The improvement of quality traits, including grain quality traits and dough rheological properties, are important goal in wheat breeding for a long time. To understand the genetic basis of key quality traits of wheat, two single-locus and five multi-locus GWAS models were performed for six grain quality traits and three dough rheological properties based on 19, 254 SNPs in 267 bread wheat accessions. As a result, 299 quantitative trait nucleotides (QTNs) within 105 regions were identified to be associated with these quality traits in four environments. Among the 105 QTN regions, 40 core QTN regions were stably detected in at least three environments, 19 of which are novel. Compared with the previous studies, these novel QTN regions explained smaller phenotypic variation, which verified the advantages of the multi-locus GWAS models in detecting important small effect QTNs associated with complex traits. After detailed function and expression analysis, 67 core candidate genes involved in protein/sugar synthesis, histone modification and transcription factor regulation were determined to be related to grain quality formation, which indicated that wheat grain quality was affected by multi-level regulation. Finally, a preliminary network of gene regulation that may affect wheat quality formation was inferred. This study verified the power and reliability of multi-locus GWAS methods in wheat quality trait research, and increased the understanding of wheat quality formation mechanisms. The detected QTN regions and candidate genes in this study could be further used for gene cloning and marker-assisted selection in high-quality breeding of bread wheat.

Background: Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacteria and abiotic stress by modulating the transmembrane transfer of amino acids. In this study, we performed a genome-wide screening to analyze the AAT genes in foxtail millet (Setaria italica L.), especially those associated with quality formation and abiotic stresses response. Results: A total number of 94 AAT genes were identified and divided into 12 subfamilies by their sequence characteristics and phylogenetic relationship. A large number (58/94, 62%) of AAT genes in foxtail millet were expanded via gene duplication, involving 13 tandem and 12 segmental duplication events. Tandemly duplicated genes had a significant impact on their functional differentiation via sequence variation, structural variation and expression variation. Further comparison in multiple species showed that in addition to paralogous genes, the expression variations of the orthologous AAT genes also contributed to their functional differentiation. The transcriptomic comparison of two millet cultivars verified the direct contribution of the AAT genes such as SiAAP1, SiAAP8, and SiAUX2 in the formation of grain quality. In addition, the qRT-PCR analysis suggested that several AAT genes continuously responded to diverse abiotic stresses, such as SiATLb1, SiANT1. Finally, combined with the previous studies and analysis on sequence characteristics and expression patterns of AAT genes, the possible functions of the foxtail millet AAT genes were predicted. Conclusion: This study for the first time reported the evolutionary features, functional differentiation, roles in the quality formation and response to abiotic stresses of foxtail millet AAT gene family, thus providing a framework for further functional analysis of SiAAT genes, and also contributing to the applications of AAT genes in improving the quality and resistance to abiotic stresses of foxtail millet, and other cereal crops.

The vacuolar type H⁺-ATPase (V-type H⁺-ATPase) plays important roles in establishing an electrochemical H⁺-gradient across tonoplast, energizing Na⁺ sequestration into the central vacuole, and enhancing salt stress tolerance in plants. In this paper, a putative E subunit of the V-type H⁺-ATPase gene, W36 was isolated from stress-induced wheat de novo transcriptome sequencing combining with 5'-RACE and RT-PCR methods. The full-length of W36 gene was 1097 bp, which contained a 681 bp open reading frame (ORF) and encoded 227 amino acids. Southern blot analysis indicated that W36 was a single-copy gene. The quantitative real-time PCR (qRT-PCR) analysis revealed that the expression level of W36 could be upregulated by drought, cold, salt, and exogenous ABA treatment. A subcellular localization assay showed that the W36 protein accumulated in the cytoplasm. Isolation of the W36 promoter revealed some cis-acting elements responding to abiotic stresses. Transgenic Arabidopsis plants overexpressing W36 were enhanced salt and mannitol tolerance. These results indicate that W36 is involved in the plant response to osmotic stress.

The excessive content of heavy metals and the deficiency of beneficial trace elements in cereals have threatened global food security and human health. As important metal transporters, Natural resistance-associated macrophage proteins (Nramps) are involved in the absorption and transport of various metal ions in plants, including beneficial elements and hazardous heavy metals, yet little is known about their roles in foxtail millet. In this study, 12 Nramps were identified in foxtail millet genome and divided into three clades. Expansion and functional differentiation of SiNramp gene family is evident in the high proportion of gene duplication as well as the diversity in protein structure and expression characteristics. The SiNramp genes exhibited different response patterns to Cd stress in different tissues. Based on the integration of ionome, RNA-seq and orthologous analysis, the association of SiNramp genes with the accumulation of different metal ions was investigated, and the possible functions of several SiNramp genes were predicted, such as SiNramp6 and SiNramp12. In general, this study provides a comprehensive theoretical framework for the study of Nramp genes in foxtail millet and other minor gramineous crops, which will lay a foundation for further research on the mechanism of metal transport and accumulation.