Background: As a perennial crop, oil-Camellia possesses a long domestication history and produces high-quality seed oil that is beneficial to human health. Camellia oleifera Abel. is a sister species to the tea plant, which is extensively cultivated for edible oil production. However, the molecular mechanism of the domestication of oil-Camellia is still limited due to the lack of sufficient genomic information. Results: To elucidate the genetic and genomic basis of evolution and domestication, here we report a chromosome-scale reference genome of wild oil-Camellia (2.95 Gb), together with transcriptome sequencing data of 221 cultivars. The oil-Camellia genome, assembled by an integrative approach of multiple sequencing technologies, consists of a large proportion of repetitive elements (76.1%) and high heterozygosity (2.52%). We construct a genetic map of high-density corrected markers by sequencing the controlled-pollination hybrids. Genome-wide association studies reveal a subset of artificially selected genes that are involved in the oil biosynthesis and phytohormone pathways. Particularly, we identify the elite alleles of genes encoding sugar-dependent triacylglycerol lipase 1, β-ketoacyl-acyl carrier protein synthase III, and stearoyl-acyl carrier protein desaturases; these alleles play important roles in enhancing the yield and quality of seed oil during oil-Camellia domestication. Conclusions: We generate a chromosome-scale reference genome for oil-Camellia plants and demonstrate that the artificial selection of elite alleles of genes involved in oil biosynthesis contributes to oil-Camellia domestication.

Camellia oleifera is a major tree species for producing edible oil. Its seed oil is well known for the high level of oleic acids; however, little is known regarding the molecular mechanism of lipid biosynthesis in C. oleifera. Here, we measured the oil contents and fatty acid (FA) compositions at four developmental stages and investigated the global gene expression profiles through transcriptomics sequencing. We identified differentially-expressed genes (DEGs) among the developmental stages and found that the distribution of numbers of DEGs was associated with the accumulation pattern of seed oil. Gene Ontology (GO) enrichment analysis revealed some critical biological processes related to oil accumulation, including lipid metabolism and phosphatidylcholine metabolism. Furthermore, we investigated the expression patterns of lipid biosynthesis genes. We showed that most of the genes were identified with single or multiple copies, and some had correlated profiles along oil accumulation. We proposed that the higher levels of stearoyl-ACP desaturases (SADs) coupled with lower activities of fatty acid desaturase 2 (FAD2) might be responsive to the boost of oleic acid at the late stage of C. oleifera seeds’ development. This work presents a comprehensive transcriptomics study of C. oleifera seeds and uncovers valuable DEGs that are associated with the seed oil accumulation.

Phenolics are a group of important plant secondary metabolites that have been proven to possess remarkable antioxidant activity and to be beneficial for human health. Pecan nuts are an excellent source of dietary phenolics. In recent years, many studies have focused on the separation and biochemical analysis of pecan phenolics, but the molecular mechanisms of phenolic metabolism in pecans have not been fully elucidated, which significantly hinders quality breeding research for this plant. Chalcone synthase (CHS) plays crucial roles in phenolic biosynthesis. In this study, three Carya illinoinensis CHSs (CiCHS1, CiCHS2, and CiCHS3), were isolated and analyzed. CiCHS2 and CiCHS3 present high expression levels in different tissues, and they are also highly expressed at the initial developmental stages of kernels in three pecan genotypes. A correlation analysis was performed between the phenolic content and CHSs expression values during kernel development. The results indicated that the expression variations of CiCHS2 and CiCHS3 are significantly related to changes in total phenolic content. Therefore, CiCHSs play crucial roles in phenolic components synthesis in pecan. We believe that the isolation of CiCHSs is helpful for understanding phenolic metabolism in C. illinoinensis, which will improve quality breeding and resistance breeding studies in this plant.

