The antioxidant properties of CGA have been associated with preventing various chronic diseases.To better understand the biosynthesis of antioxidants in blueberry fruit, we identified homologs of previously characterized genes in other species involved in ascorbate, flavonols, chlorogenic acid, and anthocyanin biosynthesis. The key biosynthetic genes for these compounds exhibited a distinct developmental-specific pattern of expression . For example, genes involved in the conversion of leucoanthocyanidins to proanthocyanidins are highly expressed in the earliest and middle developmental fruit stages but not in ripening fruit . Conversely, genes involved in the conversion of leucoanthocyanidins to anthocyanins were highly expressed in mature and ripe fruit but not during early fruit developmental stages . Additionally, paralogs encoding the same anthocyanin pathway enzymes and genes involved in vacuolar localization of proanthcyanidins exhibited similar developmental stage-specific expression patterns. For example, the transcription factor complex MYB-bHLH-WD regulates expression of anthocyanin biosynthetic genes in eudicots. Using the Plant Transcription Factor Database v.4.0 , we identified homologs of transcription factors belonging to 55 gene families, and members of some of these gene families were predicted to be involved in the developmental regulation of flavonoid biosynthesis during blueberry fruit growth , including R2- R3-MYBs, R3-MYBs, bHLHs, and WDRs . These transcription factors also exhibit fruit development-specific expression patterns. In addition, we performed a gene co-expression network analysis to identify meta modules of genes that appear coregulated during fruit development, specifically genes that are associated with phytonutrient biosynthesis. Our analysis identified 1,988 meta modules of co-expressed genes, nft hydroponic of which 428 metamodules contained at least one of the 57 Pfam domains that have been previously categorized as associated with specialized metabolic pathways in plants.
Our analysis revealed that 142 of 428 meta modules were more highly expressed in developing fruit compared to other plant Thissues. Some meta modules showed clear trends of being highly expressed during either early or late fruit development. For example, METAMOD00377 is expressed early in fruit development and contains homologs to known anthocyanin genes OMT, HCT, PAL, and HQT as well as 31 homologs to known transcription factors. In contrast, METAMOD01221 is expressed late in fruit development and contains homologs of HCT, TT19, UFGT, and OMT and contains 10 homologs to known transcription factors. Moreover, we also examined meta modules for genes associated with other biosynthetic pathways that impart unique blueberry fruit characteristics. We identified two meta modules where genes appear to be co-regulated. Metamodule METAMOD00377, which contains Pfam domains associated with terpene, saccharide, and alkaloid specialized metabolism, and METAMOD01221, which contains terpene and saccharide metabolism. These meta modules contained genes that are differentially expressed during fruit development. Overall, the developmental-specific expression patterns of key bio-synthetic genes and their putative transcriptional regulators emphasize the tight regulation of production, conversion, and transport of precursor compounds that lead to the accumulation of antioxidant-related metabolites in blue Berry.The coregulation of genes involved in the biosynthesis of terpenes and saccharides during early and late fruit development described above reflects a coordinated interplay between these metabolites during fruit growth. Both terpenes and sugars contribute to the characteristic flavor of ripened fruit . In blueberry, two components play a central role in flavor perception: taste, which is a balance of sweetness and acidity, and aroma. Blueberry aroma is a complex blend of volatiles that include aldehydes, esters, terpenes, ketones, and alcohols. Previous reports in blueberry showed that the aroma profile varies greatly across different blueberry ecotypes and cultivars . For example, the aroma of high bush blueberry is primarily driven by terpene hydrocarbons and aldehydes -2-hexenal, -2-hexenol, -3-hexenol. Both linalool and geraniol are associated with sweet floral flavor. However, linalool was reported to largely impart the characteristic blueberry flavor when combined with certain aldehydes . Here, we also identified and examined the expression of genes involved in the biosynthesis of linalool. Four of the linalool synthase homologs in tetraploid blueberry are highly expressed during late fruit development .
