Dianxing Wu

Gene identification and allele-specific marker development for two allelic low phytic acid mutations in rice (Oryza sativa L.)

Phytic acid (PA, myo-inositol 1,2,3,4,5,6-hexakisphosphate) is an important anti-nutritional component in cereal and legume grains. PA forms of phosphorus (P) and its salts with micronutrient cations, such as iron and zinc, are indigestible in humans and non-ruminant animals, and hence could affect food/feed nutritional value and cause P pollution of ground water from animal waste. We previously developed a set of low phytic acid (LPA) rice mutants with the aim to increase their nutritional quality. Among them, one line, i.e., Os-lpa-XQZ-1 (hereafter lpa 1-2), was identified to have a mutation allelic to the KBNT lpa 1-1 mutation (hereafter lpa 1-1), which was already delimited to a 47-kb region on chromosome 2. In this study, we searched the candidate gene for these two allelic LPA mutations using T-DNA insertion mutants, mutation detection by CEL I facilitated mismatch cleavage, and gene sequencing. The TIGR locus LOC_Os02g57400 was revealed as the candidate gene hosting these two mutations. Sequence analysis showed that the lpa 1-1 is a single base pair substitution mutation, while lpa 1-2 involves a 1,475-bp fragment deletion. A CAPS marker (LPA1_CAPS) was developed for distinguishing the lpa 1-1 allele from lpa 1-2 and WT alleles, and InDel marker (LPA1_InDel) was developed for differentiating the lpa 1-2 allele from lpa 1-1 and WT ones. Analysis of two populations derived from the two mutants with wild-type varieties confirmed the complete co-segregation of these two markers and LPA phenotype. The LOC_Os02g57400 is predicted to encode, through alternative splicing, four possible proteins that are homologous to the 2-phosphoglycerate kinase reported in hyperthermophilic and thermophilic bacteria. The identification of the LPA gene and development of allele-specific markers are of importance not only for breeding LPA varieties, but also for advancing genetics and genomics of phytic acid biosynthesis in rice and other plant species.

Critical roles of soluble starch synthase SSIIIa and granule-bound starch synthase Waxy in synthesizing resistant starch in rice

Significance Resistant starch (RS) has the potential to protect against diabetes and reduce the incidence of diarrhea, inflammatory bowel disease, colon cancer, and chronic renal and hepatic diseases. In this study, we identified two critical starch synthase genes which together regulate RS biosynthesis in rice, and we explored their potential interactions as part of a network of starch biosynthetic enzymes. The findings hold promise for applications in breeding varieties with improvement of RS in hot cooked rice and may also have general implications for understanding RS biosynthesis in other major cereal crops. Changes in human lifestyle and food consumption have resulted in a large increase in the incidence of type-2 diabetes, obesity, and colon disease, especially in Asia. These conditions are a growing threat to human health, but consumption of foods high in resistant starch (RS) can potentially reduce their incidence. Strategies to increase RS in rice are limited by a lack of knowledge of its molecular basis. Through map-based cloning of a RS locus in indica rice, we have identified a defective soluble starch synthase gene (SSIIIa) responsible for RS production and further showed that RS production is dependent on the high expression of the Waxya (Wxa) allele, which is prevalent in indica varieties. The resulting RS has modified granule structure; high amylose, lipid, and amylose–lipid complex; and altered physicochemical properties. This discovery provides an opportunity to increase RS content of cooked rice, especially in the indica varieties, which predominates in southern Asia.

High photosynthetic efficiency of a rice (Oryza sativa L.) xantha mutant

Comparative analysis revealed that a xantha rice mutant (cv. Huangyu B) had higher ratios of chlorophyll (Chl) a/b and carotenoids/Chl, and higher photosynthetic efficiency than its wild type parent (cv. II32 B). Unexpectedly, the mutant had higher net photosynthetic rate (PN) than II32 B. This might have resulted from its lower non-photochemical quenching (qN) but higher maximal photochemical efficiency (FV/FM), higher excitation energy capture efficiency of photosystem 2 (PS2) reaction centres (FV′/FM′), higher photochemical quenching (qP), higher effective PS2 quantum yield (ΦPS2), and higher non-cyclic electron transport rate (ETR). This is the first report of a chlorophyll mutant that has higher photosynthetic efficiency and main Chl fluorescence parameters than its wild type. This mutant could become a unique material both for the basic research on photosynthesis and for the development of high yielding rice cultivars.

