Abstract
BackgroundA number of QTL studies reported that one genomic region was associated with several traits, indicating linkage and/or pleiotropic effects. The question of pleiotropy versus tight linkage in these studies should be solved using a large-size population combined with high-density mapping. For example, if each of the 2 parents has a TGW-increasing or SPP-increasing QTL that is tightly linked, complementary combination of the 2 beneficial QTLs by using molecular markers could produce higher yields compared to the 2 parents. However, a pleiotropic QTL with opposite effects on the SPP and 1,000-grain weight (TGW) is complicated and challenging in terms of its application to rice improvement.ResultsIn this study, using a series of BC5F4 nearly isogenic lines (NILs) that were derived from a cross between the Korean japonica cultivar Hwayeongbyeo and Oryza rufipogon, we demonstrated that 2 QTLs, qSPP5 for spikelets per panicle (SPP) and qTGW5 for grain weight (TGW), are tightly linked on chromosome 5. Alleles from the O. rufipogon parent increased the SPP and decreased TGW in the Hwayeongbyeo background. qSPP5 was located within a 803-kb interval between the simple sequence repeat (SSR) markers INDEL3 and RM18076. Based on the map position, qTGW 5 seemed to be the same gene as qSW5, which controls grain morphology. The additive effect of the O. rufipogon allele at qSPP5 was 10–15 SPP, and 33.0% of the phenotypic variance could be explained by the segregation of the SSR marker RM18058. Yield trials with BC5F4 NILs showed that lines that contained a homozygous O. rufipogon introgression at the qSPP5 region out-yielded sibling NILs that contained Hwayeongbyeo DNA by 15.3% and out-yielded the Hwayeongbyeo parent by 7.3%.ConclusionBased on the finding that the O. rufipogon allele for the SPP was beneficial in the japonica and indica cultivar backgrounds, the qSPP5 allele could be valuable for improving rice yields. In addition, the NIL populations and molecular markers are useful for cloning qSPP5.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-33) contains supplementary material, which is available to authorized users.
Highlights
A number of QTL studies reported that one genomic region was associated with several traits, indicating linkage and/or pleiotropic effects
The grain width (GW) of Hwayeongbyeo was larger than that of CR6, whereas no significant differences in the grain thickness (GT) and grain length (GL) were detected between the 2 parents
The genotypes of the BC5F2 plants were determined at RM194 and the phenotypic variances that were explained by the marker were 37.0%, 13.9%, 9%, and 20.0%, respectively
Summary
A number of QTL studies reported that one genomic region was associated with several traits, indicating linkage and/or pleiotropic effects. Several QTLs for the SPP have been identified in wild relatives (Thomson et al, 2003; Suh et al, 2005; Onishi et al, 2007) These QTLs are located across the chromosomes and provide valuable information on the genes that control the SPP in different populations. SPP QTLs have been mapped as a single Mendelian factor (Zhang et al, 2006, 2009) and were rarely found on chromosomes 5 and 10 (Thomson et al, 2003; Tan et al, 2008) These studies showed that the wild rice allele leads to increased or decreased number of SPP
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