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Nitrogen (N) deficiency is one of the factors limiting crop productivity worldwide. As major forms of N, nitrate (NO3−) and ammonium (NH4+) regulate plant growth as signals. Although there are abundant studies on the response of many plants to N stress, the mechanism by which wheat (Triticum aestivum L.) roots adapt to low N, especially to low-NH4+ stress, has not been fully elucidated. In this study, wheat seedlings were planted in 1/2-strength Hoagland’s solution containing 5 mM NO3−, 0.1 mM NO3−, or 0.1 mM NH4+ to characterize root physiological responses to N deficit. Under low-N stress, root fresh weight, lateral root number increased compared with those under control conditions. Moreover, the concentrations of indole-3-acetic acid (IAA), cytokinins (CKs), gibberellin (GA3), and jasmonic acid (JA) increased, while the salicylic acid (SA) concentration decreased under low-N stress. Assays using enzyme-linked immunosorbent assay (ELISA) and non-invasive micro-test technology (NMT) showed that H+-ATPase activity, the H+ efflux, and the IAA influx increased, while N influx decreased under low-N stress. Further study revealed that low-NO3− stress increased nitrate reductase and glutamine synthetase activities, while low-NH4+ stress increased the activities of glutamine synthetase and glutamate synthase. In conclusion, low-N stress altered root IAA, CKs, GA3, JA, and SA concentrations; increased H+-ATPase activity and H+ efflux; promoted an increase in lateral root number and thus N absorption area. Besides, low-N stress increased the activities of key enzymes related to N assimilation, promoted protein biosynthesis, and ultimately enhanced root growth.

Summary Fine mapping QTLs and identifying candidate genes for cotton fibre‐quality and yield traits would be beneficial to cotton breeding. Here, we constructed a high‐density genetic map by specific‐locus amplified fragment sequencing (SLAF‐seq) to identify QTLs associated with fibre‐quality and yield traits using 239 recombinant inbred lines (RILs), which was developed from LMY22 (a high‐yield Gossypium hirsutumL. cultivar) × LY343 (a superior fibre‐quality germplasm with G. barbadenseL. introgressions). The genetic map spanned 3426.57 cM, including 3556 SLAF‐based SNPs and 199 SSR marker loci. A total of 104 QTLs, including 67 QTLs for fibre quality and 37 QTLs for yield traits, were identified with phenotypic data collected from 7 environments. Among these, 66 QTLs were co‐located in 19 QTL clusters on 12 chromosomes, and 24 QTLs were detected in three or more environments and determined to be stable. We also investigated the genomic components of LY343 and their contributions to fibre‐related traits by deep sequencing the whole genome of LY343, and we found that genomic components from G. hirsutum races (which entered LY343 via its G. barbadense parent) contributed more favourable alleles than those from G. barbadense. We further identified six putative candidate genes for stable QTLs, including Gh_A03G1147 (GhPEL6), Gh_D07G1598 (GhCSLC6) and Gh_D13G1921 (GhTBL5) for fibre‐length QTLs and Gh_D03G0919 (GhCOBL4), Gh_D09G1659 (GhMYB4) and Gh_D09G1690 (GhMYB85) for lint‐percentage QTLs. Our results provide comprehensive insight into the genetic basis of the formation of fibre‐related traits and would be helpful for cloning fibre‐development‐related genes as well as for marker‐assisted genetic improvement in cotton.

Peanut (Arachis hypogaea) is an important oil crop cultivated across the world. Abiotic stresses are the major constraint factors that defect its yield, especially in the rainfed peanut cultivation areas. Aquaporins are proteins that form a large family of more than 30 members in higher plants and play key roles in plant water balance under abiotic stress conditions. To comprehensively understand the functions of aquaporins in peanut, we identified their family genome-wide and characterized the phylogenetics, gene structure, and the conserved motif of the selective filter. In total, 64 aquaporin isoforms were identified, the NIPs were firstly categorized into NIP1s and NIP2s groups based on the phylogenetic analysis and the selective filter structure classification system. Further, we analyzed the gene expression pattern under the salt-stress conditions and found that a TIP3 member is strongly induced by salt stress, which in turn contributed to improved seed germination under salt stress when expressed in Arabidopsis. Our study thus provides comprehensive profiles on the MIP superfamily and their expression and function under salt-stress conditions. We believe that our findings will facilitate the better understanding of the roles of aquaporins in peanuts under salt salt-stress conditions.

Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome structure, number and type of genes, codon usage, and repeat sequences of 20 Eragrostideae species were analyzed. The length of these chloroplast genomes varied from 130,773 bp to 135,322 bp. These chloroplast genomes showed a typical quadripartite structure, including a large single-copy region (77,993&ndash, 80,643 bp), a small single-copy region (12,410&ndash, 12,668 bp), and a pair of inverted repeats region (19,394&ndash, 21,074 bp). There were, in total, 129&ndash, 133 genes annotated in the genome, including 83&ndash, 87 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Forward and palindromic repeats were the most common repeat types. In total, 10 hypervariable regions (rpl22, rpoA, ndhF, matK, trnG&ndash, UCC-trnT&ndash, GGU, ndhF&ndash, rpl32, ycf4&ndash, cemA, rpl32&ndash, trnL&ndash, UAG, trnG&ndash, GCC&ndash, trnfM&ndash, CAU, and ccsA&ndash, ndhD) were found, which can be used as candidate molecular markers for Eragrostideae. Phylogenomic studies concluded that Enneapogon diverged first, and Eragrostis including Harpachne is the sister to Uniola. Furthermore, Harpachne harpachnoides is considered as a species of Eragrostis based on morphological and molecular evidence. In addition, the interspecies relationships within Eragrostis are resolved based on complete chloroplast genomes. This study provides useful chloroplast genomic information for further phylogenetic analysis of Eragrostideae.

As one of the most severe environmental stresses, salt stress can cause a series of changes in plants. In salt tolerant plant Zoysia macrostachya, germination, physiology, and genetic variation under salinity have been studied previously, and the morphology and distribution of salt glands have been clarified. However, no study has investigated the transcriptome of such species under salt stress. In the present study, we compared transcriptome of Z. macrostachya under normal conditions and salt stress (300 mmol/L NaCl, 24 h) aimed to identify transcriptome responses and molecular mechanisms under salt stress in Z. macrostachya. A total of 8703 differently expressed genes (DEGs) were identified, including 4903 up-regulated and 3800 down-regulated ones. Moreover, a series of molecular processes were identified by Gene Ontology (GO) analysis, and these processes were suggested to be closely related to salt tolerance in Z. macrostachya. The identified DEGs concentrated on regulating plant growth via plant hormone signal transduction, maintaining ion homeostasis via salt secretion and osmoregulatory substance accumulation and preventing oxidative damage via increasing the activity of ROS (reactive oxygen species) scavenging system. These changes may be the most important responses of Z. macrostachya under salt stress. Some key genes related to salt stress were identified meanwhile. Collectively, our findings provided valuable insights into the molecular mechanisms and genetic underpinnings of salt tolerance in Z. macrostachya.

Photosynthesis in non-foliar organs plays an important role in crop growth and productivity, and it has received considerable research attention in recent years. However, compared with the capability of photosynthetic CO2 fixation in leaves, the distinct attributes of photosynthesis in the non-foliar organs of wheat (a C3 species) are unclear. This review presents a comprehensive examination of the photosynthetic characteristics of non-foliar organs in wheat. Compared with leaves, non-foliar organs had a higher capacity to refix respired CO2 , higher tolerance to environmental stresses and slower terminal senescence after anthesis. Additionally, whether C4 photosynthetic metabolism exists in the non-foliar organs of wheat is discussed, as is the advantage of photosynthesis in non-foliar organs during times of abiotic stress. Introducing the photosynthesis-related genes of C4 plants into wheat, which are specifically expressed in non-foliar organs, can be a promising approach for improving wheat productivity.

