# The Wx/SSIIa and GS3/GW7 Alleles, Both Individually and in Combination, Can Significantly Distinguish Rice Germplasm Quality

## TL;DR

This study identifies key rice genes that influence cooking, eating, and appearance quality traits, helping improve rice quality through marker-assisted breeding.

## Contribution

The study introduces new allele-specific markers and reveals gene interactions affecting rice quality traits.

## Key findings

- Wx-In1 and SSIIa-Ex8 are major loci for amylose content, gel consistency, and alkali spreading value.
- GS3-Ex2 and GW7-Pro significantly influence chalkiness and other appearance traits.
- Combining alleles at these loci can enhance rice quality through synergistic effects.

## Abstract

As living standards rise, there has been a growing emphasis on quality traits related to rice’s taste potential. Recent studies explored correlations among quality traits, but the influence of major genes governing a specific quality trait on other quality traits remains elusive. Here, we report on the application of grain quality genes, two of Waxy (Wx) and Starch synthase II-a (SSIIa), which dominates in rice cooking and eating quality, and two grain length/width-related genes, grain size 3 (GS3) and grain width 7 (GW7), on appearance quality traits. Five allele-specific markers for these genes were developed, and used to stack the desirable alleles at these loci. The effects of individual or combined alleles at the loci were evaluated using a set of 156 rice germplasm. We found that the Wx-In1 (Intron 1) locus exerts a major effect in controlling both amylose content and gel consistency, while the SSIIa-Ex8 (Exon 8) locus primarily governs alkali spreading value. The impact on chalkiness-related traits follows the hierarchy of Wx-In1 > SSIIa-Ex8 > Wx-Ex10 (Exon 10). GS3-Ex2 (Exon 2) has a highly significant impact on chalkiness-related traits, and the GW7-Pro (Promoter) locus exerts a synergistic effect. The GS3-Ex2 locus exerts an effect in controlling both gel consistency and alkali spreading value, while the GW7-Pro locus governs amylose content. The data for newly developed allele-specific markers will facilitate the improvement of rice quality in rice.