Xiaoli Shu

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.

Genome-wide Association Study of Resistant Starch (RS) Phenotypes in a Barley Variety Collection

Barley is primarily grown for feed and malt, but in some regions of the world it is also considered to be a staple food. Some barley types such as high-amylose barley have also gained importance as health-promoting foods. Starch that is not readily digested in the upper mammalian gastrointestinal system, or resistant starch (RS), is considered to be valuable because it prevents some diet-related diseases such as colon cancer. RS was quantified in a diverse collection of 209 spring barley varieties released in Europe during the past 100 years. The RS content varied from <1% to >15% in the collection, with 13 varieties having high RS content (>11%) and 15 varieties below 1%. Combined with genome-wide association scanning (GWAS), SNP markers and candidate genes controlling the RS content in grains were identified. This identified 40 SNP markers with a LOD score above 2, located on chromosomes 2H, 3H, 5H, and 6H, respectively. Among these SNPs, 10 genes with a known role in starch biosynthesis were associated on the basis of synteny conservation to the rice genome. The β-glucan content was quantified in 61 varieties selected to represent extreme as well as medium RS values. The β-glucan amount in the 15 varieties with RS <1% ranged from 1.7 to 3.2%, ranged from 1.76 to 2.54% in the 13 varieties with RS >11%, and ranged from 1.95 to 2.82% for those with 1%< RS < 11%. No statistically significant correlation between RS content and β-glucan content was found. This association analysis of commercial varieties revealed a large variation in RS content and identified a number of SNP markers that can be explored for selection and further dissection of the pathway and control of RS phenotype.

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.

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.