17, 82, 13, and 51) in clades II, XI, and IX acted on kernel maturation. We have characterized the NAC genes in siberian apricot during this study. Our results will provide resources for future research of the biological roles of PsNACs in fruit and kernel development in siberian apricot.

Fruit size is one of the essential quality traits and influences the economic value of apricots. To explore the underlying mechanisms of the formation of differences in fruit size in apricots, we performed a comparative analysis of anatomical and transcriptomics dynamics during fruit growth and development in two apricot cultivars with contrasting fruit sizes (large-fruit Prunus armeniaca ‘Sungold’ and small-fruit P. sibirica ‘F43’). Our analysis identified that the difference in fruit size was mainly caused by the difference in cell size between the two apricot cultivars. Compared with ‘F43’, the transcriptional programs exhibited significant differences in ‘Sungold’, mainly in the cell expansion period. After analysis, key differentially expressed genes (DEGs) most likely to influence cell size were screened out, including genes involved in auxin signal transduction and cell wall loosening mechanisms. Furthermore, weighted gene co-expression network analysis (WGCNA) revealed that PRE6/bHLH was identified as a hub gene, which interacted with 1 TIR1, 3 AUX/IAAs, 4 SAURs, 3 EXPs, and 1 CEL. Hence, a total of 13 key candidate genes were identified as positive regulators of fruit size in apricots. The results provide new insights into the molecular basis of fruit size control and lay a foundation for future breeding and cultivation of larger fruits in apricot.

Background Prunus pedunculata Pall, the deciduous shrub of Amygdalus subgenus in Rosaceae, is a new kind of desert oil-bearing tree. It has a long story of being planted in the West and North of China for sand fixation and desert control. In addition, the seeds of P. pedunculata are rich of oil, especially the monounsaturated fatty acid and polyunsaturated fatty acid. However, little is known about the molecular mechanisms of oil accumulation during the seed development of P. pedunculata. Results The seeds of P. pedunculata from three independent plants at 10, 18, 24, 31, 39, 45, 59 and 73 days after flowering (DAF) were obtained and the oil compositions were evaluated. It showed that oleic acid was the dominant type of oil content in the mature seeds (from 32.724% at 10DAF to 72.06% at 73DAF). Next, transcriptome sequencing for the developing seeds produced 988.795 million high quality reads and TRINITY assembled 326,271 genes for the first transcriptome for P. pedunculata. After the assembled transcriptome was evaluated by BUSCO with 85.9% completeness, we identified 195,342, 109,850 and 121,897 P. pedunculata genes aligned to NR, GO and KEGG pathway databases, respectively. Then, we predicted 23,229 likely proteins from the assembled transcriptome and identified 1917 signal peptides and 5512 transmembrane related proteins. In the developing seeds we detected 91,362 genes (average FPKM > 5) and correlation analysis indicated three possible development stages – early (10 ~ 24DAF), middle (31 ~ 45DAF) and late (59 ~ 73DAF). We next analyzed the differentially expressed genes (DEGs) in the developing seeds. Interestingly, compared to 10DAF the number of DEGs was increased from 4406 in 18DAF to 27,623 in 73DAF. Based on the gene annotation, we identified 753, 33, 8 and 645 DEGs related to the fatty acid biosynthesis, lipid biosynthesis, oil body and transcription factors. Notably, GPAT, DGD1, LACS2, UBC and RINO were highly expressed at the early development stage, ω6-FAD, SAD, ACP, ACCA and AHG1 were highly expressed at the middle development stage, and LACS6, DGD1, ACAT1, AGPAT, WSD1, EGY2 and oleosin genes were highly expressed at the late development stage. Conclusions This is the first time to study the developing seed transcriptome of P. pedunculata and our findings will provide a valuable resource for future studies. More importantly, it will improve our understanding of molecular mechanisms of oil accumulation in P. pedunculata.

