Genetic Analysis for Cooking and Eating Quality of Super Rice and Fine Mapping of a Novel Locus qGC10 for Gel Consistency

Abstract

Rice (Oryza sativa L.) is an important cereal that provides food for more than half of the world's population. Besides grain yield, improving grain quality is also essential to rice breeders. Amylose content (AC), gelatinization temperature (GT) and gel consistency (GC) are considered to be three indicators for cooking and eating quality in rice. Using a genetic map of RILs derived from the super rice Liang-You-Pei-Jiu with high-density SNPs, we detected 3 QTLs for AC, 3 QTLs for GT, and 8 QTLs for GC on chromosomes 3, 4, 5, 6, 10, and 12. Wx locus, an important determinator for AC and GC, resided in one QTL cluster for AC and GC, qAC6 and qGC6 here. And a novel major QTL qGC10 on chromosome 10 was identified in both Lingshui and Hangzhou. With the BC₄F₂ population derived from a CSSL harboring the segment for qGC10 from 93-11 in PA64s background, it was fine mapped between two molecular markers within 181 kb region with 27 annotated genes. Quantitative real-time PCR results showed that eight genes were differentially expressed in endosperm of two parents. After DNA sequencing, only LOC_Os10g04900, which encodes a F-box domain containing protein, has 2 bp deletion in the exon of PA64s, resulting in a premature stop codon. Therefore, LOC_Os10g04900 is considered to be the most likely candidate gene for qGC10 associated with gel consistency. Identification of qGC10 provides a new genetic resource for improvement of rice quality.

Keywords: QTL analysis; cooking and eating quality; fine mapping; gel consistency; rice.

FIGURE 1

Phenotype of amylose content (AAC, A), gelatinization temperature (ASV, B) and gel consistency (C) in parents 93-11 and PA64s. The error bar for each value represents mean ± SD (n = 6). * and ** indicate at 5 and 1% significant level compared to 93-11 according to t-test (n = 6), respectively.

FIGURE 2

Location of QTLs for AC, GT, and GC on SNP map. Number indicates genetic distance (cM) along each chromosome.

FIGURE 3

GC phenotype and Rapid Visco Analyzer (RVA) profile characteristic values in 93-11, PA64s and CSSL-qGC10. (A) GC phenotype in 93-11, PA64s and CSSL-qGC10. Rice flour becomes rice paste glue after dilute alkali and heat treatment. It has a certain degree of extension when cooling in the horizontal tube with total length of 100 mm, and the extended length represents GC value. (B) RVA profile characteristic values in 93-11, PA64s and CSSL-qGC10. The RVA spectrum simulates the process of rice cooking and reflects the taste and texture of rice. RVA is represented by Relative Viscosity Units (RVU).

FIGURE 4

Fine mapping of qGC10. (A) qGC10 was narrowed down to a 181 kb interval defined by markers IND-4 and SNP-1. Values represent means ± SD (n ≥ 3). Different letters represent significant differences (P < 0.05) by t-test. (B) All the 27 predicted genes in the target region. (C) Structure and mutated sites of the most likely candidate gene. LOC_Os10g04900 consist of one exon (represent with black box). Arrow indicates the deletion of 2 bp in the position of PA64s compared to 93-11.

FIGURE 5

Relative expression of 8 genes in the endosperm of 93-11 and PA64s. The error bar for each value represents mean ± SD (n = 3). ** indicate at 1% significant level compared to PA64s according to t test.