Genome-wide comprehensive analysis of transcriptomes and small RNAs offers insights into the molecular mechanism of alkaline stress tolerance in a citrus rootstock

Alkaline stress has serious-negative effects on citrus production.Ziyang xiangcheng(Citrus junos Sieb.ex Tanaka)(Cj)is a rootstock that is tolerant to alkaline stress and iron deficiency.Trifoliate orange(Poncirus trifoliata(L.)Raf.)(Pt),the most widely used rootstock in China,is sensitive to alkaline stress.To investigate the molecular mechanism underlying the tolerance of Cj to alkaline stress,next-generation sequencing was employed to profile the root transcriptomes and small RNAs of Cj and Pt seedlings that were cultured in nutrient solutions along a three pH gradient.This two-level regulation data set provides a system-level view of molecular events with a precise resolution.The data suggest that the auxin pathway may play a central role in the inhibitory effect of alkaline stress on root growth and that the regulation of auxin homeostasis under alkaline stress is important for the adaptation of citrus to alkaline stress.Moreover,the jasmonate(JA)pathway exhibits the opposite response to alkaline stress in Cj and Pt and may contribute to the differences in the alkaline stress tolerance and iron acquisition between Cj and Pt.The dataset provides a wealth of genomic resources and new clues to further study the mechanisms underlying alkaline stress resistance in Cj.

Genomic and transcriptomic analyses of Citrus sinensis varieties provide insights into Valencia orange fruit mastication trait formation

Valencia orange(Citrus sinensis Osbeck)(VO)is a type of late-ripening sweet orange whose ripening occurs 4 to 5 months later than that of the mid-ripening common sweet orange(CO).Notably,the mastication trait of VO fruit is inferior to that of CO fruit.To date,how inferior pulp mastication trait forms in VO has not been determined.In this study,13 VO varieties and 12 CO varieties were subjected to whole-genome resequencing.A total of 2.98 million SNPs were identified from 25 varieties,and a SNP molecular marker was developed to distinguish VO and CO.Moreover,144 and 141 genes identified by selective sweep analysis were selected during VO and CO evolution,respectively.Based on gene functional enrichment analysis,most of the selected VO genes were related to the stress response and lignin biosynthesis.Simultaneously,we comparatively analyzed the transcriptome profiles of peel and pulp tissues among three VO varieties and three CO varieties,and the results demonstrated differences in lignin biosynthesis between VO and CO fruits.Furthermore,coexpression network analysis was performed to identify hub genes of lignin-related and variety-specific networks,which included CsERF74,CsNAC25,CsHSFB3,CsSPL4/13,etc.Overall,this study provides important insights into the mastication trait formation of Valencia orange fruit.

The miR159a-DUO1 module regulates pollen development by modulating auxin biosynthesis and starch metabolism in citrus

Achieving seedlessness in citrus varieties is one of the important objectives of citrus breeding.Male sterility associated with abnormal pollen development is an important factor in seedlessness.However,our understanding of the regulatory mechanism underlying the seedlessness phenotype in citrus is still limited.Here,we determined that the miR159a-DUO1 module played an important role in regulating pollen development in citrus,which further indirectly modulated seed development and fruit size.Both the overexpression of csi-miR159a and the knocking out of DUO1 in Hong Kong kumquat(Fortunella hindsii)resulted in small and seedless fruit phenotypes.Moreover,pollen was severely aborted in both transgenic lines,with arrested pollen mitotic I and abnormal pollen starch metabolism.Through additional cross-pollination experiments,DUO1 was proven to be the key target gene for miR159a to regulate male sterility in citrus.Based on DNA affinity purification sequencing(DAP-seq),RNA-seq,and verified interaction assays,YUC2/YUC6,SS4 and STP8 were identified as downstream target genes of DUO1,those were all positively regulated by DUO1.In transgenic F.hindsii lines,the miR159a-DUO1 module down-regulated the expression of YUC2/YUC6,which decreased indoleacetic acid(IAA)levels and modulated auxin signaling to repress pollen mitotic I.The miR159a-DUO1 module reduced the expression of the starch synthesis gene SS4 and sugar transport gene STP8 to disrupt starch metabolism in pollen.Overall,this work reveals a new mechanism by which the miR159a-DUO1 module regulates pollen development and elucidates the molecular regulatory network underlying male sterility in citrus.

Regulation of hypoxic stress and oxidative stress in bone grafting: Current trends and future perspectives

Tissue engineering aims to offer large-scale replacement of damaged organs using implants with the com-bination of cells,growth factors and scaffolds.However,the intra/peri-implant region is exposed to se-vere hypoxic stress and oxidative stress during the early stage of implantation with bone graft materials,which endangers the survival,proliferation and differentiation of seed cells within the implants as well as the host cells surrounding the implants.If the bone graft material could spontaneously and intelligently regulate the hypoxic stress and oxidative stress to a moderate level,it will facilitate the vascularization of the implants and the rapid regeneration of the bone tissue.In this review,we will first introduce the signaling pathways of cellular response under hypoxic stress and oxidative stress,then present the clas-sical material designs and examples in response to hypoxic stress and oxidative stress.And finally,we will address the important role of epigenetic mechanisms in the regulation of hypoxic stress and oxida-tive stress and describe the potential applications and prospective smart bone graft materials based on novel epigenetic factors against hypoxic stress and oxidative stress in bone repair.The main content of this review is summarized in the following graphical abstract.