Grain Shape Genes:Shaping the Future of Rice Breeding

The main goals of rice breeding nowadays include increasing yield,improving grain quality,and promoting complete mechanized production to save labor costs.Rice grain shape,specified by three dimensions,including grain length,width and thickness,has a more precise meaning than grain size,contributing to grain appearance quality as well as grain weight and thus yield.Furthermore,the divergence of grain shape characters could be utilized in mechanical seed sorting in hybrid rice breeding systems,which has been succeeded in utilizing heterosis to achieve substantial increase in rice yield in the past decades.Several signaling pathways that regulate rice grain shape have been elucidated,including G protein signaling,ubiquitination-related pathway,mitogen-activated protein kinase signaling,phytohormone biosynthesis and signaling,micro RNA process,and some other transcriptional regulatory pathways and regulators.This review summarized the recent progress on molecular mechanisms underlying rice grain shape determination and the potential of major genes in future breeding applications.

Long noncoding RNAs:new insights in modulating mammalian spermatogenesis

Spermatogenesis is a complex differentiating developmental process in which undifferentiated spermatogonial germ cells differentiate into spermatocytes,spermatids,and finally,to mature spermatozoa.This multistage developmental process of spermatogenesis involves the expression of many male germ cell-specific long noncoding RNAs(lncRNAs)and highly regulated and specific gene expression.LncRNAs are a recently discovered large class of noncoding cellular transcripts that are still relatively unexplored.Only a few of them have postmeiotic;however,lncRNAs are involved in many cellular biological processes.The expression of lncRNAs is biologically relevant in the highly dynamic and complex program of spermatogenesis and has become a research focus in recent genome studies.This review considers the important roles and novel regulatory functions whereby lncRNAs modulate mammalian spermatogenesis.

Integrated analysis of miRNA and mRNA expression profiles in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis

Insect gut microbiota has been reported to participate in regulating host multiple biological processes including metabolism and reproduction.However,the corresponding molecular mechanisms remain largely unknown.Recent studies suggest that microRNAs(miRNAs)are involved in complex interactions between the gut microbiota and the host.Here,we used next-generation sequencing technology to characterize miRNA and mRNA expression profiles and construct the miRNA–gene regulatory network in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis.A total of 3016 differentially expressed genes(DEGs)and 18 differentially expressed miRNAs(DEMs)were identified.Based on the integrated analysis of miRNA and mRNA sequencing data,229 negatively correlated miRNA-gene pairs were identified from the miRNA-mRNA network.Gene ontology enrichment analysis indicated that DEMs could target several genes involved in the metabolic process,oxidation-reduction process,oogenesis,and insulin signaling pathway.Finally,real-time quantitative polymerase chain reaction further verified the accuracy of RNA sequencing results.In conclusion,our study provides the profiles of miRNA and mRNA expressions under antibiotics treatment and provides an insight into the roles of miRNAs and their target genes in the interaction between the gut microbiota and its host.

An Uncanonical CCCH-Tandem Zinc-Finger Protein Represses Secondary Wall Synthesis and Controls Mechanical Strength in Rice

Secondary walls, which represent the bulk of biomass, have a large impact on plant growth and adaptation to environments. Secondary wall synthesis is switched and regulated by a sophisticated signaling transduction network. However, there is limited understanding of these regulatory pathways. Here, we report that ILAl-interacting protein 4 （lIP4） can repress secondary wall synthesis, lIP4 is a phosphorylation sub- strate of an Raf-like MAPKKK, but its function is unknown. By generating lip4 mutants and relevant transgenic plants, we found that lesions in lIP4 enhance secondary wall formation. Gene expression and transactivation activity assays revealed that lIP4 negatively regulates the expression of MYB61 and CESAs but does not bind their promoters, lIP4 interacts with NAC29/NAC31, the upstream regulators of secondary wall synthesis, and suppresses the downstream regulatory pathways in plants. Mutagenesis analyses showed that phosphomimic UP4 proteins translocate from the nucleus to the cytoplasm, which releases interacting NACs and attenuates its repression function. Moreover, we revealed that liPs are evolutionarily conserved and share unreported CCCH motifs, referred to as uncanonical CCCH-tandem zinc-finger proteins. Collectively, our study provides mechanistic insights into the control of secondary wall synthesis and presents an opportunity for improving relevant agronomic traits in crops.

