Background: The auxin indole-3-acetic acid (IAA) is a vital phytohormone that influences plant growth and development. Our previous work showed that IAA content decreased during flower development in the medicinally important orchid Dendrobium officinale, while Aux/IAA genes were downregulated. However, little information about auxin-responsive genes and their roles in D. officinale flower development exists. Results: This study validated 14 DoIAA and 26 DoARF early auxin-responsive genes in the D. officinale genome. A phylogenetic analysis classified the DoIAA genes into two subgroups. An analysis of cis-regulatory elements indicated that they were related by phytohormones and abiotic stresses. Gene expression profiles were tissue-specific. Most DoIAA genes (except for DoIAA7) were sensitive to IAA (10 μmol/L) and were downregulated during flower development. Four DoIAA proteins (DoIAA1, DoIAA6, DoIAA10 and DoIAA13) were mainly localized in the nucleus. A yeast two-hybrid assay showed that these four DoIAA proteins interacted with three DoARF proteins (DoARF2, DoARF17, DoARF23). Conclusions: The structure and molecular functions of early auxin-responsive genes in D. officinale were investigated. The DoIAA-DoARF interaction may play an important role in flower development via the auxin signaling pathway.

The present study investigated the dynamic changes in vitamin E and gene expression within its biosynthetic pathway during three germination periods of four brown rice cultivars with different seed coat colors. The results reveal that the vitamin E content increased during the germination process of all brown rice cultivars. Moreover, the content of α-tocopherol, α-tocotrienol, and β-tocopherol significantly increased at the later stage of germination. The expression levels of DXS1 and γ-TMT genes in all cultivars were significantly increased, whilst the HGGT gene expression levels of G6 and XY cultivars increased significantly at the later stage of brown rice germination. In addition, the expression levels of MPBQ/MT2 in G1 and G6 cultivars, and TC expression levels in G2 and G6 cultivars were substantially increased at the later stage of germination. Overall, the up-regulation of MPBQ/MT2, γ-TMT, and TC genes doubled the content of α-tocopherol, α-tocotrienol, and β-tocopherol, and the total vitamin E content of brown rice was at its highest at 96HAT. The utilization of the germination period can effectively improve the nutritional value of brown rice, which can be used for the development and utilization of brown rice for healthy rice products.

Waxy corn kernels with different colors have high phenolic content and good application potential in medicine and food healthcare. In our work, the content changes of phenolic and anthocyanins profiles were related to genes in the anthocyanin biosynthesis pathway, and the antioxidant activities of three different colors of waxy corn kernels (black, white, and yellow) were determined during kernel development. Results showed that growing temperature and light intensity could affect the accumulation of phytochemicals and antioxidant activities in waxy corns during maturation. Phenolic and antioxidant activities decreased over kernel maturation, and spring had higher nutrition levels during the best harvest time (20 and 25 days after pollination in the spring and autumn, respectively) for waxy corns. Cyanidin-3-O-glucoside and pelargonidin-3-O-glucoside were the main anthocyanins detected in the black waxy corns. The contents of cyanidin are higher than pelargonidin followed by peonidin in the autumn, while on the other hand, pelargonidin had a slightly higher content compared to cyanidin in the spring. DFR, CF1, and ANS were the key genes affecting anthocyanin accumulation. This work provided information on the best harvest time for the pigment of waxy corn in order to achieve relatively high phenolic profiles and antioxidant activities. It also illustrated the possible relationship between weather conditions, gene expression levels, and phenolic content during kernel development.

Theindicarice variety XYXZ carries elite traits including appearance and eating quality. Here, we report the de novo assembly of XYXZ using Illumine paired-end whole-genome shotgun sequencing and Nanopore sequencing. We annotated 39,722 protein-coding genes in the 395.04 Mb assembly. In comparison to other cultivars, XYXZ showed a larger gene size including the transcripts and introns, and more exons per gene. And hundreds of ultra-long genes were also detected. A total of 4362 complete LTRs were annotated, and among them, many were located next to or in protein-coding genes including several genes related to rice quality. We observed the different distributions of LTRs in these genes among XYXZ, Nipponbare, and R498, implying these LTRs might potentially affect expressions of the proximal genes and rice quality. Overall, This chromosome-length genome assembly of XYXZ provides a valuable resource for gene discovery, genetic variation and evolution, and the breeding of high-quality rice.