In present study, we identified the members of small auxin-up RNA (SAUR) gene family in Prunus sibirica (P. sibirica) and analyzed their localization, phylogeny, duplication, cis-elements in the promoter, and expression patterns. In total, 57 PsSAURs were identified, randomly distributed along eight chromosomes. Among them, eight and ten pairs of segmentally duplicated genes and tandem duplication genes were found in 13 and 21 PsSAURs, respectively. Phylogenetic analysis indicated that the PsSAURs were divided into five groups (Group A-E). Light-responsive cis-elements, methyl jasmonate, abscisic acid, salicylic acid, and gibberellin, as well as low-temperature responsiveness, and defense and stress responsiveness were identified by analyzing PsSAURs promoter sequences. Expression pattern analysis showed that PsSAURs had different tissue and stage expression patterns. This study provided a foundation for further investigations for the functional analyses of SAURs in P. sibirica.

Background Apricot is cultivated worldwide because of its high nutritive content and strong adaptability. Its flesh is delicious and has a unique and pleasant aroma. Apricot kernel is also consumed as nuts. The genome of apricot has been sequenced, and the transcriptome, resequencing, and phenotype data have been increasely generated. However, with the emergence of new information, the data are expected to integrate, and disseminate. Results To better manage the continuous addition of new data and increase convenience, we constructed the apricot genomic and phenotypic database (AprGPD, http://apricotgpd.com). At present, AprGPD contains three reference genomes, 1692 germplasms, 306 genome resequencing data, 90 RNA sequencing data. A set of user-friendly query, analysis, and visualization tools have been implemented in AprGPD. We have also performed a detailed analysis of 59 transcription factor families for the three genomes of apricot. Conclusion Six modules are displayed in AprGPD, including species, germplasm, genome, variation, product, tools. The data integrated by AprGPD will be helpful for the molecular breeding of apricot.

Prunus mira, an important economic fruit crop and ancestral peach species, is widely distributed along the Yarlung Zangbo Grand Canyon and tributary basins in the Tibetan plateau. Due to infrastructure construction and deforestation, natural habitat of P. mira has been severely damaged, leading to reduction in its distribution range and population size and it is listed as a critically endangered species in China’s list of National Key Protected Wild Plants. In this study, 85 novel single nucleotide polymorphism (SNP) markers were developed based on restriction-site associated DNA sequencing. The minor allele frequency, observed heterozygosity, and expected heterozygosity ranged from 0.064 to 0.748, 0.086 to 0.846, and 0.126 to 0.562, respectively. The PIC ranged from 0.117 to 0.423. Ten loci showed significant deviations from the Hardy–Weinberg equilibrium after Bonferroni correction (p

Armeniaca sibirica L. (Rosaceae) was once an economically important species in China, but the amount of natural germplasm of A. sibirica recently declined dramatically as a consequence of habitat fragmentation and overharvesting; this species has now been listed as endangered in the China Plant Red Data Book. In this study, 72 polymorphic single nucleotide polymorphism (SNP) markers were developed in A. sibirica based on its transcriptome and characterized by genotyping 70 individuals using the SNaPshot method. The minor allele frequency varied from 0.102 to 0.516, and the observed heterozygosity, expected heterozygosity, and polymorphism information content ranged from 0.052 to 0.649, 0.186 to 0.617, and 0.105 to 0.452, respectively. Among these SNPs, seven loci deviated significantly from the Hardy–Weinberg equilibrium after Bonferroni correction (p

Siberian apricot (Prunus sibirica L.) is a traditional nut tree species in East Asia and Siberia and is a possible contribution to healthy diets. However, it has attracted little research attention and information on the nutritional value of its kernel is limited. In this study, the profile, nutritional value and variation of amino acids were investigated in eight provenances. The kernels contained 29 × 10−2 g/g protein and were rich in glutamic acid (26.5%), aspartic acid (11.3%) and arginine (10.1%). They showed higher essential amino acids (EAA) than similar protein values for almonds. The variation coefficients of amino acids ranged from 3.8 to 43.7%, and the levels of seven amino acids were significantly different among the eight provenances. The proportion of essential amino acids to total amino acids and amino acid score were also quite different. Protein was negatively correlated with some amino acids and protein quality values. In conclusion, there were two superior provenances (Wanjiagou and Horinger County) with high EAA contents and protein quality, and could be used in the large-scale development of this species.

