Studies on rice seed quality through analysis of a large-scale T-DNA insertion population

Abstract

A rice (Oryza sativa) T-DNA insertion population, which included more than 63 000 independent transgenic lines and 8 840 identified flanking sequence tags (FSTs) that were mapped onto the rice genome, was developed to systemically study the rice seed quality control. Genome-wide analysis of the FST distribution showed that T-DNA insertions were positively correlated with expressed genes, but negatively with transposable elements and small RNAs. In addition, the recovered T-DNAs were preferentially located at the untranslated region of the expressed genes. More than 11 000 putative homozygous lines were obtained through multi-generations of planting and resistance screening, and measurement of seed quality of around half of them, including the contents of starch, amylose, protein and fat, with a nondestructive near-infrared spectroscopy method, identified 551 mutants with unique or multiple altered parameters of seed quality. Analysis of the corresponding FSTs showed that genes participating in diverse functions, including metabolic processes and transcriptional regulation, were involved, indicating that seed quality is regulated by a complex network. IntroductionRice (Oryza sativa), as a wholesome and nutritious cereal grain, provides the staple food for more than half of the world's population [1]. Along with the growth of economies and population throughout the world, there is an increasing demand for high-yield and high-quality rice. The grain quality of rice, including that of milling, appearance, cooking and eating, and nutrition, is determined by multiple physicochemical properties [2], and studies on the involved key genes and relevant regulatory mechanisms will help to illustrate the regulatory networks of rice quality control and benefit for the breeding efforts.Starch, which is composed of amylose and amylopectin, comprises ∼90% of dry endosperm of rice seed.The apparent amylose content (AAC) is recognized as an important determinant of the appearance and texture of grain [3]. Thai jasmine rice (KDML 105), one of the best-quality rice with good cooking and eating qualities, has low amylose content (AC) and medium gel consistency (GC) [4].The nutritional quality includes the proportions of protein, fat, mineral and other substances [5]. The rice protein is rich in methionine and cysteine, and compares favorably with proteins of other cereals, but is poor in lysine and threonine, making it an incomplete protein source for human infants [6]. Storage triacylglycerols are stored in oil bodies containing phospholipids and oleosins at the surface [7], and oil bodies are abundant in embryo and aleurone layer of rice seed. However, the aleurone layer is usually removed by milling because it turns rancid upon storage [8]. In addition, oil also influences other aspects of seed quality, and a recent report showed that the quality and viability of Arabidopsis seeds can be enhanced by suppressing phospholipase D [9].The near-infrared spectroscopy (NIRS) technology, which is based on the fact that several natural pr...

Rice ABI5-Like1 Regulates Abscisic Acid and Auxin Responses by Affecting the Expression of ABRE-Containing Genes

“…A search of the Shanghai T-DNA insertion population (http://ship.plantsignal.cn; Fu et al, 2009) resulted in the identification of a putative mutant line in which the insertion is located at the first intron of ABL1 ( Fig. 2A, top panel).…”

Dynamic Cytology and Transcriptional Regulation of Rice Lamina Joint Development

“…To further study the mechanism of auxin effects in regulating lamina joint development, a gain-of-function mutant, lc1-D (leaf inclination 1; which encodes OsGH3-1, an IAA amino synthetase), which was identified from the Shanghai T-DNA Insertion Population (Fu et al, 2009) and which presents a reduced auxin level and enlarged leaf angles due to the increased cell elongation in the adaxial surface of the lamina joint (Zhao et al, 2013), was used. Comparison of transcriptomes of the lamina joint of lc1-D and its corresponding original cultivar control, cv ZH11, identified 319 up-regulated and 254 down-regulated genes in lc1-D. Interestingly, 55% of the up-regulated genes (175) and 34% of the down-regulated genes (86) in lc1-D are detected in DEGs along with lamina joint development ( Fig.…”

SEMI-ROLLED LEAF1 Encodes a Putative Glycosylphosphatidylinositol-Anchored Protein and Modulates Rice Leaf Rolling by Regulating the Formation of Bulliform Cells

“…Characterization of Additional Alleles of srl1-1 srl1-2 was identified from SHIP (Fu et al, 2009) with the line ID SHIP_ZSF4805. Rice sp.…”

“…Additional srl1 mutant alleles were searched against the T-DNA flanking sequences in Shanghai T-DNA insertion population (SHIP; Fu et al, 2009). A candidate mutant with T-DNA located at the fifth intron of SRL1 was identified and named as srl1-2.…”