Comparative Transcriptome Analysis Reveals Differential Regulation of Flavonoids Biosynthesis Between Kernels of Two Pecan Cultivars

Abstract

Flavonoids influence the flavor and nutritional value of pecan nuts. However, limited information is available regarding the molecular mechanisms underlying pecan flavonoid biosynthesis. Here, we used a high (“YLC28”) and a low (“Oconee”) flavonoid content cultivar as the research objects. The changes in flavonoid content and the gene transcription patterns during kernel development were identified. Different accumulation patterns of total flavonoids (TF) and condensed tannins (CT) were observed between the two cultivars. The contents of TF and CT in “YLC28” were 1.76- and 2.67-fold higher levels than that of “Oconee” on 150 days after full bloom of female flowers, respectively. In total, 30 RNA-Seq libraries were constructed and sequenced. The upregulated genes in “YLC28” were highly enriched in flavonoid-related pathways. Thirty-three structural genes were identified, and the expression of two phenylalanine ammonia lyases, one chalcone synthase, one flavonoid 3’,5’-hydroxylase, and one flavonol synthase exhibited high correlation (r ≥ 0.7, p < 0.01) with the condensed tannin content in “YLC28.” A putative MYB transcription factor, CIL1093S0100, might act as a flavonoid biosynthesis repressor during kernel development. Altogether, these results will be useful for uncovering the molecular mechanisms of flavonoid biosynthesis and subsequently accelerating quality pecan breeding.

Metabolomics and Transcriptomics Analyses Reveal Regulatory Networks Associated with Fatty Acid Accumulation in Pecan Kernels

“…Aapigenin, phloretin, catechin, and procyanidin B2 levels exhibited similar trends, with high content during the first and third developmental stage. In our previous study, we reported that the lowest level of apigenin occurred during the middle developmental stage of pecan kernels …”

“…In our previous study, we reported that the lowest level of apigenin occurred during the middle developmental stage of pecan kernels. 17 Correlation Analysis of Metabolites. To explore the correlation between the different metabolites, a metabolite− metabolite Pearson correlation matrix was generated (Figure 4).…”

“…Furthermore, knowing the approximate proportions of these nutrients can facilitate the determination of the accurate nutritional value of pecan nuts. However, to date, only a few studies have been performed to identify the concentration variations of nutrients in pecan kernels, and they have reported that the content of FAs, proteins, phenolics, flavonoids, and tocopherols varied with genotypes and embryo developmental stages. − Despite the several bioactive components analyzed during pecan kernel development, to the best of our knowledge, the comprehensive metabolite variations and regulatory networks associated with different metabolites remain unknown.…”

Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting

“…The PRJNA533506 project provided the raw data regarding the pistillate flower of 'Pawnee' at five stages: flower bud 1 (FB1), FB2, FB3, flower 1 (FL1), and FL2 in timing order [32]. The PRJNA792564 project offered the RNA-seq raw data of a developing kernel that collected from 'YLC28' trees 100, 114, 121, 135, and 150 d after pistillate flower full bloom [33]. The downloaded raw data were filtered via standard quality control to generate clean reads for mapping.…”