High-resolution phenotyping for investigating the genotype-phenotype association in rice grains
Journal
2016 American Society of Agricultural and Biological Engineers Annual International Meeting
ISBN
9781510828759
Date Issued
2016
Author(s)
Abstract
Abstract. Rice (Oryza sativa L.) shows remarkable variation in grains. The phenotypic information of the rice grains needs to be quantified accurately as the first step to investigate the association between the phenotypes and genotypes. This study proposed a procedure to phenotype rice grains of various cultivars in high resolution. In the process, rice seeds of more than 200 cultivars were acquired from Genetic Stocks Oryza. The genotypic variations (i.e., single nucleotide polymorphisms) of these cultivars are publicly available. The images of the grains were acquired in high resolution by microscopy (approximately 95 pixels per millimeter). Phenotypic traits were next quantified from the grain images automatically using image processing. The traits included morphological and color traits for the grain body, sterile lemmas, and brush. These traits were subsequently used for investigating the association between the phenotypic and genotypic variations of the cultivars using generalized linear model and mixed linear model. The analysis identified several candidate loci affecting morphological and color characters of the rice grains.
Type
conference paper