QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects

Abstract

Grain length in rice plays an important role in determining rice appearance, milling, cooking and eating quality. In this study, the genetic basis of grain length was dissected into six main-effect quantitative trait loci (QTLs) and twelve pairs of epistatic QTLs. The stability of these QTLs was evaluated in four environments using an F7 recombinant inbred line (RIL) population derived from the cross between a Japonica variety, Asominori, and an Indica variety, IR24. Moreover, chromosome segment substitution lines (CSSLs) harboring each of the six main-effect QTLs were used to evaluate gene action of QTLs across eight environments. A major QTL denoted as qGL-3a, was found to express stably not only in the isogenic background of Asominori but also in the recombinant background of Asominori and IR24 under multiple environments. The IR24 allele at qGL-3a has a positive effect on grain length. Based on the test of advanced backcross progenies, qGL-3a was dissected as a single Mendelian factor, i.e., long rice grain was controlled by a recessive gene gl-3. High-resolution genetic and physical maps were further constructed for fine mapping gl-3 by using 11 simple sequence repeat (SSR) markers designed using sequence information from seven BAC/PAC clones and a BC4F2 population consisting of 2,068 individuals. Consequently, the gl-3 gene was narrowed down to a candidate genomic region of 87.5 kb long defined by SSR markers RMw357 and RMw353 on chromosome 3, which provides a basis for map-based cloning of this gene and for marker-aided QTL pyramiding in rice quality breeding.

Quantitative Trait Loci for Grain Yield and Adaptation of Durum Wheat (Triticum durum Desf.) Across a Wide Range of Water Availability

“…Accordingly, the stable expression of a QTL across a broad range of agrometeorological conditions is a critical factor when breeding for wide adaptation and yield stability. Examples of such QTL have been reported in bread wheat (Quarrie et al 2007), rice (Wan et al 2005(Wan et al , 2006, pearl millet (Yadav et al 2002), and maize (Landi et al 2007).…”

【Short Report】Identification of Chromosome Regions Affecting Leaf Area with Rice Chromosome Segment Substitution Lines

“…Sink size, another determining factor of yield is given by the product of grain number and weight. In addition to many quantitative trait loci (QTLs), plural genes related to sink size, such as fc1, Gn1 and GS3 have been identified (Ashikari et al, 2005;Goto et al, 2005;Fan et al, 2006;Wan et al, 2006). It is possible to accomplish huge sink size with this information, but partial development in sink size causes a relatively low supply by source and hence does not impact on yield (Peng et al, 1999;Takai et al, 2005).…”

Descriptive statistics and correlation analysis of agronomic traits in a maize recombinant inbred line population

“…Of course, these populations are associated with longer time commitments and higher costs for population construction than F 2 and backcross populations (Wan et al, 2008). Currently, the studies using an RIL as a mapping population are focused on a few crops, including rice (Wan et al, 2006), soybean (Fu et al, 2006), and wheat (Ma et al, 2007). Only limited reports were found in maize in the literature (Bouchez et al, 2002;Ordas et al, 2008), especially in China (Ding et al, 2008).…”