Water deficit is one of the major factors limiting crop productivity worldwide. Plant roots play a key role in uptaking water, perceiving and transducing of water deficit signals to shoot. Although the mechanisms of drought-tolerance have been reported recently, the transcriptional regulatory network of wheat root response to water stress has not been fully understood. In this study, drought-tolerant cultivar JM-262 and susceptible cultivar LM-2 are planted to characterize the root transcriptional changes and physiological responses to water deficit. A total of 8197 drought tolerance-associated differentially expressed genes (DEGs) are identified, these genes are mainly mapped to carbon metabolism, flavonoid biosynthesis, and phytohormone signal transduction. The number and expression level of DEGs involved in antioxidative and antiosmotic stresses are more enhanced in JM-262 under water stress. Furthermore, we find the DEGs related to root development are much more induced in JM-262 in phytohormone signal transduction and carbon metabolism pathway. In conclusion, JM-262 may alleviate the damage of drought by producing more osmoprotectants, ROS scavengers, biomass and energy. Interestingly, hormone signaling and cross-talk probably play an important role in promoting JM-262 greater root systems to take up more water, higher capabilities to induce more drought-related DEGs and higher resisitance to oxidative stresse.

Seed germination and formation are the beginning and ending, respectively, of a plant life cycle. These two processes are under fine regulation by the internal genetic information. Previously, we demonstrated that Arabidopsis MIDASIN 1 (MDN1) is required for ribosome biogenesis, and its dysfunction leads to pleiotropic developmental phenotypes, including impaired embryogenesis and slow seed germination. In this study, we further found that the weak mutant of MDN1, mdn1-1, exhibits an increased seed size phenotype. Seed proteomic analysis reveals that a number of proteins involved in seed development and response to external environments are mis-regulated by the MDN1 dysfunction. Many 2S seed storage proteins (SSPs) and late embryogenesis abundant (LEA) proteins are over-accumulated in the dry seeds of mdn1-1. Further, some genes encoding seed storage reserves are also upregulated in mdn1-1 seedlings. More interestingly, abscisic acid-insensitive 5 (ABI5) is over-accumulated in mdn1-1 seeds, and the loss of its function partially rescues the low seed germination rate of mdn1-1. Together, this study further demonstrates that MDN1 is essential for establishing a normal seed proteome, and its mutation triggers ABI5-mediated repression of seed germination.

As one of the most common abiotic stresses, salt stress seriously impairs crop yield. Brachypodium distachyon (L.) Beauv. is a model species for studying wheat and other grasses. In the present investigation, the physiological responses of B. distachyon treated with different concentrations of NaCl for 24 h were measured. Therefore, the control and the seedlings of B. distachyon treated with 200 mM NaCl for 24 h were selected for transcriptome analysis. Transcriptome differential analysis showed that a total of 4116 differentially expressed genes (DEGs) were recognized, including 3120 upregulated and 996 downregulated ones. GO enrichment assay indicated that some subsets of genes related to the active oxygen scavenging system, osmoregulatory substance metabolism, and abscisic-acid (ABA)-induced stomatal closure were significantly upregulated under salt stress. The MapMan analysis revealed that the upregulated genes were dramatically enriched in wax metabolic pathways. The expressions of transcription factor (TF) family members such as MYB, bHLH, and AP2/ERF were increased under salt stress, regulating the response of plants to salt stress. Collectively, these findings provided valuable insights into the mechanisms underlying the responses of grass crops to salt stress.

In recent years, black testa peanut (Arachis hypogaea L.) has been favored because of its nutritional value and health function. To explore the genetic basis of peanut testa color, high-throughput sequencing technology was used to sequence the transcriptome of black testa peanut ‘ZH9ʹ and pink testa peanut ‘ZH8.ʹ Over 18 million high-quality reads were assembled into 49,404–52,578 genes for these two cultivars using a combined assembly strategy. Totally, 4,122 differentially expressed genes (DEGs) were identified between ZH8 and ZH9, among which 1317 (32%) were up-regulated and 2805 (68%) were down-regulated. KEGG analysis showed that the pathways of anthocyanin biosynthesis, isoflavonoid biosynthesis, flavone and flavonol biosynthesis, and phenylpropanoid biosynthesis were in the top 20 differentially expressed genes enriched pathways. Further analysis showed that the formation of the black color of ZH9 testa was mainly due to the reduction of lignin biosynthesis and isoflavonoid biosynthesis, and as a result, more substrate flow to anthocyanin biosynthesis. The up-regulation of all genes associated with DFR, a key enzyme determining flavonoid synthesis or anthocyanin synthesis in the flavonoid metabolic pathway, is also a strategy for increasing dihydroflavonol, a substrate for anthocyanin and flavonol biosynthesis. In addition, we identified three up-regulated R2R3MYB transcription factors associated with anthocyanin biosynthesis in ZH9. Finally, we verified the expressions of 15 genes that encode key enzymes and transcription factors using quantitative real-time PCR (qRT-PCR).

