RNA-Seq Reveals Flavonoid Biosynthesis-Related Genes in Pecan (Carya illinoinensis) Kernels

Abstract

Pecan (Carya illinoinensis) is an important tree nut throughout the world. The high concentration of flavonoid in its kernels makes it an excellent food with health benefits. However, the molecular basis of flavonoid biosynthesis in pecan remains unclear, which hinders quality breeding in this plant. Therefore, in order to find the crucial genes involved in flavonoid biosynthesis, the changes in flavonoid profiles and the transcriptomes of pecan kernels at four developmental stages (late water, gel, dough, and mature stages) were analyzed. As a result, the highest levels of total phenolic, condensed tannin, and flavan-3-ols were observed at the "late water stage". Catechin was the most abundant flavan-3-ol at different development stages. In total, 64 773 unigenes were obtained, and 46 924 (72.44%) unigenes were annotated. After differentially expressed gene (DEG) analysis, 12 750 unique DEGs were identified. Flavonoid-related DEGs of 36 structural genes and eight MYBs were obtained. The structural gene set contained three PALs, three CHSs, two CHIs, one F3H, two F3′Hs, two F3′5′Hs, one DFR, one ANS, two LARs, and two ANRs. The expression patterns of most of the structural genes were consistent with the changes in flavonoid profiles during kernel development. We believe that this RNA-Seq data set will provide valuable resources for unraveling the molecular mechanism of flavonoid metabolism in pecan and will significantly promote genetic studies and quality breeding in this plant.

Isolation and Characterization of Three Chalcone Synthase Genes in Pecan (Carya illinoinensis)

“…Thus, many studies have focused on the separation of phenolics and characterization of antioxidant capacity of different components in pecan [6,7,8,9]. However, the molecular basis of phenolic biosynthesis in pecan has not been fully elucidated [10]. Recently, an RNA-Seq dataset of pecan kernels was released, and in total, 36 putative structural genes involved in flavonoid synthesis were reported [10].…”

Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis)

“…Recently, next and third-generation sequencing technologies have been employed to investigate molecular mechanisms of key traits and construct a reference genome in pecan [3,4,12,28]. Transcriptomes and draft genomes offered an opportunity to identify SSR sites on a large scale.…”

“…The genus Carya consists of 17 species [1], of which pecan, hickory, C. hunanensis, and C. dabieshanensis have significant economic values in China [3]. However, the molecular markers in these species are far from sufficient.…”

“…K. Koch), native to North America, is an important crop worldwide [1]. Pecan nuts are rich in unsaturated fatty acids, phenolics, and flavonoids and have good nutritional and health benefits [2][3][4]. The nut shell contains high levels of bioactive compounds, including tocopherols, phytosterols, total phenolics, and condensed tannins, and shows antioxidant, antimicrobial, and potential anticancer activity [5,6].…”

“…In recent years, transcriptome and genome data of pecan have been published [3,4,28,29], offering a good opportunity to discover and develop SSRs on a large scale. Compared to genic SSRs, genomic SSRs (gSSRs) are more abundant [30].…”