Osteoporosis:A Silent Disease with Complex Genetic Contribution

Osteoporosis is the most common multifactorial metabolic bone disorder worldwide with a strong genetic component. In this review, the evidence for a genetic contribution to osteoporosis and related phenotypes is summarized alongside with methods used to identify osteoporosis susceptibility genes. The key biological pathways involved in the skeleton and bone development are discussed with a particular focus on master genes clustered in these pathways and their mode of action. Furthermore, the most studied single nucleotide polymorphisms （SNPs） analyzed for their importance as genetic markers of the disease are presented. New data generated by next- generation sequencing in conjunction with extensive meta-analyses should contribute to a better understanding of the genetic basis of osteoporosis and related phenotype variability. These data could be ultimately used for identifying at-risk patients for disease prevention by both controlling environmental factors and providing possible therapeutic targets.

Long noncoding RNA(lncRNA)HOTAIR:Pathogenic roles and therapeutic opportunities in gastric cancer

Gastric cancer is one of the first malignant cancers in the world and a large number of people die every year due to this disease.Many genetic and epigenetic risk factors have been identified that play a major role in gastric cancer.HOTAIR is an effective epigenetic agent known as long noncoding RNA(lncRNA).HOTAIR has been described to have biological functions in biochemical and cellular processes through interactions with many factors,leading to genomic stability,proliferation,survival,invasion,migration,metastasis,and drug resistance.In the present article,we reviewed the prognostic value of the molecular mechanisms underlying the HOTAIR regulation and its function in the development of Gastric Cancer,whereas elucidation of HOTAIR–protein and HOTAIR–DNA interactions can be helpful in the identification of cancer processes,leading to the development of potential therapeutic strategies.

Systematic identification and functional analysis of long noncoding RNAs involved in indoxacarb resistance in Spodoptera litura

Long noncoding RNAs(lncRNAs)are noncoding transcripts that are more than 200 nucleotides long.They play essential roles in regulating a variety of biological processes in many species,including insects,and some lncRNAs have been found to be associated with insecticide resistance.However,the characteristics and biological func-tions of lncRNAs involved in indoxacarb resistance are unknown in Spodoptera litura.We performed RNA sequencing in the SS,InRS,and FInRS of S.litura and identified 11978 lncRNAs,including 3136 intergenic lncRNAs,7393 intronic lncRNAs,and 1449 anti-sense lncRNAs.Compared with the SS,51 lncRNAs were upregulated and 134 lncRNAs were downregulated in the two resistant strains,and 908 differentially expressed mRNAs were predicted as the target genes of the 185 differentially expressed lncRNAs.Further analysis showed that 112 of differentially expressed lncRNAs may be associated with in-doxacarb resistance by regulating the expression of 14 P450s,seven CCEs,one GST,six UGTs,five ABC transporters,and 24 cuticle protein genes,and 79 of differentially ex-pressed lncRNAs may regulate the expression of 14 detoxification genes and 19 cuticle protein genes to participate in indoxacarb resistance by sponging 10 microRNAs.Interest-ingly,47 of differentially expressed lncRNAs may mediate indoxacarb resistance through both lncRNA-mRNA and lncRNA-miRNA-mRNA regulatory pathways.Furthermore,quantitative PCR,RNA interference,and indoxacarb bioassay analyses indicated that over-expressed LNC_004867 and LNC_006576 were involved in indoxacarb resistance.This study provides comprehensive information for lncRNAs of S.litura,and presents evidence that lncRNAs havekey roles in conferring insecticide resistance in S.litura.