Fine mapping of a quantitative trait locus for grain number per panicle from wild rice (Oryza rufipogon Griff.)

Abstract

SIL040, an introgression line (IL) developed by introgressing chromosomal segments from an accession of Oryza rufipogon into an indica cultivar Guichao 2, showed significantly less grains per panicle than the recurrent parent Guichao 2. Quantitative trait locus (QTL) analysis in F2 and F3 generations derived from the cross between SIL040 and Guichao 2 revealed that gpa7, a QTL located on the short arm of chromosome 7, was responsible of this variation. Alleles from O. rufipogon decreased grains per panicle. To fine mapping of gpa7, a high-resolution map with 1,966 F2 plants derived from the cross between SIL040 and Guichao 2 using markers flanking gpa7 was constructed, and detailed quantitative evaluation of the structure of main panicle of each of F3 families derived from recombinants screened was performed. By two-step substitution mapping, gpa7 was finally narrowed down to a 35-kb region that contains five predicted genes in cultivated rice. The fact that QTLs for five panicle traits (length of panicle, primary branches per panicle, secondary branches per panicle, grains on primary branches and grains on secondary branches) were all mapped in the same interval as that for gpa7 suggested that this locus was associated with panicle structure, showing pleiotropic effects. The characterizing of panicle structure of IL SIL040 further revealed that, during the domestication from common wild allele to cultivated rice one at gpa7, not only the number of branches and grains per panicle increased significantly, more importantly, but also the ratio of secondary branches per panicle to total branches per panicle and the ratio of grains on secondary branches per panicle to total grains per panicle increased significantly. All these results reinforced the idea that gpa7 might play an important role in the regulation of grain number per panicle and the ratio of secondary branches per panicle during the domestication of rice panicle.

QTL mapping of agronomic traits using an RIL population derived from a cross between temperate japonica cultivars in rice (Oryza sativa L.)

“…Among the 27 QTLs detected in the present study, nineteen have been detected in previous QTL studies (www.gramene.org). These include the QTLs for days to heading, dth6 (Yano et al 2000), for panicle length, pl6 and pl7, in the Lemont × Teqing RI population (Mei et al 2005), for grain yield, gy7 (Tian et al 2006), and for grain width gw7 (Redoña and Mackill 1998). However, the other eight QTLs, cl10 for culm length, spp10 for spikelets per panicle, gt7 for grain thickness, gl8 and gl12 for grain length and gs4, gs7 and gs12 for grain shape were identified for the first time in this study, indicating that these QTLs might be specific to temperate japonica rice.…”

“…So far, most QTLs have been detected using intersubspecific and inter-specific crosses (Aluko et al 2004, Tian et al 2006. This is due to the fact that wide crosses possessed a higher level of DNA polymorphism than intrasubspecific crosses and thereby contributed to increase mapping efficiency (Causse et al 1994); however, this presented a disadvantage for determining the utility of a QTL for a breeding program that exclusively utilized a japonica germplasm.…”

Construction of a new set of rice chromosome segment substitution lines and identification of grain weight and related traits QTLs

“…Some examples of major genes identified in this way are spd6 (panicle size and plant height) (Shan et al 2009) and gpa7 (grain number per panicle) (Tian et al 2006a) from Oryza rufipogon Griff., and GIF1 (grain-filling and yield) and PROG1 (growth habit, grain number and grain yield) (Tan et al 2008) from cultivated rice. Although CSSL populations represent a useful tool for genetic analysis, they have not been widely utilized in breeding practice, probably because most CSSL parental lines are not themselves elite varieties, and hence are associated with poor overall performance (Shan et al 2009, Tian et al 2006a.…”

Selecting a set of wild barley introgression lines and verification of QTL effects for resistance to powdery mildew and leaf rust

“…Several reports for different crop species underline the usefulness of ILs for these purposes. By means of ILs, yield-associated QTLs were fine-mapped in tomato (Eshed and Zamir 1995), rice (Tian et al 2006b), and wheat (Röder et al 2008). Two studies in tomato focused on the dissection of regions containing QTLs for fruit quality and shape (Yates et al 2004;van der Knaap et al 2004, respectively).…”