Abstract
BackgroundAn ideal appearance is of commercial value for rice varieties. Chalkiness is one of the most important appearance quality indicators. Therefore, clarification of the heredity of chalkiness and its molecular mechanisms will contribute to reduction of rice chalkiness. Although a number of QTLs related to chalkiness were mapped, few of them have been cloned so far.ResultsIn this study, using recombinant inbred lines (RILs) of PA64s and 9311, we identified 19 QTLs associated with chalkiness on chromosomes 1, 4, 6, 7, 9 and 12, which accounted for 5.1 to 30.6 % of phenotypic variations. A novel major QTL qACE9 for the area of chalky endosperm (ACE) was detected in Hainan and Hangzhou, both mapped in the overlapping region on chromosome 9. It was further fine mapped to an interval of 22 kb between two insertion-deletion (InDel) markers IND9-4 and IND9-5 using a BC4F2 population. Gene prediction analysis identified five putative genes, among which only one gene (OsAPS1), whose product involved in starch synthesis, was detected two nucleotide substitutions causing amino acid change between the parents. Significant difference was found in apparent amylose content (AAC) between NILqACE9 and 9311. And starch granules were round and loosely packed in NILqACE9 compared with 9311 by scanning electron microscopy (SEM) analysis.ConclusionsOsAPS1 was selected as a novel candidate gene for fine-mapped qACE9. The candidate gene not only plays a critical role during starch synthesis in endosperm, but also determines the area of chalky endosperm in rice. Further cloning of the QTL will facilitate the improvement of quality in hybrid rice.
Highlights
An ideal appearance is of commercial value for rice varieties
Normal distributions and bimodal distributions were observed in the recombinant inbred lines (RILs) population for area of chalky endosperm (ACE), DEC and percentage of grains with chalkiness (PGWC) in Hangzhou and Hainan, respectively (Fig. 1b), indicating the three traits were controlled by multi-genes in Hangzhou and one or two major genes in Hainan
In Hangzhou, we identified qACE6-2, qDCE6 and qPGWC6, explained respectively up to 9.2, 30.6 and 30.5 % of the phenotypic variation and located within 10.92 ~ 22.12 cM on chromosome 6
Summary
An ideal appearance is of commercial value for rice varieties. Chalkiness is one of the most important appearance quality indicators. Clarification of the heredity of chalkiness and its molecular mechanisms will contribute to reduction of rice chalkiness. A number of QTLs related to chalkiness were mapped, few of them have been cloned so far. Rice is one of the most important food crops, and fed more than half of the population in the world. With the increase of living standard, more and more attention has been paid on rice quality, including the appearance quality, processing quality, nutritional quality, and cooking and eating quality, etc. Chalkiness is an important indicator of the appearance quality for rice. Several rice mutants associated with chalkiness have been identified and a few genes have been cloned. The OsPPDKB gene, which control carbon flow into starch and lipid biosynthesis during grain filling and starch synthase IIIa (SSIIIa), whose product plays an
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