QTL identification for cooking and eating quality in indica rice (Oryza sativa L.) using multi-parent advanced generation intercross (MAGIC) population
2016
Ponce, K.S.
The choice of mapping population and mapping method are the key factors in understanding the genetic basis of complex traits as it highly influences power and resolution of quantitative trait locus (QTL) mapping. Association mapping (AM) using multi-parent advanced generation intercross (MAGIC) population provides a promising tool in genetic dissection of economically important quantitative traits. In this study, QTLs were identified for ten physicochemical properties related to cooking and eating quality via AM using 479 F sub 6¬ MAGIC lines. The whole population including the eight founder lines were genotyped with 6K Illumina Infinium HD Assay. All traits had a large genetic variation and high heritability estimates. Highly significant phenotypic correlations were present between traits. High genetic diversity was observed among founder lines and in the MAGIC population. The linkage disequilibrium (LD) decayed cleanly and rapidly below critical level (r sup 2) 0.2 at about 1.25 Mb. Cryptic kinship and the presence of two population structure were also observed. The association analysis based on PK model identified 18 QTLs for all the physicochemical traits, five of which corresponded to GBSSI/Wx gene, the major gene responsible for starch biosynthesis. The identified QTLs showed multi-trait association and revealed small to modest effects, where the highest percentage of phenotypic variance explained was 17.18%. These QTLs are directly relevant and useful in breeding for improved cooking and eating quality in indica rice. The results also confirmed that QTL mapping via AM using MAGIC population is a powerful method in detecting alleles affecting cooking and eating properties. Moreover, the results supported previous studies that MAGIC populations are indeed valuable resource in genetic analysis of complex traits.
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