Association Analysis of Three Diverse Rice (Oryza sativa L.) Germplasm Collections for Loci Regulating Grain Quality Traits

Abstract

Core Ideas We characterized core and minicore subsets of the USDA National Small Grains Collection of global rice accessions for grain quality. We identified loci and candidate genes for grain quality and grain chalk traits in rice diversity panels. We detected loci with pleiotropic effects across multiple grain quality and agronomic traits. We demonstrated the utility for genome‐wide association (GWA) discovery in a minicore selected to maximize diversity with a minimal panel size. Rice (Oryza sativa L.) end‐use cooking quality is vital for producers and billions of consumers worldwide. Grain quality is a complex trait with interacting genetic and environmental factors. Deciphering the complex genetic architecture associated with grain quality provides essential information for improved breeding strategies to enhance desirable traits that are stable across variable climatic and environmental conditions. In this study, genome‐wide association (GWA) analysis of three rice diversity panels, the USDA rice core subset (1364 accessions), the minicore (MC) (173 accessions after removing non‐sativa), and the high density rice array–MC (HDMC) (383 accessions), with simple sequence repeats, single nucleotide polymorphic markers, or both, revealed large‐ and small‐effect loci associated with known genes and previously uncharacterized genomic regions. Clustering of the significant regions in the GWA results suggests that multiple grain quality traits are inherited together. The 11 novel candidate loci for grain quality traits and the seven candidates for grain chalk identified are involved in the starch biosynthesis pathway. This study highlights the intricate pleiotropic relationships that exist in complex genotype–phenotypic associations and gives a greater insight into effective breeding strategies for grain quality improvement.

Enhancing the searchability, breeding utility, and efficient management of germplasm accessions in the USDA−ARS rice collection

“…In the subpopulation analysis, all controls from the USDA Rice Core Subset were correctly assigned to their subpopulations indicating that the 19 markers used in the structure analysis were in agreement with subpopulation assignment as determined with the 72 markers used in previous studies (Agrama et al., 2010; Huggins et al., 2019). The subpopulation structure analysis showed the Indica subspecies represents the majority of the accessions in the 2K panel, with 48.4% IND and 9.6% AUS.…”

“…A SNP located in Waxy exon 10, Wx Ex10, was used to distinguish starch viscosity profiles important for cooked rice texture (Traore, McClung, Chen, & Fjellstrom, 2011). The GC/TT SNP in the Alk gene (Huggins et al., 2019) was used to predict gelatinization temperature (Bao et al., 2006b). A marker was developed to detect the 8‐bp deletion in the BADH2 gene that is associated with the presence of 2‐acetyl‐1‐pyrroline that results in a buttery or nutty fragrance (Kovach et al., 2009).…”

“…Genotyping of diversity panels (The 3,000 Rice Genomes Project, 2014; Agrama et al., 2009; Bryant et al., 2011; Eizenga et al., 2014; X. Li et al., 2010; McCouch et al., 2016; Wang et al., 2016; D. R. Wang et al., 2018; W. Wang et al., 2018; Zhao et al., 2011) and mapping in various biparental populations led to the development of TSMs important to rice cultivar development. Some of the markers relevant to U.S. breeding programs include five rice blast ( Magnaporthe oryzae B. Couch) resistance genes (Fjellstrom et al., 2004, 2006; Wang et al., 2010), pubescence (Eizenga, Chen, Jia, Jackson, & Edwards, 2019; W. Li et al., 2010), apparent amylose content (Ayres et al., 1997, Chen, Bergman, Pinson, & Fjellstrom, 2008), starch pasting properties (Chen, Fjellstrom, Christensen, & Bergman, 2010), starch gelatinization temperature (Bao, Corke, & Sun, 2006b; Huggins et al., 2019), the fragrance ( frg ) gene associated with 2‐acetyl‐1‐pyrroline (2‐AP), the characteristic compound found in aromatic rice (Fitzgerald, Sackville Hamilton, Calingacion, Verhoeven, & Butardo, 2008; Kovach, Calingacion, Fitzgerald, & McCouch, 2009), red pericarp color as determined by genes involved in proanthocyanidin synthesis (Furukawa et al., 2007; Sweeney, Thomson, Pfeil, & McCouch, 2006; Wu et al., 2019), and an induced mutation for herbicide resistance (Kadaru, Zhang, Yadav, & Oard, 2008). Although molecular markers are available for these economically important traits, they have not been used to systematically characterize the rice NSGC prior to this study.…”

Registration of the Estrela × NSFTV199 Rice Recombinant Inbred Line Mapping Population

“…These 20 RILs were genotyped with 63 of the 132 markers used for the QTL mapping. The 63 markers were peak markers for the QTL identified in this population (Eizenga et al, 2019) or near SNPs associated with marker‐trait associations for chalk (Huggins et al, 2019). The entire population was genotyped with the segregating dominant marker for the rice blast fungal disease gene Pi‐z on chr.…”

Phylogenetic origin and dispersal pattern of Taiwan weedy rice

“…Thirty‐eight simple sequence repeat (SSR) loci distributed among the 12 rice chromosomes, which showed high polymorphism in previous research, were chosen for the study (Table ). Four previously developed functional markers were used to detect the functional polymorphism for amylose content ( WxIn1 and WxEx6 ), gelatinization temperature ( ALK ), and bran color ( Rc ) . Four new functional markers were developed for plant height ( sd1 ) and red bran ( Rd ) .…”