Abstract
Rice eating and cooking quality is largely determined by starch physicochemical properties. The diverse accessions in the USDA rice mini-core collection (URMC) facilitate extensive association analysis of starch physicochemical properties with molecular markers specific to starch biosynthesis related genes. To identify significant trait-marker associations that can be utilized in rice breeding programs for improved starch quality, we conducted two association analyses between 26 molecular markers derived from starch biosynthesis related genes and 18 parameters measured of starch physicochemical properties in two sets of the mini-core accessions successfully grown in two environments in China. Many significant trait-marker associations (P < 0.001) were detected in both association analyses. Five markers of Waxy gene, including the (CT)n repeats, the G/T SNP of intron 1, the 23 bp sequence duplication (InDel) of exon 2, the A/C SNP of exon 6, and the C/T SNP of exon 10, were found to be primarily associated with starch traits related to apparent amylose content (AAC), and two markers targeting the 4,329–4,330 bp GC/TT SNPs and 4,198 bp G/A SNP of SSIIa gene were mainly associated with traits related to gelatinization temperature (GT). Two new haplotypes were found in the mini-core collection based on the combinations of the 23 bp InDel and three SNPs (G/T of intron 1, A/C of exon 6, and C/T of exon 10) of Waxy gene. Furthermore, our analyses indicated that the (CT)n polymorphisms of Waxy gene had a non-negligible effect on AAC related traits, as evidenced by significant variation in AAC related traits among rice accessions with the same Waxy SNPs but different (CT)n repeats. As the five Waxy markers and the two SSIIa markers showed consistent major effects on starch quality traits across studies, these markers should have priority for utilization in marker-assisted breeding.
Highlights
As the major component in rice grain, starch accounts for over 90% of endosperm weight, and the physicochemical properties of starch have foremost influence on rice eating and cooking quality
Following Li et al (2010), the 217 accessions in the minicore were divided into seven ancestry groups, and the polymorphism information content (PIC) of the 26 markers in each group was calculated in the present study (Table 1)
We found that the 23 bp InDel in exon 2 and (CT)n microsatellite polymorphisms were most strongly associated with Apparent amylose content (AAC) while intron 1, exon 6, and exon 10 were less significant as suggested by the P-values (Table 2), and these findings were confirmed by both association analyses
Summary
As the major component in rice grain, starch accounts for over 90% of endosperm weight, and the physicochemical properties of starch have foremost influence on rice eating and cooking quality. Amylose content and the fine structure of amylopectin are the main determinants of rice eating and cooking quality (Juliano, 1985; Bao et al, 2009; Syahariza et al, 2013; Kong et al, 2015). Additional indicators have been developed for more precise evaluation of grain quality, such as pasting viscosity profile, thermal, and retrogradation properties. All these starch physicochemical properties could be grouped as AAC-related traits and GT-related traits according to previous studies (Wang et al, 2007; Yang et al, 2014)
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