03044naa a2200385 a 450000100080000000500110000800800410001902200140006002400410007410000140011524501520012926000090028150003040029052016560059465000170225065000090226765300150227665300220229165300220231365300130233565300160234865300190236470000190238370000190240270000170242170000230243870000160246170000180247770000200249570000170251570000180253270000160255070000210256677300710258710596132019-03-12       2018    bl uuuu     u00u1 u    #d  a1940-33727 a10.3835/plantgenome2017.08.00762DOI1 aQUERO, G.  aGenome-wide association study using historical breeding populations discovers genomic regions involved in high-quality rice.h[electronic resource]  c2018  aArticle history: Received: Aug 25, 2017 // Accepted: Apr 09, 2018 // Published: July 12, 2018. Permissions: This is an open access article under the CC BY-NC-ND license. Proper attribution is required for reuse. No permissions are needed for reuse unless it is derivative or for commercial purposes.  aAbstract.  Rice (Oryza sativa L.) is one of the most important staple food crops in the world; however, there has recently been a shift in consumer demand for higher grain quality. Therefore, understanding the genetic architecture of grain quality has become a key objective of rice breeding programs. Genomewide association studies (GWAS) using large diversity panels have successfully identified genomic regions associated with complex traits in diverse crop species. Our main objective was to identify genomic regions associated with grain quality and to identify and characterize favorable haplotypes for selection. We used two locally adapted rice breeding populations and historical phenotypic data for three rice quality traits: yield after milling, percentage of head rice recovery, and percentage of chalky grain. We detected 22 putative quantitative trait loci (QTL) in the same genomic regions as starch synthesis, starch metabolism, and cell wall synthesis-related genes are found. Additionally, we found a genomic region on chromosome 6 in the tropical japonica population that was associated with all quality traits and we identified favorable haplotypes. Furthermorethis region is linked to the OsBEI gene that codes for a starch branching enzyme I, which is implicated in starch granule formation. In tropical japonica, we also found two putative QTL linked to OsBEII, OsDEP1, and OsDEP2. Our study provides an insight into the genetic basis of rice grain chalkiness, yield after milling, and head rice, identifying favorable haplotypes and molecular markers for selection in breeding programs.  © 2018 Crop Science Society of America  aORYZA SATIVA  aRICE  aFOOD GRAIN  aGENETIC SELECTION  aGENETIC VARIATION  aGENETICS  aMILLED RICE  aPLANT BREEDING1 aGUTIÉRREZ, L.1 aMONTEVERDE, E.1 aBLANCO, P.H.1 aPÉREZ DE VIDA, F.1 aROSAS, J.E.1 aFERNANDEZ, S.1 aGARAYCOCHEA, S.1 aMC COUCH, S.1 aBERBERIAN, N.1 aSIMONDI, S.1 aBONNECARRERE, V.  tPlant Genome, 2018, Volume 11, Article number 170076. Open Access.