QTL Identification for Cooking and Eating Quality in indica Rice Using Multi-Parent Advanced Generation Intercross (MAGIC) Population.

Kimberly S Ponce,Guoyou Ye,Xiangqian Zhao

doi:10.3389/fpls.2018.00868

Abstract

Association mapping using a multi-parent advanced generation intercross (MAGIC) population provides a promising tool in genetic dissection of rice cooking and eating quality (CEQ). In this study, QTLs were identified for ten physicochemical properties related to CEQ using 508 F6 MAGIC lines. The whole population and eight founder lines were genotyped with 6K Illumina Infinium HD Assay. All traits had high heritability estimates and showed a large genetic variation in the MAGIC population. Highly significant phenotypic correlations were present between traits. AC was significantly positively correlated with PKT, TV, FV, SBV, PKT, and RT but significantly negatively correlated with GC and BDV. Seventeen QTLs were identified for all traits. GBSSI locus was hosted or closely to nine QTLs, qAC6, qGC6.1, qPKT6.1, qPKV6, qBDV6.1, qTV6.1, qFV6, qSBV6, and qRT6, suggesting that GBSSI impacts the overall CEQ. Another locus closed to SSIIa, located at 6.99 Mb, affects five traits, GC, PKT, BDV, SBV, and PT. The identified QTLs 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 CEQ in indica rice. These results also confirmed that QTL mapping via association mapping using a MAGIC population is a powerful method in genetic analysis of complex traits.

Highlights

Grain quality is one of the most important quantitative traits in rice
SAGC-08, FFZ1, and IR 02A127 were under low amylose content (AC) class (10–20%) while CT 16658-5-2-2SR-2-3-6MP, BP1976B-2-3-7-TB-1-1, HHZ 5-SAL 9Y 3-Y 1, and IR 68 were under intermediate AC class (20–25%)
AC was significantly positively correlated with peak time (PKT), trough viscosity (TV), final viscosity (FV), setback viscosity (SBV), PKT, and RT but significantly negative correlated with gel consistency (GC) and breakdown viscosity (BDV), which indicate that disruption of starch molecules become harder as AC increase

Summary

Introduction

Grain quality is one of the most important quantitative traits in rice. It is a multi-faceted trait involving physical and biochemical aspects relating to milling, appearance, cooking and eating quality (CEQ), and nutrition (He et al, 1999; Fitzgerald et al, 2009; Bao, 2014). CEQ mainly affects the easiness of cooking, firmness, and cohesiveness of cooked rice and CEQ is directly related to four physicochemical properties, the amylose content (AC), gel consistency (GC), gelatinization temperature (GT), and pasting viscosity (PV) (Dela Cruz and Khush, 2000; Fitzgerald et al, 2009; Bao, 2014).

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