# Genome-Wide Association Study on Grain Length and Grain Width of Rice

## TL;DR

This study identifies genetic regions and gene variants in rice that control grain shape, which is important for yield and quality, and highlights useful resources for rice breeding.

## Contribution

The study discovers four QTLs and candidate genes for rice grain shape, including a novel locus and haplotype combinations in slender-grain rice.

## Key findings

- Four QTLs (qGL3.1, qGL3.2, qGL11, qGW4) were identified as associated with rice grain length and width.
- Haplotype analysis revealed that specific gene combinations are linked to the slender-grain phenotype in eight rice accessions.
- The study provides genetic resources for marker-assisted breeding to improve rice grain shape.

## Abstract

Rice grain morphology, especially grain shape, is one of the major indicators determinant of yield potential and is controlled by an interconnected gene regulatory network. It also affects rice processing and quality, which are critical for market competitiveness. To achieve higher and more stable rice yields, it is crucial to identify and utilize favorable genetic resources associated with grain shape, and to understand the underlying mechanisms of these genes. Therefore, investigating the genetic regions responsible for rice grain shape is of great importance for both scientific research and rice breeding. In this study, 231 different rice varieties were grown under two different nitrogen conditions, and their grain shapes were measured at maturity. The grain shape data were then correlated with the varieties’ genomic information to identify regions controlling grain shape, along with potential genes and their variants in those regions. Our findings highlight valuable rice accessions and beneficial gene variants enabling breeders to more efficiently generate rice lines exhibiting the desired grain shapes.

The morphology of rice grains represents one of the most vital agronomic characteristics, significantly impacting both grain productivity and the subsequent milling and nutritional quality of the crop. A comprehensive understanding of the genetic basis and molecular drivers of grain shape is vital for the targeted breeding of high-performance rice lines with consistent yield stability. To pinpoint the genomic regions influencing grain dimensions, we conducted a genome-wide association analysis across a panel of 231 distinct rice accessions, focusing on the discovery of loci associated with length and width. Our analysis revealed four consistent quantitative trait loci (QTLs) distributed across chromosomes 3, 4, and 11. Notably, grain length was associated with qGL3.1, qGL3.2, and qGL11. The first two were co-localized with GS3 and SMG3, respectively, whereas qGL11 likely constitutes a novel locus. One QTL, qGW4, which governs grain width, was found to co-localize with the gene OsOFP14. Haplotype analysis further revealed that the characteristic haplotypes of the candidate genes for qGL3.1, qGL3.2, and qGW4 were enriched in eight germplasm accessions (including Newbonnet, Skybonnet, and Lemont), all of which exhibit a slender-grain phenotype. This finding suggests that the specific combination of these characteristic haplotypes is a common genetic signature of slender-grain rice, serving as a potential gene combination for the targeted improvement of rice grain shape. Our results reveal valuable QTLs and candidate genes and highlight specific germplasm resources that can be readily applied in marker-assisted breeding to improve rice grain shape.