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Summary: Self‐incompatibility (SI) is a widespread prezygotic mechanism for flowering plants to avoid inbreeding depression and promote genetic diversity. Citrus has an S‐RNase‐based SI system, which was frequently lost during evolution. We previously identified a single nucleotide mutation in Sm‐RNase, which is responsible for the loss of SI in mandarin and its hybrids. However, little is known about other mechanisms responsible for conversion of SI to self‐compatibility (SC) and we identify a completely different mechanism widely utilized by citrus. Here, we found a 786‐bp miniature inverted‐repeat transposable element (MITE) insertion in the promoter region of the FhiS2‐RNase in Fortunella hindsii Swingle (a model plant for citrus gene function), which does not contain the Sm‐RNase allele but are still SC. We demonstrate that this MITE plays a pivotal role in the loss of SI in citrus, providing evidence that this MITE insertion prevents expression of the S‐RNase; moreover, transgenic experiments show that deletion of this 786‐bp MITE insertion recovers the expression of FhiS2‐RNase and restores SI. This study identifies the first evidence for a role for MITEs at the S‐locus affecting the SI phenotype. A family‐wide survey of the S‐locus revealed that MITE insertions occur frequently adjacent to S‐RNase alleles in different citrus genera, but only certain MITEs appear to be responsible for the loss of SI. Our study provides evidence that insertion of MITEs into a promoter region can alter a breeding strategy and suggests that this phenomenon may be broadly responsible for SC in species with the S‐RNase system. [ABSTRACT FROM AUTHOR]

Summary: Carotenoids contribute to fruit coloration and are valuable sources of provitamin A in the human diet. Abscisic acid (ABA) plays an essential role in fruit coloration during citrus fruit ripening, but little is known about the underlying mechanisms. Here, we identified a novel bZIP transcription activator called CsbZIP44, which serves as a central regulator of ABA‐mediated citrus carotenoid biosynthesis. CsbZIP44 directly binds to the promoters of four carotenoid metabolism‐related genes (CsDXR, CsGGPPs, CsBCH1 and CsNCED2) and activates their expression. Furthermore, our research indicates that CsHB5, a positive regulator of ABA and carotenoid‐driven processes, activates the expression of CsbZIP44 by binding to its promoter. Additionally, CsHB5 interacts with CsbZIP44 to form a transcriptional regulatory module CsHB5‐CsbZIP44, which is responsive to ABA induction and promotes carotenoid accumulation in citrus. Interestingly, we also discover a positive feedback regulation loop between the ABA signal and carotenoid biosynthesis mediated by the CsHB5‐CsbZIP44 transcriptional regulatory module. Our findings show that CsHB5‐CsbZIP44 precisely modulates ABA signal‐mediated carotenoid metabolism, providing an effective strategy for quality improvement of citrus fruit and other crops. [ABSTRACT FROM AUTHOR]

Somatic embryogenesis ( SE) is a process of somatic cells becoming dedifferentiated and generating embryos. SE has been widely used in biotechnology as a powerful way of regeneration and a model system for studying plant embryogenesis, but the controlling mechanisms of SE are far from clear. Here, we show the genomewide profiles of mi RNAs/si RNAs and their target genes in nonembryogenic and embryogenic tissues of 'Valencia' sweet orange. By high-throughput sequencing ( HTS) of small RNAs and RNA degradome tags, we identified 50 known and 45 novel mi RNAs, 130 miniature inverted-repeat transposable elements ( MITEs) derived, 94 other and 235 phased small interfering RNAs (si RNAs), as well as 203 target genes. The majority of the abundantly expressed mi RNAs/si RNAs exhibit lower expression levels in embryogenic callus ( EC) or during SE process than in nonembryogenic callus ( NEC), which is supposed to derepress the target genes that are involved in development and stress response, thus to activate the biological processes required for cell differentiation. However, the conserved csi-miR156a/b, miR164b and 171c directed suppression of specific transcription factors ( TFs) are supposed to inactivate the postembryonic growth thus to maintain normal SE. In this study, mi RNA- and si RNA-mediated silencing of target genes was found under sophisticated regulation in citrus SE system; the enhancement effect of specific conserved mi RNAs on SE was discussed, providing new clues for future investigation of mechanisms that control SE. [ABSTRACT FROM AUTHOR]