Auxin plays an important role in regulating leaf senescence. Auxin response factors (ARFs) are crucial components of the auxin signaling pathway; however, their roles in leaf senescence in cereal crops are unknown. In this study, we identified TaARF15-A1 as a negative regulator of senescence in wheat (Triticum aestivum L.) by analyzing TaARF15-A1 overexpression (OE) and RNA interference lines and CRISPR/Cas9-based arf15 mutants. OE of TaARF15-A1 delayed senescence, whereas knockdown lines and knockout mutants showed accelerated leaf senescence and grain ripening. RNA-seq analysis revealed that TaARF15-A1 delays leaf senescence by negatively regulating senescence-promoting processes and positively modulating senescence-delaying genes including senescence-associated phytohormone biosynthesis and metabolism genes as well as transcription factors (TFs). We also demonstrated that TaARF15-A1 physically interacts with TaMYC2, a core jasmonic acid (JA) signaling TF that positively modulates wheat senescence. Furthermore, TaARF15-A1 suppressed the expression of TaNAM-1 (TaNAM-A1 and TaNAM-D1) via protein–protein interaction and competition with TaMYC2 for binding to its promoter to regulate senescence. Finally, we identified two haplotypes of TaARF15-A1 in global wheat collections. Association analysis revealed that TaARF15-A1-HapI has undergone strong selection during wheat breeding in China, likely owing to its earlier maturity. Thus, we identify TaARF15-A1 as a negative regulator of senescence in common wheat and present another perspective on the crosstalk between auxin and JA signaling pathways in regulating plant senescence.

Flag-leaf-related traits including length (FLL), width (FLW), area (FLA), thickness (FLT), and volume (FLV) of flag leaves are the most important determinants of plant architecture and yield in wheat. Understanding the genetic basis of these traits could accelerate the breeding of high yield wheat varieties. In this study, we constructed a doubled haploid (DH) population and analyzed flag-leaf-related traits in five experimental locations/years using the wheat 90K single-nucleotide polymorphism array. It’s worth noting that a novel method was used to measure FLT and FLV easily. Leaf thickness at two-thirds of the leaf length from tip to collar represented the average leaf thickness as measured with freehand sections and was used to calculate the leaf volume. In addition, flag-leaf-related traits showed positive correlations with yield related traits under two different water regimes. A total of 79 quantitative trait loci (QTL) controlling the five traits were detected among all chromosomes except 4D and 5A, explaining 3.09–14.52% of the phenotypic variation. Among them, 15 stable QTL were identified in more than three environments, including two major QTL for FLT, six for FLW, three for FLA, two for FLT and two for FLV. DH lines with positive alleles at both QTL regions had an average FLL (9.90%), FLW (32.87%), FLT (6.62%), FLA (18.47%), and FLV (20.87%) greater than lines with contrasting alleles. QFLT-2B, QFLV-2A, and QFLV-7D were co-located with yield-related traits. The 15 QTL were validated by tightly linked kompetitive allele specific PCR (KASP) markers in a recombinant inbred line (RIL) population derived from a different cross. QFLL-4A, QFLW-4B, QFLA-5D.1, QFLA-7A, QFLA-7D.1, QFLT-2B, QFLT-6A, QFLV-2A, and QFLV-7D are likely novel loci. These results provide a better understanding of the genetic basis underlying flag-leaf-related traits. Also, target regions for fine mapping and marker-assisted selection were identified and these will be valuable for breeding high yielding bread wheat.

The synonymous codons usage shows a characteristic pattern of preference in each organism. This codon usage bias is thought to have evolved for efficient protein synthesis. Synonymous codon usage was studied in genes of the hexaploid wheat Triticum aestivum (AABBDD) and its progenitor species, Triticum urartu (AA), Aegilops tauschii (DD), and Triticum turgidum (AABB). Triticum aestivum exhibited stronger usage bias for G/C-ending codons than did the three progenitor species, and this bias was especially higher compared to T. turgidum and Ae. tauschii. High GC content is a primary factor influencing codon usage in T. aestivum. Neutrality analysis showed a significant positive correlation (p<0.001) between GC12 and GC3 in the four species with regression line slopes near zero (0.16–0.20), suggesting that the effect of mutation on codon usage was only 16–20%. The GC3s values of genes were associated with gene length and distribution density within chromosomes. tRNA abundance data indicated that codon preference corresponded to the relative abundance of isoaccepting tRNAs in the four species. Both mutation and selection have affected synonymous codon usage in hexaploid wheat and its progenitor species. GO enrichment showed that GC biased genes were commonly enriched in physiological processes such as photosynthesis and response to acid chemical. In some certain gene families with important functions, the codon usage of small parts of genes has changed during the evolution process of T. aestivum.

Walnut oil is an excellent source of essential fatty acids. Systematic evaluation of walnut lipids has significance for the development of the nutritional and functional value of walnut. Ultra-performance liquid chromatography/Orbitrap high-resolution mass spectrometry (UHPLC-Orbitrap HRMS) was used to characterize the lipids of walnut. A total of 525 lipids were detected and triacylglycerols (TG) (18:2/18:2/18:3) and diacylglycerols (DG) (18:2/18:2) were the main glycerolipids present. Essential fatty acids, such as linoleic acid and linolenic acid, were the main DG and TG fatty acid chains. Many types of phospholipids were observed with phosphatidic acid being present in the highest concentration (5.58%). Using a combination of metabolome and transcriptome analysis, the present study mapped the main lipid metabolism pathway in walnut. These results may provide a theoretical basis for further study and specific gene targets to enable the development of walnut with increased oil content and modified fatty acid composition.

N⁶-methyladenine (6mA) DNA modification has been detected in several eukaryotic organisms, where it plays important roles in gene regulation and epigenetic memory maintenance. However, the genome-wide distribution patterns and potential functions of 6mA DNA modification in woodland strawberry (Fragaria vesca) remain largely unknown. Here, we examined the 6mA landscape in the F. vesca genome by adopting single-molecule real-time sequencing technology and found that 6mA modification sites were broadly distributed across the woodland strawberry genome. The pattern of 6mA distribution in the long non-coding RNA was significantly different from that in protein-coding genes. The 6mA modification influenced the gene transcription and was positively associated with gene expression, which was validated by computational and experimental analyses. Our study provides new insights into the DNA methylation in F. vesca.