In this chapter, we continue to focus on the on the rotation invariance of Uniform LSP in the identification of Gramineous Grass Seeds. Fusing with GLCM, the texture characteristics of grass seeds to identify the seeds whose color, shape, sizeand other characteristics are very similar can be extracted.

The research of grassland digitalization is to manage grassland information in a digital mode. The purpose of designing and implementation of a digital platform of grassland and forage is to provide a public communication path for scientific researchers, grassland workers.

The classical plant classification is mainly based on the external morphology of plants, taking advantages of simple observation tools, the experts analyze and compare plants indoors or in the field for their similarity and variability.

When we focus on seed identification and quality assessment of forage, it is interesting to note that similar seeds, especially in some closely species of the same family (genus), are hard to be identified correctly, even for the experts.

Image mosaic is originated from human photography knowledge. When the camera's field is smaller than that of human, people will naturally consider splicing multiple photos into a large one for a broader field. However, due to technical and cost constraints, e.g. hardware equipment.

In this chapter, we investigated the seed identification for gramineous grass with an approach integrated LSP and LDA to extract the textural features as the input of supervised classification for automatic seed identification of gramineous grass.

Prunus mira Koehne belonging to family Rosaceae, is an indigenous species distributed in Tibet, China. De novo assembly with low coverage whole genome sequencing data facilitated to generate the complete chloroplast (cp) genome of P. mira in this study. The genome was a circular DNA molecule with 158,153 bp in length. It exhibited a typical quadripartite structure comprising a large single-copy region (LSC, 86,319 bp), a small single-copy region (SSC, 19,022 bp) and a pair of inverted repeat regions (IRs, 26,406 bp each). A total of 112 genes were predicted, which included 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis indicated that P. mira was the most ancestral and basal lineage within the subgenus Amygdalus (Prunoideae subfamily), which is conform to the traditional classification.

Background Bud dormancy in deciduous fruit trees enables plants to survive cold weather. The buds adopt dormant state and resume growth after satisfying the chilling requirements. Chilling requirements play a key role in flowering time. So far, several chilling models, including ≤ 7.2 °C model, the 0–7.2 °C model, Utah model, and Dynamic Model, have been developed; however, it is still time-consuming to determine the chilling requirements employing any model. This calls for efficient tools that can analyze data. Results In this study, we developed novel software Chilling and Heat Requirement (CHR), by flexibly integrating data conversions, model selection, calculations, statistical analysis, and plotting. Conclusion CHR is a tool for chilling requirements estimation, which will be very useful to researchers. It is very simple, easy, and user-friendly.

Body size parameters of sheep can reflect its growth development, production performance and genetic characteristics. Therefore, the body size measurement is great significance in sheep breeding. In this study, a measuring method based on vision image analysis for the body size of sheep is proposed, which can be practically applied in farm environment without disturbing the animals. This approach is based on computer-assisted visual image capture in a position-limit apparatus, and based on an automatic foreground area extraction algorithm known as simple linear iterative clustering (SLIC) SuperPixels and Fuzzy c-means (FCM) clustering, a center line of flexible symmetrical body extraction algorithms, as well as measuring points extraction algorithms. The test results for 27 small-tailed Han sheep chosen randomly from herd show that the method for foreground extraction can get segmentation images with well-remained boundaries. Detection algorithm of the center line of sheep body in top view has a relatively high adaptability. The extraction of measurement points in different postures for sheep's body size has a better stability and accuracy, the maximum average relative errors between the detected and measured values of body height, rump height, body length, chest depth, chest width and rump width are 1.13%, 1.54%, 2.03%, 4.45%, 2.25% and 2.41%, respectively. The use of both left view and right view can improve the precision of the measurement, and the values from one test may have a greater deviation from the actual values due to the variety of sheep body posture, but the accuracy can be improved by averaging the measurements repeated for many times. The results also show that measurement of sheep size based on vision image analysis is feasible, and it can ensure accuracy, reduce workload and sheep stress compared to the method conducted by man. Prediction result of live-sheep weight based on body size shown that the parameters got by image processing can be used for monitoring the growth of sheep.