This pattern of expression coincides with previous reports of linalool accumulation in ripened blueberry fruit . On the other hand, one homolog of linalool synthase, although it was expressed during fruit growth, did not show a clear fruit development-specific pattern. Investigating the underlying factors regulating these enzymes will facilitate genetic manipulations that may lead to further improving blueberry flavor in the future.Superior fruit quality is also associated with sugar levels. During fruit ripening, sugar levels of the endocarp increase by importing hexose symplastically and/or apoplastically. Sugar transporters , sucrose transporter, and tonoplast sugar transporter have been demonstrated to regulate intercellular sugar transport in phloem and fruit. In A. thaliana, all clade III SWEET play a role in sucrose transport, with AtSWEET9 primarily functioning in nectary secretion, while AtSWEET15 is required for seed filling by acting with SWEET11 and SWEET12. In blueberry, the clade III SWEET transporters 9 and 10 were highly expressed during early fruit growth, while clade III SWEET transporter 15 was mainly expressed in ripe fruit . interestingly, one of the blueberry SWEET15 homologs showed a distinct pattern of expression compared to the other three homologs. To the best of our knowledge, we are the first to report on the potential role of these genes during blueberry fruit development. In addition, homologs of A. thaliana TST1 and watermelon ClTST1 and ClTST3 were expressed during fruit ripening in blueberry. Elevated expression of a ClTST1 homolog was observed throughout fruit development, but the ClTST3 homolog showed very low expression. Another gene that is highly expressed during fruit maturation is vacuolar invertase. As described in other systems, its upregulation during fruit ripening coincided with the breakdown of starch to sucrose or a mixture of glucose and fructose, suggesting that it may be involved in the regulation of sugar accumulation in blueberry fruit. It was previously reported that vacuolar invertase modulates the hexose to sucrose ratio in ripening frui. In addition, there are also two sugar transport protein homologs that exhibited developmental specific expression. However, their function remains largely unknown, thus, their potential role in sugar accumulation in the developing berry requires further investigation.
Tandemly duplicated genes arise as a result of unequal crossing over or template slippage during DNA repair, exhibit high birth-death rates, and typically are in co-regulated clusters in the genome. Smallerscale duplications , which include tandem duplicates, are highly biased toward certain gene families including those involved in specialized metabolism. Furthermore, tandem duplications often results in the increased dosage of gene products and may improve the metabolic flux of rate limiting steps in certain bio-synthetic pathways. Most genes associated with the biosynthesis of antioxidants have at least one tandem duplicate present in the high bush blueberry genome, with tandem array sizes ranging from 2 to 10 gene copies . The largest tandem arrays were found for HQT and HCT genes, which are co-regulated and involved in the CGA pathway . Differences in tandem array sizes were also observed between homoeologous chromosomes for various genes. For example, the C3H gene, which is involved in CGA biosynthesis , was present on all four homoeologous chromosomes but with varying tandem array sizes. One of the homoeologous chromosomes had two copies of C3H, while the other three homoeologous chromosomes had four copies. This suggests that copy number differences of C3H among sub genomes may be due to either selection for gene duplication or loss or, in the case of allopolyploidy, may be due to preexisting gene content differences among the diploid progenitor species. Genes in the anthocyanin pathway with other unique duplication patterns include CHS, CHI, OMT, and UFGT. The gene CHS, involved in the conversion of 4-coumaryl-CoA to naringenin chalcone, has two copies, and both have tandem duplicates in at least three of the homoeologous chromosomes. interestingly, the gene CHI has a single preserved tandem gene duplicate on only one of the homoeologous chromosomes. However, nft system additional copies of CHI were also identified more distantly away from the syntenic ortholog on another homoeologous chromosome, likely involving a transposition event following tandem duplication. The OMT and UFGT genes all have tandem duplicates on all of the homoeologous chromosomes, although with varying array sizes, while the ANR gene involved in the conversion of anthocyanidin to proanthocyanidin is single copy on all homoeologous chromosomes. DFR gene, which is involved inthe conversion of