Background: Camellia oleifera (C.oleifera) is one of the most important wood oil species in the world. C.oleifera was propagated by nurse seedling grafting. Since the morphology of rootstocks has a significant impact on grafting efficiency and seedling quality, it is necessary to understand the molecular mechanism of morphogenesis for cultivating high-quality and controllable rootstocks. However, the genomic resource for this species is relatively limited, which hinders us from fully understanding the molecular mechanisms of seed germination in C.oleifera. Results: In this paper, using transcriptome sequencing, we measured the gene expression in the C.oleifera cotyledon in different stages of development and the global gene expression profiles. Approximately 45.4 gigabases (GB) of paired-end clean reads were assembled into 113,582 unigenes with an average length of 396 bp. Six public protein databases annotate 61.5% (68,217) of unigenes. We identified 11,391 differentially expressed genes (DEGs) throughout different stages of germination. Enrichment analysis revealed that DEGs were mainly involved in hormone signal transduction and starch sucrose metabolism pathways. The gravitropism regulator UNE10, the meristem regulators STM, KNAT1, PLT2, and root-specific transcription factor WOX11 all have higher gene expression levels in the CAM2 stage (seed soaking), which indicates that the cotyledon-regulated program for germination had initiated when the seeds were imbibition. Our data showed differentially reprogrammed to multiple hormone-related genes in cotyledons during C.oleifera seed germination. Conclusion: Cotyledons play vital roles, both as the main nutrient provider and as one primary instructor for seed germination and seedling growth. Together, our study will significantly enrich the genomic resources of Camellia and help us understand the molecular mechanisms of the development in the seed germination and seedling growth of C.oleifera. It is helpful to culture standard and superior quality rootstock for C.oleifera breeding.

A comprehensive method for evaluating kernel quality was established by estimating in detail the kernel quality of 27 pecan cultivars introduced into China and by exploring the major trait differences among the different cultivars of pecan. The contents of crude fat, crude protein, soluble sugar, and tannin; the fatty acid composition; the amino acid composition; and the mineral element composition of 27 pecan cultivars were analyzed and tested using the national standards for principal component analysis (PCA), and orthogonal partial least-squares discriminant analysis (OPLS-DA) was used to comprehensively evaluate the 34 characteristic indicators. The fatty acids in the kernel were dominated by unsaturated fats, with oleic acid having the highest content relative to linoleic acid; the amino acid composition was dominated by medicinal amino acids; and potassium, magnesium, and calcium were the predominant mineral elements. Systematic cluster analysis revealed that the 27 pecan cultivars could be classified into three categories (relatively optimal, general, and poorest kernel quality) and 21 indexes, including oleic, linoleic, linolenic, crude fat, soluble sugars, aspartic acid, and threonine, served as indexes of the differences among the 27 tested cultivars. Combined with principal component analysis and stepwise regression analysis, a kernel quality evaluation model was established and verified, and reliable evaluation results were obtained. In addition, Nos. 9, 65, 66, 72, 8, and 21, which had the best quality, were further ranked using the probability ranking method within the third category of optimal quality cultivars. There were obvious differences in kernel characteristics among the different cultivars of pecan. Six cultivars with potential to be developed into excellent cultivars were preliminarily screened out. It was found that the organic combination of cluster analysis, principal component analysis, and orthogonal partial least-squares discriminant analysis can provide a reliable method for the quality evaluation of pecans.

The outbreak of anthracnose caused by Colletotrichum spp. represents a devastating epidemic that severely affects oil tea (Camellia oleifera) production in China. However, the unknown resistance mechanism to anthracnose in C. oleifera has impeded the progress of breeding disease-resistant varieties. In this study, we investigated the physiological responses of resistant and susceptible lines during C. gloeosporioides infection. Our results showed that the accumulation of malondialdehyde (MDA), catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) in both disease-resistant and susceptible lines increased by C. gloeosporioides infection. Also, disease-resistant lines exhibited lower MDA, but higher POD, SOD, and CAT activities compared to susceptible lines. The accumulation of flavonoids in both resistant and susceptible C. oleifera leaves increased following C. gloeosporioides infection, and the increase was greater in resistant lines. Further, we identified and functionally characterized the dihydroflavonol 4-reductase (CoDFR) from the resistant C. oleifera line. We showed that the full-length coding sequence (CDS) of CoDFR is 1044 bp encoding 347 amino acids. The overexpression of CoDFR in tobacco altered the expression of flavonoid biosynthetic genes, resulting in an increased flavonoid content in leaves. CoDFR transgenic tobacco plants exhibited increased anthracnose resistance. Furthermore, the transgenic plants had higher salicylic acid content. These findings offer potential insights into the pivotal role of CoDFR involved in flavonoid-mediated defense mechanisms during anthracnose invasion in resistant C. oleifera.