Integrative analysis of transcriptome and miRNAome reveals molecular mechanisms regulating pericarp thickness in sweet corn during kernel development

Pericarp thickness affects the edible quality of sweet corn (Zea mays L. saccharata Sturt.). Therefore, breeding varieties with a thin pericarp is important for the quality breeding of sweet corn. However, the molecular mechanisms underlying the pericarp development remain largely unclear. We performed an integrative analysis of mRNA and miRNA sequencing to elucidate the genetic mechanism regulating pericarp thickness during kernel development (at 15 days, 19 days, and 23 days after pollination) of two sweet corn inbred lines with different pericarp thicknesses (M03, with a thinner pericarp and M08, with a thicker pericarp). A total of 2,443 and 1,409 differentially expressed genes (DEGs) were identified in M03 and M08, respectively. Our results indicate that phytohormone-mediated programmed cell death (PCD) may play a critical role in determining pericarp thickness in sweet corn. Auxin (AUX), gibberellin (GA), and brassinosteroid (BR) signal transduction may indirectly mediate PCD to regulate pericarp thickness in M03 (the thin pericarp variety). In contrast, abscisic acid (ABA), cytokinin (CK), and ethylene (ETH) signaling may be the key regulators of pericarp PCD in M08 (the thick pericarp variety). Furthermore, 110 differentially expressed microRNAs (DEMIs) and 478 differentially expressed target genes were identified. miRNA164-, miRNA167-, and miRNA156-mediated miRNA–mRNA pairs may participate in regulating pericarp thickness. The expression results of DEGs were validated by quantitative real-time PCR. These findings provide insights into the molecular mechanisms regulating pericarp thickness and propose the objective of breeding sweet corn varieties with a thin pericarp

Physiological and Molecular Characteristics of Southern Leaf Blight Resistance in Sweet Corn Inbred Lines

Southern corn leaf blight is one of the most widespread foliar diseases in maize-producing areas worldwide and can seriously reduce the yield and quality of sweet corn. However, the molecular mechanisms underlying the disease in sweet corn have not been widely reported. In this study, two sweet corn inbred lines, resistant K13 (RK13) and susceptible K39 (SK39), were used to explore the disease resistance mechanism of southern leaf blight. We observed morphological characteristics and assessed the changes in protective enzymatic activity in sweet corn leaves after inoculation of C. heterostrophus. RNA-seq was performed to elucidate the transcriptional dynamics and reveal the key pathways involved in southern leaf blight resistance without pathogens (Mock) and at 1 and 3 days post inoculation (1 and 3 dpi). Differentially expressed genes (DEGs) were identified in the SK39 group (including three pairwise combinations: SK39−0d_vs_SK39−1d, SK39−1d_vs_SK39−3d and SK39−1d_vs_SK39−3d), the RK13 group (including three pairwise combinations: RK13−0d_vs_RK13−1d, RK13−1d_vs_RK13−3d and RK13−1d_vs_RK13−3d), and the SK39_vs_RK13 group (including three pairwise combinations: SK39−0d_vs_RK13−0d, SK39−1d_vs_RK13−1d, and SK39−3d_vs_RK13−3d). In our study, 9455 DEGs from the RK13 group, 9626 from the SK39 group, and 9051 DEGs from the SK39_vs_RK13 group were obtained. Furthermore, 2775, 163, and 185 DEGs were co-expressed at SK39_vs_RK13, RK13, and SK39, respectively. A functional analysis of the DEGs revealed that five pathways—i.e., photosynthesis, plant hormone signal transduction, MAPK signaling pathway, phenylpropanoid biosynthesis, and biosynthesis of secondary metabolites—and transcription factor families play crucial roles in disease resistance. The results from the present study enabled the identification of the JA and SA signaling pathways, which are potentially involved in the response to southern leaf blight in maize. Our findings also highlight the significance of ZIM transcription factors and pathogenesis-related (PR) genes during pathogen infection. This study preliminarily explored the molecular mechanisms of the interaction between sweet corn and C. heterostrophus and provides a reference for identifying southern leaf blight resistance genes in the future

Population Genetic Analysis of a Bread Wheat Panel from Northern and Huang-Huai Agro-Ecological Regions in China

Bread wheat (Triticum aestivum L.) is one of the most extensively cultivated cereal crops around the world. Here, we investigated the population structure and genetic diversity of a panel mainly originated from two wheat agro-ecological regions (northern winter wheat region, NW; and the Huang-Huai River Valley’s facultative wheat region, HH) in China based on a 15K SNP array. Population genetic analysis revealed that the optimal population number (K) was three, and the three groups were roughly related to ecological regions, including NW (mainly Hebei), HH1 (Henan-Shaanxi), and HH2 (Shandong). Within HH, HH1 had a higher nucleotide diversity (π = 0.31167), minor allele frequency (MAF = 0.2663), polymorphism information content (PIC = 0.2668), and expected heterozygosity (Hexp = 0.3346) than HH2. Furthermore, our results demonstrated that genetic diversity decreases with the advancement of wheat breeding. Finally, inference of ancestry informative markers indicated that the genomes of the three pure groups from the three provinces (Hebei, Henan, and Shandong) of the two regions have genomic regions with different mosaic patterns derived from the two landrace groups. These findings may facilitate the development of wheat breeding strategies to target novel desired alleles in the future