Abstract
Rice quality is mainly related to the following two starch components, apparent amylose content (AAC) and resistant starch (RS). The former affects grain cooking properties, while RS acts as a prebiotic. In the present study, a Genome Wide Association Scan (GWAS) was performed using 115 rice japonica accessions, including tropical and temperate genotypes, with the purpose of expanding the knowledge of the genetic bases affecting RS and AAC. High phenotypic variation was recorded for the two traits, which positively correlated. Moreover, both the parameters correlated with seed length (positive correlation) and seed width (negative correlation). A correlational selection according to human preferences has been hypothesized for the two starch traits and grain size. In addition, human selection has been proposed as the causal agent even for the different phenotypes related to starch and grain size showed by the tropical and temperate japonica accessions utilized in this study. The present GWAS led to the identification of 11 associations for RS on seven chromosomes and five associations for AAC on chromosome 6. Candidate genes and co-positional relationships with quantitative trait loci (QTLs) previously identified as affecting RS and AAC were identified for 6 associations. The candidate genes and the new RS- and/or AAC-associated regions detected provide valuable sources for future functional characterizations and for breeding programs aimed at improving rice grain quality.
Highlights
Rice provides more than 1/5 of calories for human worldwide populations and, in the last decades, the economic development and the improvement of lifestyle has brought more concerns about rice quality
Data were reported as RS and TS (RSTS) ratio percentages, which allowed the quantification of resistant starch (RS) content based on the corresponding total starch (TS) value
A significant positive correlation was found between apparent amylose content (AAC) and RS, according to the observation that AAC represents one of the main determinants of RS in rice seeds [24], and between these two starch-related traits and grain shape
Summary
Rice provides more than 1/5 of calories for human worldwide populations (http://faostat.fao.org) and, in the last decades, the economic development and the improvement of lifestyle has brought more concerns about rice quality. The grains of high AAC rice varieties remain firm and separate, whereas low AAC genotypes result. AAC in rice grains is directly associated with the amounts of the granule bound starch synthase I (GBSSI) enzyme, which regulates starch accumulation in the endosperm of developing caryopsis [4]. This enzyme is encoded by the Waxy (Wx) gene and, as extensively reported, different alleles at this locus correspond to different AAC percentages [1,4,5,6,7]
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