Multi-omics Strategies to Analyze Complex Agronomic Traits in Plants

High temperature stress is regarded as one of the significant abiotic stresses affecting the composition and distribution of natural habitats and the productivity of agriculturally significant plants worldwide. The HSF family is one of the most important transcription factors (TFs) families in plants and capable of responding rapidly to heat and other abiotic stresses. In this study, 29 AgHSFs were identified in celery and classified into three classes (A, B, and C) and 14 subgroups. The gene structures of AgHSFs in same subgroups were conserved, whereas in different classes were varied. AgHSF proteins were predicted to be involved in multiple biological processes by interacting with other proteins. Expression analysis revealed that AgHSF genes play a significant role in response to heat stress. Subsequently, AgHSFa6-1, which was significantly induced by high temperature, was selected for functional validation. AgHSFa6-1 was identified as a nuclear protein, and can upregulate the expression of certain downstream genes (HSP98.7, HSP70-1, BOB1, CPN60B, ADH2, APX1, GOLS1) in response to high-temperature treatment. Overexpression of AgHSFa6-1 in yeast and Arabidopsis displayed higher thermotolerance, both morphologically and physiologically. In response to heat stress, the transgenic plants produced considerably more proline, solute protein, antioxidant enzymes, and less MDA than wild-type (WT) plants. Overall, this study revealed that AgHSF family members perform a key role in response to high temperature, and AgHSFa6-1 acts as a positive regulator by augmenting the ROS-scavenging system to maintain membrane integrity, reducing stomatal apertures to control water loss, and upregulating the expression level of heat-stress sensitive genes to improve celery thermotolerance.

Maize (Zea mays) inbred lines vary greatly in flowering time, but the genetic basis of this variation is unknown. In this study, three maize flowering-related traits (DTT, days to tasselling; DTP, days to pollen shed; DTS, days to silking) were evaluated with an association panel consisting of 226 maize inbred lines and an F_2:3 population with 120 offspring from a cross between the T32 and Qi319 lines in different environments. A total of 82 significant single nucleotide polymorphisms (SNPs) and 117 candidate genes were identified by genome-wide association analysis. Twenty-one quantitative trait loci (QTLs) and 65 candidate genes were found for maize flowering time by linkage analysis with the constructed high-density genetic map. Transcriptome analysis was performed for Qi319, which is an early-maturing inbred line, and T32, which is a late-maturing inbred line, in two different environments. Compared with T32, Qi319 showed upregulation of 3815 genes and downregulation of 3906 genes. By integrating a genome-wide association study (GWAS), linkage analysis and transcriptome analysis, 25 important candidate genes for maize flowering time were identified. Together, our results provide an important resource and a foundation for an enhanced understanding of flowering time in maize.

Gibberellin (GA) is an important phytohormone that can participate in various developmental processes of plants. The study found that application of GA₃ can induce parthenocarpy fruit and improve fruit set. However, the use of GA₃ affects endogenous hormones in fruits, thereby affecting fruit quality. This study mainly investigates the effect of exogenous GA₃ on endogenous hormones in sweet cherries. The anabolic pathways of each hormone were analyzed by metabolome and transcriptome to identify key metabolites and genes that affect endogenous hormones in response to exogenous GA₃ application. Results showed that exogenous GA₃ led to a significant increase in the content of abscisic acid (ABA) and GA and affected jasmonic acid (JA) and auxin (IAA). At the same time, the key structural genes affecting the synthesis of various hormones were preliminarily determined. Combined with transcription factor family analysis, WRKY genes were found to be more sensitive to the use of exogenous GA₃, especially the genes belonging to Group III (PaWRKY16, PaWRKY21, PaWRKY38, PaWRKY52, and PaWRKY53). These transcription factors can combine with the promoters of NCED, YUCCA, and other genes to regulate the content of endogenous hormones. These findings lay the foundation for the preliminary determination of the mechanism of GA₃’s effect on endogenous hormones in sweet cherry and the biological function of WRKY transcription factors.