Abstract
Identification of Quantitative Trait Loci (QTL) has been a challenge for complex traits due to the use of populations with narrow genetic base. Most of QTL mapping studies were carried out from crosses made within the subspecies, either indica × indica or japonica × japonica. In this study we report advantages of using Multi-parent Advanced Generation Inter-Crosses global population, derived from a combination of eight indica and eight japonica elite parents, in QTL discovery for yield and grain quality traits. Genome-wide association study and interval mapping identified 38 and 34 QTLs whereas Bayesian networking detected 60 QTLs with 22 marker-marker associations, 32 trait-trait associations and 65 marker-trait associations. Notably, nine known QTLs/genes qPH1/OsGA20ox2, qDF3/OsMADS50, PL, QDg1, qGW-5b, grb7-2, qGL3/GS3, Amy6/Wx gene and OsNAS3 were consistently identified by all approaches for nine traits whereas qDF3/OsMADS50 was co-located for both yield and days-to-flowering traits on chromosome 3. Moreover, we identified a number of candidate QTLs in either one or two analyses but further validations will be needed. The results indicate that this new population has enabled identifications of significant QTLs and interactions for 16 traits through multiple approaches. Pyramided recombinant inbred lines provide a valuable source for integration into future breeding programs.
Highlights
Rice is a major food crop for over half of the world population, accounting for almost 90% of production of global rice by Asian countries[1]
Most of the economically important traits display complex genetic architecture that are under polygenic control and often influenced by extensive genotype × environment (G×E) interactions
Www.nature.com/scientificreports with high-throughput genotyping, agronomic Quantitative Trait Loci (QTL) and grain quality QTLs have been mapped by high-dense Single Nucleotide Polymorphism (SNP) markers through genome-wide association study (GWAS) 22–25
Summary
Rice is a major food crop for over half of the world population, accounting for almost 90% of production of global rice by Asian countries[1]. An alternative approach is to create multi-parental populations derived from elite parents in which each line represents a combination of alleles inherited from multiple parents This allows the broadening of the genetic base and creates agronomically superior breeding lines through strategic recombination of genes/QTLs, thereby helps to select best lines suitable for targeted breeding programs. MAGIC involves intercrossing a number of parental lines for “n” generations in a mating design to combine the genomes of all parents in the progeny lines It can be used for coarse mapping with low marker densities on lines derived from an early generation and for fine mapping QTL using lines derived from more advanced generation[32]. Based on the QTL identified, tightly linked SNP markers can be used by breeders for marker-aided selection to precisely introduce beneficial QTLs into elite lines for crop improvement
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