Background Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis. Results To investigate the functions of the dynamic DNA methylation during the early development of the peanut pod, global methylome and gene expression analyses were carried out by Illumina high throughput sequencing. A novel mapping strategy of reads was developed and used for methylome and gene expression analysis. Differentially methylated genes, such as nodulin, cell number regulator-like protein, and senescence-associated genes, were identified during the early developmental stages of the peanut pod. The expression levels of gibberellin-related genes changed during this period of pod development. From the stage one (S1) gynophore to the stage two (S2) gynophore, the expression levels of two key methyltransferase genes, DRM2 and MET1, were up-regulated, which may lead to global DNA methylation changes between these two stages. The differentially methylated and expressed genes identified in the S1, S2, and stage 3 (S3) gynophore are involved in different biological processes such as stem cell fate determination, response to red, blue, and UV light, post-embryonic morphogenesis, and auxin biosynthesis. The expression levels of many genes were co-related by their DNA methylation levels. In addition, our results showed that the abundance of some 24-nucleotide siRNAs and miRNAs were positively associated with DNA methylation levels of their target loci in peanut pods. Conclusion A novel mapping strategy of reads was described and verified in this study. Our results suggest that the methylated modes of the S1, S2, and S3 gynophore are different. The methylation changes that were identified during early peanut pod development provide useful information for understanding the roles of epigenetic regulation in peanut pod development. Electronic supplementary material The online version of this article (10.1186/s12870-018-1546-4) contains supplementary material, which is available to authorized users.

Strophostyles helvola is a close relative to common bean (Phaseolus vulgaris) and inhabits both coastal and non-coastal regions in North America. However, the mechanism of saline adaptation in S. helvola remains unclear. A transcriptome profiling would facilitate dissecting the underlying molecular mechanisms in salinity-adapted S. helvola. In this study, we reported the RNA-seq analyses of two genotypes (a salt-tolerant beach genotype and a salt-sensitive inland genotype) of S. helvola stressed with salt. S. helvola plants were grown in pots and treated with half lethal-guided dose of NaCl solution for 3 h, 24 h, and 7d. The plants supplied with the same amount of water were used as controls. The whole roots sampled from the three time points were equally pooled as one biological replicate, and three replicates were used for library construction and transcriptome sequencing on Illumina Hiseq 2500. The comparative analyses of root transcriptomes presented here provides a valuable resource for discovery of genes and networks involved in salt tolerance in S. helvola.

A plethora of evidence highlights that the dysbiosis of gut microbiota is a critical factor for inflammatory bowel disease (IBD). Both in vivo and in vitro studies have demonstrated that quinoa possesses potential prebiotic effects. The present study aims to examine the potential in using quinoa to ameliorate the dysbiosis and colitis induced by dextran sodium sulfate (DSS). A total of 40 C57BL/6 mice were fed either an AIN-93M diet or a quinoa-based diet, separately. Colitis was induced for 10 animals/dietary group with a 5-days exposure to 2.5% DSS. The clinical symptoms were monitored every other day, and the gut microbiota was characterized by 16S rRNA gene sequencing. The results indicated that consumption of quinoa lessened clinical symptoms as indicated by the reduced disease activity index and the degree of histological damage (P Proteobacteria, and decreased overgrowth of genera Escherichia/Shigella and Peptoclostridium (P Firmicutes and Bacteroidetes were less altered in mice fed with quinoa comparing to those mice fed the AIN-93M diet. In summary, the consumption of quinoa suppressed the dysbiosis of gut microbiota and alleviated clinical symptoms induced by DSS, indicating the potential to utilize quinoa as a dietary approach to improve intestinal health.