Fruit color is an important economic trait. The color of red walnut cultivars is mainly attributed to anthocyanins. The aim of this study was to explore the differences in the molecular mechanism of leaf and peel color change between red and green walnut. A reference transcriptome of walnut was sequenced and annotated to identify genes related to fruit color at the ripening stage. More than 290 million high-quality reads were assembled into 39,411 genes using a combined assembly strategy. Using Illumina digital gene expression profiling, we identified 4568 differentially expressed genes (DEGs) between red and green walnut leaf and 3038 DEGs between red and green walnut peel at the ripening stage. We also identified some transcription factor families (MYB, bHLH, and WD40) involved in the control of anthocyanin biosynthesis. The trends in the expression levels of several genes encoding anthocyanin biosynthetic enzymes and transcription factors in the leaf and peel of red and green walnut were verified by quantitative real-time PCR. Together, our results identified the genes involved in anthocyanin accumulation in red walnut. These data provide a valuable resource for understanding the coloration of red walnut.

Background: Fruit aroma is an important quality with respect to consumer preference, but the most important aroma compounds and their genetic regulatory mechanisms remain elusive. Results: In this study, we qualitatively analysed volatile compounds in the pulp and skin of five table grape cultivars with three aroma types (muscat, strawberry, and neutral) using solid-phase microextraction gas chromatography/mass spectrometry. We identified 215 aroma compounds, including 88 esters, 64 terpenes, and 29 alcohols, and found significant differences in the number of compounds between the pulp and skin, especially for terpenes. Skin transcriptome data for the five grape cultivars were generated and subjected to aroma compound-gene correlation analysis. The combined transcriptomic analysis and terpene profiling data revealed 20 candidate genes, which were assessed in terms of their involvement in aroma biosynthetic regulation, including 1 VvCYP (VIT_08s0007g07730), 2 VvCCR (VIT_13s0067g00620, VIT_13s0047g00940), 3 VvADH (VIT_00s0615g00010, VIT_00s0615g00030, VIT_ 00s0615g00020), and 1 VvSDR (VIT_08s0040g01200) in the phenylpropanoids synthesis pathway, and 1 VvDXS (VIT_05s0020g02130) and 6 VvTPS (VIT_13s0067g00370, Vitis_vinifera_newGene_3216, VIT_13s0067g00380, VIT_13s0084g00010, VIT_00s0271g00010, and VIT_13s0067g00050) in the methylerythritol phosphate pathway (involved in the production and accumulation of aromatic compounds). Additionally, 2 VvMYB (VIT_17s0000g07950, VIT_03s0063g02620) and 1 VvGATA (VIT_15s0024g00980) transcription factor played important regulatory roles in the accumulation of key biosynthetic precursors of these compounds in grapes. Our results indicated that downstream genes, specifically 1 VvBGLU (VIT_03s0063g02490) and 2 VvUGT (VIT_17s0000g07070, VIT_17s0000g07060) are involved in regulating the formation and volatilization of bound compounds in grapes. Conclusions: The results of this study shed light on the volatile compounds and “anchor points” of synthetic pathways in the pulp and skin of muscat and strawberry grapes, and provide new insight into the regulation of different aromas in grapes.

The breeding of new soft-seeded pomegranate cultivars provides new products for the market and increases farmers’ incomes, yet the genetic architecture mediating seed hardness is largely unknown. Here, the seed hardness and hundred-seed weights of 26 cultivars were determined in 2 successive years. We conducted miRNA and mRNA sequencing to analyse the seeds of two varieties of Punica granatum: soft-seeded Tunisia and hard-seeded Sanbai, at 60 and 120 d after flowering. Seed hardness was strongly positively correlated with hundred-seed weight. We detected 25 and 12 differentially expressed miRNA–mRNA pairs with negative regulatory relationships between the two genotypes at 60 and 120 d after flowering, respectively. These miRNA–mRNA pairs mainly regulated seed hardness by altering cell wall structure. Transcription factors including NAC1, WRKY and MYC, which are involved in seed hardness, were targeted by differentially expressed mdm-miR164e and mdm-miR172b. Thus, seed hardness is the result of a complex biological process regulated by a miRNA–mRNA network in pomegranate. These results will help us understand the complexity of seed hardness and help to elucidate the miRNA-mediated molecular mechanisms that contribute to seed hardness in pomegranate.

The Tiller Angle Control 1 (TAC1) gene belongs to the IGT family, which mainly controls plant branch angle, thereby affecting plant form. Two members of MdTAC1 are identified in apple; the regulation of apple branch angle by MdTAC1 is still unclear. In this study, a subcellular localization analysis detected MdTAC1a in the nucleus and cell membrane, but MdTAC1b was detected in the cell membrane. Transgenic tobacco by overexpression of MdTAC1a or MdTAC1b showed enlarged leaf angles, the upregulation of several genes, such as GA 2-oxidase (GA2ox), and a sensitive response to light and gravity. According to a qRT-PCR analysis, MdTAC1a and MdTAC1b were strongly expressed in shoot tips and vegetative buds of weeping cultivars but were weakly expressed in columnar cultivars. In the MdTAC1a promoter, there were losses of 2 bp in spur cultivars and 6 bp in weeping cultivar compared with standard and columnar cultivars. An InDel marker specific to the MdTAC1a promoter was developed to distinguish apple cultivars and F₁ progeny. We identified a protein, MdSRC2, that interacts with MdTAC1a, whose encoding gene which was highly expressed in trees with large branch angles. Our results indicate that differences in the MdTAC1a promoter are major contributors to branch-angle variation in apple, and the MdTAC1a interacts with MdSRC2 to affect this trait.