Open AccessGenome‐Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High‐Quality Rice
Author(s) -
Quero Gastón,
Gutiérrez Lucía,
Monteverde Eliana,
Blanco Pedro,
Pérez de Vida Fernando,
Rosas Juan,
Fernández Schubert,
Garaycochea Silvia,
McCouch Susan,
Berberian Natalia,
Simondi Sebastián,
Bonnecarrère Victoria
Publication year - 2018
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2017.08.0076
Subject(s) - biology , quantitative trait locus , oryza sativa , association mapping , genome wide association study , grain quality , haplotype , population , genetic architecture , genome , genetics , genetic association , microbiology and biotechnology , gene , allele , agronomy , genotype , single nucleotide polymorphism , demography , sociology
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. Genome‐wide 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. Furthermore, this 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.