SQUAMOSA promoter binding protein-like (SPL) genes are a type of plant-specific transcription factors that play crucial roles in the regulation of phase transition, floral transformation, fruit development, and various stresses. Although SPLs have been characterized in several model species, no systematic analysis has been studied in pecans, an important woody oil tree species. In this study, a total of 32 SPL genes (CiSPLs) were identified in the pecan genome. After conducting phylogenetic analysis of the conserved SBP proteins from Arabidopsis, rice, and poplar, the CiSPLs were separated into eight subgroups. The CiSPL genes within the same subgroup contained very similar exon-intron structures and conserved motifs. Nine segmentally duplicated gene pairs in the pecan genome and 16 collinear gene pairs between the CiSPL and AtSPL genes were identified. Cis-element analysis showed that CiSPL genes may regulate plant meristem differentiation and seed development, participate in various biological processes, and respond to plant hormones and environmental stresses. Therefore, we focused our study on the expression profiles of CiSPL genes during flower and fruit development. Most of the CiSPL genes were predominantly expressed in buds and/or female flowers. Additionally, quantitative real time PCR (qRT-PCR) analyses confirmed that CiSPL genes showed distinct spatiotemporal expression patterns in response to drought and salt treatments. The study provides foundation for the further exploration of the function and evolution of SPL genes in pecan.

To understand the genetic relationships of Castanea species, 16 phenotypic traits were measured, simple sequence repeat (SSR) markers were analyzed, and molecular identity cards (IDs) were constructed for 118 Castanea materials using fluorescent capillary electrophoresis. The coefficient of variation values of the 16 morphological traits of the test materials ranged from 11.11% to 60.38%. A total of 58 alleles were detected using six pairs of SSR core primers, with an average number of 9.7 alleles per locus. The average number of valid alleles per locus was 3.9419 and the proportion of valid alleles was 40.78%. A total of 105 genotypes were detected, and the number of genotypic species that could be amplified per primer pair ranged from 8 to 26. The mean value of the observed heterozygosity was 0.4986. The variation in the He, H, and PIC values was similar; the size of I value was approximately 2.21 times larger, and its mean number of variations was 0.7390, 0.7359, 0.6985, and 1.6015, respectively. The classification of 118 Castanea species was performed using three analytical methods: structure analysis, neighbor-joining (NJ) cluster analysis, and principal coordinate analysis (PCoA), and the results of the three methods were in high agreement. Six pairs of SSR core primers with high polymorphism and strong discriminatory properties were used to identify 118 Castanea plants, and a unique molecular ID card was constructed for each material. These results provide insight into the genetic diversity and population structure of Castanea plants and a theoretical basis for improving the phenomenon of mixed varieties and substandard plants in the Castanea plant market.

Fruit black spot (FBS), a fungal disease of pecan (Carya illinoinensis (Wangenh) K. Koch) caused by the pathogen Pestalotiopsis microspora, is a serious disease and poses a critical threat to pecan yield and quality. However, the details of pecan responses to FBS infection at the transcriptional level remain to be elucidated. In present study, we used RNA-Seq to analyze differential gene expression in three pecan cultivars with varied resistance to FBS infection: Xinxuan-4 (X4), Mahan (M), and Wichita (W), which were categorized as having low, mild, and high susceptibility to FBS, respectively. Nine RNA-Seq libraries were constructed, comprising a total of 58.56 Gb of high-quality bases, and 2420, 4380, and 8754 differentially expressed genes (DEGs) with |log2Fold change| ≥ 1 and p-value < 0.05 were identified between M vs. X4, W vs. M, and W vs. X4, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed to further annotate DEGs that were part of specific pathways, which revealed that out of 134 total pathways, MAPK signaling pathway, plant–pathogen interaction, and plant hormone signal transduction were highly enriched. Transcriptomic profiling analysis revealed that 1681 pathogen-related genes (PRGs), including 24 genes encoding WRKY transcription factors, potentially participate in the process of defense against Pestalotiopsis microspora infection in pecan. The correlation of WRKY TFs and PRGs was also performed to reveal the potential interaction networks among disease-resistance/pathogenesis-related genes and WRKY TFs. Expression profiling of nine genes annotated as TIFY, WRKY TF, and disease-resistance protein-related genes was performed using qRT-PCR, and the results were correlated with RNA-Seq data. This study provides valuable information on the molecular basis of pecan–Pestalotiopsis microspora interaction mechanisms and offers a repertoire of candidate genes related to pecan fruit response to FBS infection.

