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The genomic basis underlying the selection for environmental adaptation and yield-related traits in maize remains poorly understood. Here we carried out genome-wide profiling of the small RNA (sRNA) transcriptome (sRNAome) and transcriptome landscapes of a global maize diversity panel under dry and wet conditions and uncover dozens of environment-specific regulatory hotspots. Transgenic and molecular studies of Drought-Related Environment-specific Super eQTL Hotspot on chromosome 8 (DRESH8) and ZmMYBR38, a target of DRESH8-derived small interfering RNAs, revealed a transposable element-mediated inverted repeats (TE-IR)-derived sRNA- and gene-regulatory network that balances plant drought tolerance with yield-related traits. A genome-wide scan revealed that TE-IRs associate with drought response and yield-related traits that were positively selected and expanded during maize domestication. These results indicate that TE-IR-mediated posttranscriptional regulation is a key molecular mechanism underlying the tradeoff between crop environmental adaptation and yield-related traits, providing potential genomic targets for the breeding of crops with greater stress tolerance but uncompromised yield.

Pepper is an important vegetable with great economic value and unique biological features. In the past few years, significant development has been made toward understanding the huge complex pepper genome; however, pepper functional genomics has not been well studied. To better understand the pepper gene structure and pepper gene regulation, we conducted full-length mRNA sequencing by PacBio sequencing and obtained 57 862 high-quality full-length mRNA sequences derived from 18 362 previously annotated and 5769 newly detected genes. New gene models were built that combined the full-length mRNA sequences and corrected approximately 500 fragmented gene models from previous annotations. Based on the full-length mRNA, we identified 4114 and 5880 pepper genes forming natural antisense transcript (NAT) genes in-cis and in-trans, respectively. Most of these genes accumulate small RNAs in their overlapping regions. By analyzing these NAT gene expression patterns in our transcriptome data, we identified many NAT pairs responsive to a variety of biological processes in pepper. Pepper formate dehydrogenase 1 (FDH1), which is required for R-gene-mediated disease resistance, may be regulated by nat-siRNAs and participate in a positive feedback loop in salicylic acid biosynthesis during resistance responses. Several cis-NAT pairs and subgroups of trans-NAT genes were responsive to pepper pericarp and placenta development, which may play roles in capsanthin and capsaicin biosynthesis. Using a comparative genomics approach, the evolutionary mechanisms of cis-NATs were investigated, and we found that an increase in intergenic sequences accounted for the loss of most cis-NATs, while transposon insertion contributed to the formation of most new cis-NATs. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at http://bigd.big.ac.cn/gsa Accession number, CRA001412.

Plant genomes encode large numbers of nucleotide-binding (NB) leucine-rich repeat (LRR) immune receptors (NLR) that mediate effector triggered immunity (ETI) and play key roles in protecting crops from diseases caused by devastating pathogens. Fitness costs are associated with plant NLR genes and regulation of NLR genes by micro(mi)RNAs and phased small interfering RNAs (phasiRNA) is proposed as a mechanism for reducing these fitness costs. However, whether NLR expression and NLR-mediated immunity are regulated during plant growth is unclear. We conducted genome-wide transcriptome analysis and showed that NLR expression gradually increased while expression of their regulatory small RNAs (sRNA) gradually decreased as plants matured, indicating that sRNAs could play a role in regulating NLR expression during plant growth. We further tested the role of miRNA in the growth regulation of NLRs using the tobacco mosaic virus (TMV) resistance gene N, which was targeted by miR6019 and miR6020. We showed that N-mediated resistance to TMV effectively restricted this virus to the infected leaves of 6-week old plants, whereas TMV infection was lethal in 1- and 3-week old seedlings due to virus-induced systemic necrosis. We further found that N transcript levels gradually increased while miR6019 levels gradually decreased during seedling maturation that occurs in the weeks after germination. Analyses of reporter genes in transgenic plants showed that growth regulation of N expression was post-transcriptionally mediated by MIR6019/6020 whereas MIR6019/6020 was regulated at the transcriptional level during plant growth. TMV infection of MIR6019/6020 transgenic plants indicated a key role for miR6019-triggered phasiRNA production for regulation of N-mediated immunity. Together our results demonstrate a mechanistic role for miRNAs in regulating innate immunity during plant growth., Author summary In plants, nucleotide-binding (NB) leucine-rich repeat (LRR) receptors (NLR) mediate pathogen-specific effector triggered immunity and are widely used in breeding to generate pathogen-resistant crops. However, dysregulation of NLR expression can inhibit plant growth and how NLR expression and function are regulated in different stages of plant growth is poorly understood. Using a high-throughput sequencing and bioinformatics approach, we found an overall increase in NLR expression, but expression of NLR-targeting sRNA during plant growth was decreased. We also used resistance to tobacco mosaic virus (TMV) mediated by the resistance gene N as a model system to study the biological significance of growth regulation of NLR by miRNAs. We found that N-mediated TMV immunity strengthened and N transcript levels increased during plant maturation. Using genetic analysis, we showed that up-regulation of N was due to transcriptional down-regulation of the N-targeting miR6019/6020 cluster during plant growth. We also showed that sRNA-mediated growth regulation of N expression and function was conserved between tobacco and tomato plants. This study therefore reveals a role for miRNAs in regulating innate immunity during plant growth.

To observe the effects of basic fibroblast growth factor (bFGF) on wound healing of bilioenteric anastomosis as to prevent postoperative biliary strictures.A model of choledochoduodenostomy in 31 dogs were constructed at first, then bFGF was administered on the local anastomosis (bFGF group) for 1 week after the operation as compared with sodium chloride solution (control group). Both groups were observed with light microscope (HE, Masson staining) and electron microscope 3 days, 1 and 3 weeks and 3 and 6 months after the operation (n=3). Hydroxyproline was measured at the same time.bFGF group healed more quickly compared with control group. Good function of cells were detected by electron microscope. Better mucosa epithelia, fibroblast, and capillary vessel proliferation were detected by histological observation in bFGF group. In bFGF group, collagen fibers were arranged orderly. Three weeks after operation, collagen fibers in control group were orderless and in whirlpool. Hydroxyproline of bFGF group was lower than that of control group (P0.05).bFGF administered in local anastomosis is an effective method to prevent postoperative anastomotic stenosis.