Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

Abstract

A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm is crucial in tailoring digestibility without sacrificing grain quality. In this study, significant association peaks on chromosomes 6 and 7 were identified through a genomewide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known genes with high correlation to the proportion of amylose and amylopectin. An SNP in the promoter region of Granule Bound Starch Synthase I was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a nonsynonymous SNP mutation on exon 5 of a bHLH transcription factor was found to elevate the proportion of amylose at the expense of reduced short-chain amylopectin. Linking starch structure with starch digestibility by determining the kinetics of cooked grain amylolysis of selected haplotypes revealed strong association of starch structure with estimated digestibility kinetics. Combining all results from grain quality genomics, systems genetics, and digestibility phenotyping, we propose target haplotypes for fine-tuning starch structure in rice through marker-assisted breeding that can be used to alter the digestibility of rice grain, thus offering rice consumers a new diet-based intervention to mitigate the impact of nutrition-related noncommunicable diseases.

Integrating a genome‐wide association study with a large‐scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice

“…In this work, we attempted to identify unique accessions with low in vitro GI and softer texture. Instead of using debranched starch structure (Butardo et al ., ), we phenotyped 305 diversity lines for in vitro GI for assessing digestibility and starch paste viscosity data as proxy measure for texture. We identified a low GI accession with softer cooked grain texture (GQ02497) by tapping into subtle allelic mutations and recombination's that occurred during the course of rice domestication.…”

“…The final viscosity (FV) was measured using a rapid viscosity analyzer (RVA) at the IRRI Grain Quality Nutrition and Services Laboratory (IRRI GQNSL) following the described standard method for rice (Butardo et al ., ). The high‐throughput amylose content (AAC) estimation was also performed as previously described (Butardo et al ., ).…”

“…In particular, mutations in starch synthase IIa and IIb ( SSIIa, SSIIb ), soluble starch synthase IIIa ( SSIIIa ) and starch branching enzymes ( SBEs ) were targeted in the background of Wx a allele to generate high amylose lines (Wei et al ., ; Yang et al ., ; Zhou et al ., ). However, high amylose rice has undesirable cooking and eating qualities (Butardo et al ., ). Studies involving low‐GI in rice that maintains the considerable organoleptic attributes are still elusive.…”

High‐Amylose Starches to Bridge the “Fiber Gap”: Development, Structure, and Nutritional Functionality

“…In HAS, it is hypothesized that amylopectin with an increased ratio of longer chains may form radially longer clusters with chains extending through multiple crystalline regions, leading to a more stable lamellar structure . This may explain the observation (Butardo et al, 2011(Butardo et al, , 2017Li et al, 2008;Regina et al, 2012;Zhu et al, 2011) that short chains may result in imperfections in the formation of crystallites, whereas starch with fewer short chains has better enzymatic resistance and heat stability.…”

“…Starch structure has been a topic of wide investigation and has been reviewed elsewhere (Wang, Bogracheva, & Hedley, ; Zobel, ). There have been increasing numbers of studies on the structural features responsible for the unique properties of HAS (for example, maize [Jane et al., ; Shi, Capitani, Trzasko, & Jeffcoat, ], wheat [Regina et al., ], barley [Regina et al., ], and rice [Butardo et al., ; Wei, Xu, et al., ]). The structural features can be categorized into 6 levels (Figure ): from the lowest level of structure, individual chains, to the highest level of structure, starch deposition in grains (Ball et al., ).…”