Genetic diversity in agronomic and grain quality traits in the USDA rice mini-core collection

Abstract

The USDA rice mini-core collection was established to capture the genetic diversity contained in the United States rice gene bank which contains over 18,700 rice accessions. The mini-core consists of 217 accessions with diverse ancestry and geographical origins, offering a wide diversity of phenotypes and genotypes for selection of favorable materials for rice breeding and gene-mining. However, this extremely valuable germplasm has not been fully explored and many grain quality traits have not been evaluated.

One of the main objectives of this study was to characterize grain quality of rice genotypes in the mini-core with a focus on eating and cooking quality of milled rice and antioxidant property of brown rice. The rice were planted in two environments in China: Hainan Island (18°N) from December 2013 to April 2014, and Hangzhou (30° N) from June to September 2014. For characterization of eating and cooking quality of milled rice, we measured apparent amylose content (AAC), pasting viscosity profile (RVA), texture, thermal and retrogradation properties of 163 accessions harvested from Hainan and 155 accessions harvested from Hangzhou. To uncover genotypic diversity of antioxidant property, we investigated total phenolic content (TPC), total flavonoid content (TFC) and ABTS^(.+) antioxidant capacity of 160 brown rice harvested from Hainan island. These data provide necessary information for selecting desirable parental materials for rice breeding programs and for genome wide association mapping.

To dissect the effects of genotype (G), environment (E) and GxE interaction on rice eating and cooking quality, 115 accessions harvested from both environments were further analyzed. In contrast with previous studies, nearly all parameters of RVA were found to be much more affected by environment than by genotype. The same rice cultivars could vary widely in RVA parameters when grown in different environments.

To investigate association analysis between gene markers and eating and cooking quality, 26 markers derived from 18 starch biosynthesis related genes were used to genotype all 217 mini-core accessions. The allele combination of the 18 gene loci was determined for each accession. The association analysis uncovered the important effect of variation in (CT)n repeats on starch traits, which tend to be overlooked in previous studies. In addition, three new Waxy haplotypes were identified in 13 accessions. These haplotypes all had a T SNP in intron 1 of Waxy gene, and 9 of the 13 accessions had AAC >18%, although rice cultivars with this T SNP were expected to have < 18% AAC according to previous reports.

In the genome-wide association mapping of antioxidant property, several simple sequence repeat (SSR) markers were identified as having high associations with antioxidant traits. However, further quantification and association mapping of individual components of antioxidant compounds need to be conducted. In summary, the data from this study will provide guidance for selecting novel materials from the mini-core accessions for rice breeding or for direct cultivation to produce more diverse grains to meet consumer demands. The association analysis of grain quality traits contributes to a better understanding of genetic basis of rice starch biosynthesis and antioxidant property.