title: QTL analysis for chalkiness of rice and fine mapping of a candidate gene for qACE9.
abstract: BACKGROUND
  An 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  OsAPS1 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.
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.|College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Gao
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Chaolei
authors.initials: C
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Anpeng
authors.initials: A
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Guojun
authors.initials: G
authors.lastname: Dong
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Lihong
authors.initials: L
authors.lastname: Xie
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Banpu
authors.initials: B
authors.lastname: Ruan
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Hong
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China.
authors.forename: Dawei
authors.initials: D
authors.lastname: Xue
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Dali
authors.initials: D
authors.lastname: Zeng
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Longbiao
authors.initials: L
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Qian
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. zygao2000@hotmail.com.
authors.forename: Zhenyu
authors.identifier: http://orcid.org/0000-0003-4808-2511
authors.initials: Z
authors.lastname: Gao
keywords: Area of chalky endosperm; Chalkiness; Fine mapping; QTL analysis; Rice