Effects of grain development on formation of resistant starch in rice.

Three rice mutants with different contents of resistant starch (RS) were selected to investigate the effects of grain filling process on the formation of resistant starch. During grain development, the content of RS was increased with grain maturation and showed negative correlations with the grain weight and the starch molecular weight (Mn, Mw) and a positive correlation with the distribution of molecular mass (polydispersity, Pd). The morphologies of starch granules in high-RS rice were almost uniform in single starch granules and exhibited different proliferation modes from common rice. The lower activities of ADP-glucose pyrophosphorylase and starch branching enzyme and the higher activity of starch synthase and starch de-branching enzyme observed in high-RS rice might be responsible for the formation of small irregular starch granules with large spaces between them. In addition, the lower molecular weight and the broad distribution of molecular weights lead to differences in the physiochemical properties of starch.

CFD analysis on a turbulence generator of medium consistency pump

Medium concentration paper suspension is a water-air-fibre three phase suspension. It has complicated physical features. When concentration exceeds 7%, it stops flowing and acts like a solid. A generator suspension is installed before the impeller to disturb the flocs and networks to make it start to flow. In this paper, CFD method is adopted to study the effects of the turbulence generator. As there is not a mature model to describe the characteristic of pulp suspension, Newtonian fluid is used to get the general property of the turbulence generator. In the CFD simulation, apparent viscosity of the pulp suspension is used to characterize the mixture. Firstly, numerical method is applied to get the turbulence generator properties in different rotational speed and different viscosity. From another point of view, air contained in the suspension is separate initially by means of centrifugal force. As it is difficult to describe a practical model of pulp suspension, it is simplified to be a water-air two-phase mixture. Several air contents are simulated to study the air distribution in the turbulence generator. The results show that there are three main effects of turbulence generator. Firstly, it has an entrainment effect of the suspension to make it into the pump. Secondly, it stirs the pulp suspension to bring it into flowing. Last, air is centralized in the shaft centre and pre-separated in the turbulence generator. So, the turbulence generator can pre-treat the pulp suspension to make the MC pump transport suspension successfully.

Genome-Wide Identification, Classification and Evolutionary Expansion of KNOX Gene Family in Rice ( Oryza sativa ) and Populus ( Populustrichocarpa )

The KNOX gene family codes for transcriptional regulators with a variety of functions in plant developmental and physiological processes. In this study, a genome-wide comparative analysis of KNOX genes in Poplar (Populustrichocarpa) and rice (Oryza sativa L. ssp. japonica) was carried out. With comprehensive computational analyses, which take into account the gene structures, phylogeny and conserved motifs, 15 and 13 KNOX genes in Poplar and rice were identified, respectively. These KNOX genes were further divided into 3 groups. The Poplar gene POPTR_0012s04040 and the rice genes LOC_Os03g47042 and LOC_Os03g47022 were classified to a new group of KNOX genes without ahomeobox domain together with KNATM, which were proposed to play potential role in plant development and pluripotency. The identification of KNATM homolog in monocotyledons (rice) provided a strong support for proposing an ancient shuffling of HOMEOBOX gene with MEINOX gene took place in the KNOX phylogeny. Using subcellular location information, GO (gene ontology) and expression profile analysis, KNOX genes in rice and poplar were proposed to function similarly to the members in Arabidopsis. Our observations may lay the foundation for future functional analysis of KNOX genes in rice and poplar to unravel their biological roles in cellular pluripotency.

Metabolite Profiling of a Zinc-Accumulating Rice Mutant

Breeding crops with high zinc (Zn) density is an effective way to alleviate human dietary Zn deficiencies. We characterized a mutant Lilizhi (LLZ) accumulating at least 35% higher Zn concentration in grain than the wild type (WT) in hydroponic experiments. The mutant stored less Zn content in the root and transported more Zn to the grain. Metabolite profiling demonstrated that, with high Zn treatment, the contents of proline, asparagine, citric acid, and malic acid were enhanced in both LLZ and the WT, which were thought to be involved in Zn transport in rice. Furthermore, the contents of cysteine, allothreonine, alanine, tyrosine, homoserine, β-alanine, and nicotianamine required for the production of many metal-binding proteins were specifically increased in LLZ. LLZ had higher capability of amino acid biosynthesis and metal cation transportation. The current research extends our understanding on the physiological mechanisms of Zn uploading into grain and provides references for further Zn biofortification breeding in rice.