Increasing evidence indicates that long non-coding RNAs (lncRNAs) play pivotal roles in regulatory networks controlling plant and animal gene expression. However, lncRNA roles in regulating rubber biosynthesis in Eucommia ulmoides, an emerging source of natural rubber (Eu-rubber), are currently unknown. Here, we report on RNA deep-sequencing of E. ulmoides fruits at two developmental stages. Based on application of a stringent pipeline, 29,103 lncRNAs and 9,048 transcripts of uncertain coding potential (TUCPs) were identified. Two differentially expressed (DE) TUCPs appear to simultaneously regulate 12 protein-coding genes involved in Eu-rubber biosynthesis (GIEBs), as well as 95 DE genes. Functional categorization of these 95 DE genes indicated their involvement in subcellular microstructures and cellular processes, such as cell wall, cell division, and growth. These DE genes may participate in the differentiation and development of laticifers, where Eu-rubber is synthesized. A model is proposed in which "commanders" (DE TUCPs) direct the "builders" (DE genes) to construct a "storehouse" of materials needed for Eu-rubber synthesis, and the "workers" (GIEBs) to synthesize Eu-rubber. These findings provide insights into both cis- and trans-polyisoprene biosynthesis in plants, laying the foundation for additional studies of this crucial process.

Eucommia ulmoides, also called hardy rubber tree, is an economically important tree; however, the lack of its genome sequence restricts the fundamental biological research and applied studies of this plant species. Here, we present a high-quality assembly of its ∼1.2-Gb genome (scaffold N50 = 1.88 Mb) with at least 26 723 predicted genes for E. ulmoides, the first sequenced genome of the order Garryales, which was obtained using an integrated strategy combining Illumina sequencing, PacBio sequencing, and BioNano mapping. As a sister taxon to lamiids and campanulids, E. ulmoides underwent an ancient genome triplication shared by core eudicots but no further whole-genome duplication in the last ∼125 million years. E. ulmoides exhibits high expression levels and/or gene number expansion for multiple genes involved in stress responses and the biosynthesis of secondary metabolites, which may account for its considerable environmental adaptability. In contrast to the rubber tree (Hevea brasiliensis), which produces cis-polyisoprene, E. ulmoides has evolved to synthesize long-chain trans-polyisoprene via farnesyl diphosphate synthases (FPSs). Moreover, FPS and rubber elongation factor/small rubber particle protein gene families were expanded independently from the H. brasiliensis lineage. These results provide new insights into the biology of E. ulmoides and the origin of polyisoprene biosynthesis.

We used RNA sequencing to identify differentially expressed genes that improve our understanding of the salt stress response in Eucommia ulmoides. The native Chinese species Eucommia ulmoides is an economically important plant that grows in a wide range of conditions, including under salt stress. However, little is known about the genes and underlying molecular mechanisms involved in their salt stress response. The objective of this study was to investigate changes in the E. ulmoides transcriptome under salt stress. Four sequencing libraries were obtained from the control and salt stress (150 mM NaCl for 24 h) groups using Illumina HiSeq 2000. Approximately 181,071,150 clean reads were assembled de novo into 107,207 unigenes with an N50 length of 1032 bp. Among 437 differentially expressed genes (DEGs) between the control and salt stress group, 214 DEGs were upregulated and 223 DEGs were downregulated. Quantitative real-time PCR showed that DEG expression profiles were consistent with those from RNA sequencing. Functional annotation analysis indicated that many DEGs could be involved in signal transduction, ion transport, osmotic regulation and reactive oxygen species scavenging. Furthermore, 79 transcription factor families in 1590 unigenes and 32,646 simple sequence repeats (SSR) in 24,582 unigenes were identified. Overall, this study provided new insights into the molecular mechanisms that control salt stress response in E. ulmoides.

