Starch physicochemical properties of rice accessions and their association with molecular markers

Abstract

The grain quality of rice has recently attracted a lot of attention around the world, including Africa. Rice germplasm in African gene banks has not been adequately characterized for its cooking and eating qualities which are mainly controlled by starch physicochemical properties. The aim of this study was to characterize two groups of rice germplasm from Africa and the U.S. for starch properties including gelatinization temperature (GT), apparent amylose content (AAC), and paste viscosity (RVA), and to determine molecular marker associations with these traits. Wide diversity was found for all traits studied. Variation in these traits was significantly associated with molecular markers for the alk and waxy genes which encodes soluble SS II (SSIIa) and granule bound synthase (GBSS) enzymes, respectively. Based on four previously reported waxy SNP haplotypes, 93.1 and 75.9% of the variation in AAC was explained for the U.S. and African germplasm, respectively. The classification of the genotypes by their SNP haplotypes helped to clarify the relationship between AAC and peak viscosity. The characterization of individual lines using physicochemical properties and functional markers, and the determination of marker‐trait associations will facilitate the breeding of rice for grain quality in Africa and elsewhere.

Association Analysis of Markers Derived from Starch Biosynthesis Related Genes with Starch Physicochemical Properties in the USDA Rice Mini-Core Collection

“…Among over twenty starch biosynthesis related genes, Waxy gene was reported as the primary gene responsible for amylose content by multiple QTL mapping studies (He et al, 1999; Tan et al, 1999; Septiningsih et al, 2003; Xu et al, 2015). In the previous association analyses, a total of five polymorphic sites in Waxy gene were reported as having important effects on AAC variation (Ayres et al, 1997; Larkin and Park, 2003; Wanchana et al, 2003; Chen et al, 2008; Asante et al, 2013; Caffagni et al, 2013). In our association analyses, we included five markers specific to all the five polymorphic sites (G/T SNP of intron 1, 23 bp InDel of exon 2, G/C SNP of exon 6 and C/T SNP of exon 10, and (CT) n repeats) in order to compare their relative importance.…”

“…Chen et al (2008) measured 53 rice accessions with this T SNP, and nearly all of them showed AAC <18%. However, several studies reported some rice cultivars with the TAC waxy haplotype had AAC > 18% (Dobo et al, 2010; Asante et al, 2013; Caffagni et al, 2013; Biselli et al, 2014). Our present result also showed that the T SNP in intron 1 of Waxy gene is not always accompanied by an AAC lower than 18% (Table 3).…”

“…In addition, our ANOVA results showed that a larger portion of variance of AAC could be explained when RM190 was included in the analysis (Table 5), indicating that RM190 also has a non-negligible effect on AAC. Some previous studies suggested that the SNPs of Waxy gene had a superior effect on AAC, hence a priority on SNPs was recommended for utilization in marker-assisted selection (Chen et al, 2008; Dobo et al, 2010; Asante et al, 2013). However, as shown in the present study (Supplementary Table 5), the portion of AAC variance explained by SNPs varied considerably among different ancestry groups, and in some groups, Waxy SNPs explained far less variance than RM190.…”

The contribution of lysophospholipids to pasting and thermal properties of nonwaxy rice starch

“…Wide variation amongst AAC, pasting and thermal parameters is observed in cultivated rice germplasm (Asante et al, 2013 Tables 1 and 2 for the abbreviations. *, ** indicate significance at P < 0.05 and 0.01 levels, respectively.…”

Effects of Different Grinding Methods on Morphological, Textural Properties and Pasting Profiles of Mr220 Rice Flour

“…Ultimately this could result in reduced retrogradation of amylose molecules [38]. High values in breakdown and low values in setback of semi-wet ground flour are indicative of high cooking quality since neither the cooked rice retrogrades nor becomes stiff upon cooling [39].…”