Pecan forests (Carya illinoinensis) are significant contributors to both food and oil production, and thrive in diverse soil environments, including coastal regions. However, the interplay between soil microbes and pecan forest health in coastal environments remains understudied. Therefore, we investigated soil bacterial and fungal diversity in coastal (Dafeng, DF) and inland (Guomei, GM) pecan plantations using high-throughput sequencing. The results revealed a higher microbial diversity in the DF plantation than in the GM plantation, significantly influenced by pH and edaphic factors. The dominant bacterial phyla were Proteobacteria, Acidobacteriota and Bacteroidota in the DF plantation, and Acidobacteriota, Proteobacteria, and Verrucomicrobiota in the GM plantation. Bacillus, Nitrospira and UTCFX1 were significantly more abundant bacterial genera in DF soil, whereas Candidatus Udaeobacter, HSB_OF53-F07 and ADurbBin063-1 were more prevalent in GM soil. Basidiomycota dominated fungal sequences in the GM plantation, with a higher relative abundance of Ascomycota in the DF plantation. Significant differences in fungal genus composition were observed between plantations, with Scleroderma, Hebeloma, and Naucoria being more abundant in DF soil, and Clavulina, Russula, and Inocybe in GM soil. A functional analysis revealed greater carbohydrate metabolism potential in GM plantation bacteria and a higher ectomycorrhizal fungi abundance in DF soil. Significantly positive correlations were detected between certain bacterial and fungal genera and pH and total soluble salt content, suggesting their role in pecan adaptation to coastal environments and saline–alkali stress mitigation. These findings enhance our understanding of soil microbiomes in coastal pecan plantations, and are anticipated to foster ecologically sustainable agroforestry practices and contribute to coastal marshland ecosystem management.

Chestnut “calcification” is the result of a series of physiological and biochemical changes during postharvest storage; however, the associated mechanisms are unclear. In this study, several potential calcification-related physicochemical parameters in chestnut, including moisture, cell wall materials, cellulose, lignin, and pectin, were measured. Transcriptome analysis was performed on chestnut seeds during different stages of storage. The results showed that the degree of calcification in the chestnut seeds was significantly negatively correlated with the moisture content (r = −0.961) at room temperature (20–25 °C) and a relative humidity of 50–60%. The accumulation of cell wall material in completely calcified seeds was 5.3 times higher than that of fresh seeds. The total content of cellulose and lignin increased during the storage process. Transcriptome analysis of 0% and 50% calcified chestnut was performed; a total of 1801 differentially expressed genes consisting of 805 up-regulated and 996 down-regulated genes were identified during the calcification process. Furthermore, response to water, water deprivation, and salt stress were most enriched by gene ontology (GO) and gene set enrichment analysis (GSEA). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to chestnut calcification included purine metabolism, RNA degradation, the mRNA surveillance pathway, starch and sucrose metabolism, arginine and proline metabolism, and fatty acid metabolism, and were detected. Most of the genes involved in cellulose synthase, lignin catabolism, and pectin catabolism were down-regulated, while only two important genes, scaffold11300 and scaffold0412, were up-regulated, which were annotated as cellulose and pectin synthase genes, respectively. These two genes may contribute to the increase of total cell wall material accumulation during chestnut calcification. The results provided new insights into chestnut calcification process and laid a foundation for further chestnut preservation.

Pecan (Carya illinoinensis) is one of the important economic forest crops which has been widely cultivated in Anhui and Jiangsu Provinces, China. Since 2019, symptoms resembling anthracnose disease...