dihydroquercetin/dihyromyricetin to leucoanthocyanidin, has a single tandem duplicate on only one of the homoeologous chromosomes. These findings suggest that there may have been greater selective pressure to retain tandem duplicates for genes encoding enzymes involved in anthocyanin production than conversion to proanthocyanidins. The vast majority of tandem duplicates are eventually lost ; however, in rare instances, some may undergo functional diversification. Gene expression analysis revealed that 83.4% of the tandem duplicates were expressed in at least one transcriptome library with 73.5% expressed in at least one of the fruit developmental stages. This suggests that a subset of these duplicate genes have non-functionalized, subfunctionalized, or neofunctionalized. Future studies are needed to more thoroughly investigate the functions of these genes with more diverse libraries and additional transcriptome analyses.Despite the economic importance of blueberry, molecular breeding approaches to produce superior cultivars have been greatly hampered by inadequate genomic resources and a limited understanding of the underlying genetics encoding important traits. This has resulted in breeders having to solely rely on traditional approaches to generate new cultivars, each with widely varying fruit quality characteristics. For example, our analysis of a diversity panel consisting of 84 cultivars and wild species revealed that ”Draper” has antioxidant levels that are up to 19x higher than other cultivars. Thus, the genome of ”Draper” should serve as a powerful resource to the blueberry community for guiding future breeding efforts aimed at improving antioxidant levels among other important fruit quality traits.
Furthermore, to our knowledge, this is not only the first genome assembly of the cultivated high bush blueberry but is also the first chromosome-scale and haplotype-phased genome for any species in the order Ericales. Ericales includes several other high-value crops and wild species with unique lift history traits . Thus, we anticipate that this reference genome, plus associated datasets, will be useful for a wide variety of evolutionary studies. Here, we also leveraged the genome to identify candidate genes and pathways that encode superior fruit quality in blueberry, including those associated with pigmentation, sugar, and antioxidant levels. Furthermore, we found that genes encoding key bio-synthetic steps in various antioxidant pathways are enriched with tandem gene duplicates. For example, tandem gene duplications have expanded gene families that are involved in the biosynthesis of anthocyanins. This suggests that, in addition to a recent whole genome duplication, tandem duplications may have greatly contributed to the metabolic diversity observed in blueberry . These tandem duplicates may have evolved new functions , possibly involved in the biosynthesis of novel compounds, and/or were selected to improve the metabolic flux of specific bio-synthetic steps that alter the dosage of certain endpoint metabolites. Future studies are needed to further investigate the possible role of tandem duplications in having modified metabolite levels and composition in wild and cultivated blueberry. Our analyses also revealed that high bush blueberry, a tetraploid, likely arose from the hybridization of two distinct parents, possibly allopolyploidy, based on the sequence divergence, unique transposable element insertions, and sub genome expression patterns. Our analyses revealed that the sub genomes in high bush blueberry may be controlling a distinct set of genetic programs . The dominantly expressed sub genome in most surveyed Thissues becomes the lowest expressed during fruit development. This observation is similar to findings in allopolyploid wheat where developmental and adaptive traits were shown to be controlled by different sub genomes. For example, cell type- and stage dependent sub genome expression dominance was observed in the developing wheat grain. We argue that both high bush blueberry and hexaploid wheat, each now with high-quality reference genomes, make excellent systems to further investigate these underlying mechanisms of sub genome dominance. sub genome dominance has far-reaching implications to numerous research areas including breeding efforts. For example, marker-assisted breeding needs to target the correct set of dominant homoeologs given the trait in polyploids that exhibit sub genome dominance. Thus, we anticipate that this genome, combined with improved insights into sub genome dominance, will greatly accelerate molecular breeding efforts in the cultivated high bush blueberry.High-molecular-weight genomic DNA was isolated from young leaf Thissue, following a 72-hour dark treatment, using a modified nuclei preparation method.