Fine mapping of grain weight QTL, tgw11 using near isogenic lines from a cross between Oryza sativa and O. grandiglumis

Abstract

In our previous study, we reported the grain weight (GW) QTL, tgw11 in isogenic lines derived from a cross between Oryza sativa ssp. Japonica cv. Hwaseong and O. grandiglumis. The O. grandiglumis allele at tgw11 decreased GW in the Hwaseong background. To fine-map tgw11, one F5 plant homozygous for the O. grandiglumis DNA in the target region on chromosome 11 was selected from F4 line, CR1242 segregating for tgw11 and crossed with Hwaseong to produce secondary F2 and F3 populations. QTL analysis using 760 F2 plants confirmed the existence of tgw11 with an R 2 value of 15.0%. This QTL explained 32.2% of the phenotypic variance for GW in 91 F3 lines. Substitution mapping with 65 F3 lines with informative recombination breakpoints in the target region was carried out to narrow down the position of the tgw11. The result indicated that tgw11 was located in the 900-kb interval between two SSR markers, RM224 and RM27358. QTLs for grain width and grain thickness were also located in the same interval suggesting that a single gene is involved in controlling these three traits. Analysis of F3 lines indicated that the variation in TGW is associated with variation in grain shape, specifically grain thickness and grain width. Genetic analysis indicated that the O. grandiglumis allele for small seed was dominant over the Hwaseong allele. SSR markers tightly linked to the GW QTL would be useful in marker-assisted selection for variation in GW in breeding program.

Genome-wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

“…Many genes/QTL for rice grain appearance quality and milling quality traits have been reported in the last decades. The GW1-1 and GW1-2 [5], qGRL1.1 [6], GS2 [7], GW3 and GW6 [8], qGL-4b [9], qPGWC-7 [10] qGL-7 [11], qGRL7.1 [6], gw8.1 [12], gw9.1 [13], tgw11 [14] have been fine mapped. The GW2 [15], GS3 [16], qGL-3 [17], qSW5 [18], GS5 [19], Chalk5 [20], TGW6 [21], GW6a [22], SRS1 [23], GL7/GW7 [24,25], GW8 [26] and CycT1;3 [27] have been cloned.…”

A Kelch Motif‐Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice

“…Hundreds of QTLs scattered throughout the whole rice genome (http://www.gramene.com) have been identified for grain shape and weight, although many of these almost certainly represent the same loci detected across different populations and environments. At the base of rudimentary mapping, some main QTLs were further fine mapped through near‐isogenic line (NIL) analysis (Li et al 2004a; Wan et al 2006; Xie et al 2006; Wan et al 2008; Xie et al 2008; Guo et al 2009; Bai et al 2010; Shao et al 2010; Liang et al 2011; Oh et al 2011).…”

Dissecting the Genetic Basis of Extremely Large Grain Shape in Rice Cultivar ‘JZ1560’

“…A few QTLs associated with grain weight, gw3.1, gw3, gw6, gw8.1, gw9.1 and tgw11, have been identified at accurate intrachromosomal locations (Li et al, 2004a;Xie et al, 2006Xie et al, , 2008Guo et al, 2009;Oh et al, 2011). GS3, gl-3, qGL7 and qGL7-2 controlling GL were fine mapped at the exact locations on chromosomes 3 and 7 (Fan et al, 2006;Wan et al, 2006;Bai et al, 2010;Shao et al, 2010).…”