Effects of starch synthesis genes and related starch structures in enhancing resistant starch content in rice

Authors: Jia, Yulin; CHEN, MING-HSUAN - Retired ARS Employee; GONZALEZ, ANA - University Of Arkansas; WANG, YAH-JANE - University Of Arkansas

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/19/2025
Publication Date: 6/30/2025
Citation: Jia, Y., Chen, M., Gonzalez, A., Wang, Y. 2025. Effects of starch synthesis genes and related starch structures in enhancing resistant starch content in rice. Crop Science. https://doi.org/10.1002/csc2.70100.
DOI: https://doi.org/10.1002/csc2.70100

Interpretive Summary: One factor that limits the consumption and sales of rice today is the fact that it is viewed as a carbohydrate-dense food with a high glycemic index (GI). One way to make rice with lower GI is to increase its content of resistant starch (RS), a type of starch that resists digestion in the gastrointestinal tract of humans and passes undigested to the colon. By resisting digestion to glucose, it does not contribute to calorie count, blood glucose, or GI. RS provides even further health benefits, however, in that when the undigested starch reaches the colon, it is a dietary fiber, and feeds health-beneficial gut microbes. Increased consumption of dietary fiber has been found associated with reduced incidence of colon cancer, gall stones, and cardiovascular disease and is recommended as a functional food treatment of inflammatory bowel disease and assists weight loss. A small portion (c. 1%) of starch in standard milled rice is RS. This informs that rice is capable of producing RS in its grains, and that, through breeding and selection of alternative forms of genes (alleles) involved in starch-synthesis, breeders can create new rice varieties that produce even higher RS. RS is measured as a percentage of total starch, which means as RS increases, the fraction of digested starch is directly decreased. Increasing RS in rice directly lowers its GI and calorie density while also increasing its dietary fiber content. The goal of this study was to identify novel genes and gene combinations that increase RS, and we found a gene combination that results in RS levels as high as 9%. We started by identifying a new mutant with altered starch-synthesis by screening 4000 mutants of the US variety Katy that were previously created by USDA-ARS scientists, with seed made available through the USDA National Germplasm Collection System. Using segregating cross progeny and molecular markers tagging the 12 rice chromosomes, this novel mutation was mapped to the SSIIIa gene locus on chromosome 8. SSIIIa is the STARCH SYNTHESIS IIIa gene, and its role in plants is to elongate the glucose chains that make up amylopectin starch. We then used cross-progeny to determine this new ssIIIa mutation’s effect on RS, alone as well as in combination with two other genes already known to impact RS (Wx and beIIb). It was hoped that combining all three genes would result in even higher RS concentrations. However, what we found was that although Wx and beIIb are complimentary, and further increase RS when combined, the new ssIIIa mutation was antagonistic with beIIb, such that plants containing both mutations had less RS than plants containing beIIb alone. Gene-by-gene interaction (epistasis) was also noted between ssIIIa and Wx. Discovery of epistasis among RS-affecting genes was novel to this study and was made possible by the fact that we studied 3 RS genes in combination, as opposed to the more typical method of studying new mutations as single individual genes. We studied changes in starch structure due to beIIb and ssIIIa and found that the epistasis we observed was because ssIIIa interfered with the biochemical changes through which beIIb increases RS. Our results inform breeders that to develop a high-RS rice variety for meeting consumer demands for healthier, nutrient dense rice, they should do so by combining the beIIb and high-amylose Wx-a alleles but should not include ssIIIa mutations which interfere with the mechanism beIIb mutants use to increase RS. This study also demonstrates the research value of creating new mutations and disseminating their seed to researchers through the USDA National Plant Germplasm System.

Technical Abstract: Rice breeders are interested in developing varieties with lower glycemic index (GI) and increased dietary fiber to meet consumer demand for healthier food. Resistant starch (RS) is a type of dietary fiber and higher RS results in lower-GI rice. With the goal of identifying novel genes and gene combinations that increase rice RS, we identified a novel starch mutant, mapped it to the soluble starch synthase IIIa (ssIIIa) locus, and used segregating cross progeny to evaluate its impact on RS individually, and in combination with two additional genes known to affect RS: Wx and BEIIb. Of the three genes, mutation in beIIb increased RS the most. The ssIIIa mutant raised RS relative to its SSIIIa counterpart when it was genetically combined with BEIIb and Wxa, known for being the highest expression Wx allele. The ssIIIa and beIIb mutations proved antagonistic rather than complimentary, with progeny containing both ssIIIa and beIIb having less RS than those containing beIIb alone, and this reduction was more notable in progeny having Wx-in than those with Wx-a. Relationships between genes, starch molecular fine structure, and RS were also investigated. Results revealed that ssIIIa interferes with the changes in starch structure through which beIIb increases RS, resulting in antagonistic epistasis between ssIIIa and beIIb that individually increase RS. Low-GI, high-RS rice varieties can be developed using molecular markers to select for Wx-a, beIIb, and wildtype SSIIIa alleles.