Eucommia ulmoides Oliver is a woody perennial dioecious species native to China and has great economic value. However, little is known about flower bud development in this species. In this study, the transcriptomes of female and male flower buds were sequenced using the Illumina platform, a next-generation sequencing technology that provides cost-effective, highly efficient transcriptome profiling. In total, 11,558,188,080 clean reads were assembled into 75,065 unigenes with an average length of 1011bp by de novo assembly using Trinity software. Through similarity comparisons with known protein databases, 47,071 unigenes were annotated, 146 of which were putatively related to the floral development of E. ulmoides. Fifteen of the 146 unigenes had significantly different expression levels between the two samples. Additionally, 24,346 simple sequence repeats were identified in 18,565 unigenes with 12,793 sequences suitable for the designed primers. In total, 67,447 and 58,236 single nucleotide polymorphisms were identified in male and female buds, respectively. This study provides a valuable resource for further conservation genetics and functional genomics research on E. ulmoides.

The Ussurian pear is the most important cultivated pear in the northern part of China. Cultivated Ussurian pears are considered to have derived from Pyrus ussuriensis Maxim. which is native to the northeast of China. In Japan, two varieties of P. ussuriensis, P. ussuriensis var. aromatica and var. hondoensis are native to the northern area and the central area of the main island respectively. In order to reveal the origin of Pyrus ussuriensis var. aromatica distributed in the northern area of main island of Japan, more than 40 explorations have been performed in Japan and in China, and more than 30 natural habitats were recognized. These natural habitats are at risk of extinction because of human development and forest degradation caused by climate change. Population structure and genetic diversity of P. ussuriensis in China and P. ussuriensis var. aromatica in Japan have been investigated using both morphological and molecular markers in order to define appropriate conservation units, and to provide a good focus for conservation management. Distant evolutionary relationships between P. ussuriensis Maxim. in China and P. ussuriensis var. aromatica in Japan inferred from population genetic structure and phylogenetic analysis are also discussed.

Increasing evidence indicates that long non-coding RNAs (lncRNAs) play pivotal roles in regulatory networks controlling plant and animal gene expression. However, lncRNA roles in regulating rubber biosynthesis in Eucommia ulmoides, an emerging source of natural rubber (Eu-rubber), are currently unknown. Here, we report on RNA deep-sequencing of E. ulmoides fruits at two developmental stages. Based on application of a stringent pipeline, 29,103 lncRNAs and 9,048 transcripts of uncertain coding potential (TUCPs) were identified. Two differentially expressed (DE) TUCPs appear to simultaneously regulate 12 protein-coding genes involved in Eu-rubber biosynthesis (GIEBs), as well as 95 DE genes. Functional categorization of these 95 DE genes indicated their involvement in subcellular microstructures and cellular processes, such as cell wall, cell division, and growth. These DE genes may participate in the differentiation and development of laticifers, where Eu-rubber is synthesized. A model is proposed in which "commanders" (DE TUCPs) direct the "builders" (DE genes) to construct a "storehouse" of materials needed for Eu-rubber synthesis, and the "workers" (GIEBs) to synthesize Eu-rubber. These findings provide insights into both cis- and trans-polyisoprene biosynthesis in plants, laying the foundation for additional studies of this crucial process.

Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%–36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau.