title: Genome-Wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm.
abstract: Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.
authors.affiliation: Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou 434025, China.
authors.forename: Xianjin
authors.initials: X
authors.lastname: Qiu
authors.affiliation: Institute of Crop Science/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Yunlong
authors.initials: Y
authors.lastname: Pang
authors.affiliation: Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou 434025, China.
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Yuan
authors.affiliation: Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou 434025, China.
authors.forename: Danying
authors.initials: D
authors.lastname: Xing
authors.affiliation: Institute of Crop Science/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.|Shenzhen Institute of Breeding & Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
authors.forename: Jianlong
authors.initials: J
authors.lastname: Xu
authors.affiliation: International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.|CIRAD, UMR AGAP, F-34398 Montpellier, France.
authors.forename: Michael
authors.initials: M
authors.lastname: Dingkuhn
authors.affiliation: Institute of Crop Science/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Zhikang
authors.initials: Z
authors.lastname: Li
authors.affiliation: International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
authors.forename: Guoyou
authors.initials: G
authors.lastname: Ye
mesh_terms: D002523:Edible Grain / Q000033:anatomy & histology*; D004777:Environment; D063427:Food Quality; D005819:Genetic Markers / Q000235:genetics; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D012275:Oryza / Q000033:anatomy & histology* / Q000166:cytology / Q000235:genetics* / Q000254:growth & development; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics
chemical_list: D005819:Genetic Markers