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The N absorption and assimilation is critical for the rice (Oryza sativa L.) yield increase when overdose N was applied in rice production. Three different rice genotypes, 'Quanliangyou 1' (Q1), 'Quanliangyou 681' (Q681) and 'Huanghuazhan' (HHZ), were selected to investigate the effects of elevated N input on the N partitioning, plant growth, grain quality and key genes involved in glutamate biosynthesis. Under increasing N inputs (0, 120, 180, 250 kg ha-1), N content in leaf, culm, seed and root were increased significantly. The increased N was preferentially deposited in leaf and culm. Tiller number, panicle number and length were also proved to be significantly promoted, but plant height and 1000-grain weight were nonsignificantly affected under elevated N input. Under high N input, seed protein content was elevated, while fatty acid and amylose content remained unchanged in comparison to low N input, but amylopectin content decreased. For the key genes in N assimilation, glutamine synthetase (OsGS1;1) could be induced by increasing N input (0 to 180 kg ha-1) but higher N input (250 kg ha-1) inhibit its expression, which showed similar response pattern with the glutamine synthetase activity. Although different rice genotypes showed similar response pattern to elevated N input, each genotype varied a lot in certain phenotypic indexes. And the response pattern of all these phenotypic characteristics to elevated N input was independent of rice genotype. These findings suggest that elevated N input could promote rice growth, reallocate N content in different tissues, and have negative impact on grain quality. This study provided physiological and molecular foundation for rice breeding and cultivation under high N input.

The phenotypic color of seeds is a complex agronomic trait and has economic and biological significance. The genetic control and molecular regulation mechanisms have been extensively studied. Here, we used a multi-omics strategy to explore the color formation in soybean seeds at a big-data scale. We identified 13 large quantitative trait loci (QTL) for color with bulk segregating analysis in recombinant inbreeding lines. GWAS analysis of colors and decomposed attributes in 763 germplasms revealed associated SNP sites perfectly falling in five major QTL, suggesting inherited genetic control on color during natural selection. Further transcriptomics analysis before and after color accumulation revealed 182 differentially expression genes (DEGs) in the five QTL, including known genes CHS, MYB, and F3’H involved in pigment accumulation. More DEGs with consistently up- or down-regulation were identified as shared regulatory genes for two or more color formations while some DEGs were only for a specific color formation. For example, five up-regulated DEGs in QTL qSC-3 were in flavonoid biosynthesis responsible for black and brown seed. The DEG (Glyma.08G085400) was identified in the purple seed only, which encodes gibberellin 2-beta-dioxygenase in the metabolism of colorful terpenoids. The candidate genes are involved in flavonoid biosynthesis, transcription factor regulation, gibberellin and terpenoid metabolism, photosynthesis, ascorbate and aldarate metabolism, and lipid metabolism. Seven differentially expressed transcription factors were also found to regulate color formation, including a known MYB. The finds expand QTL and gene candidates for color formation, which could guide to breed better cultivars with designed colors.