Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations

Abstract

To understand the types of gene action controlling seven quantitative traits in rice, QTL mapping was performed to dissect the main effect (M-QTLs) and digenic epistatic (E-QTLs) QTLs responsible for the trait performance of 254 recombinant inbred lines (RILs) of "Lemont/Teqing", and two testcross (TC) F(1) populations derived from these RILs. The correlation analyses reveal a general pattern, i.e. trait heritability in the RILs was negatively correlated to trait heterosis in the TC hybrids. A large number of M-QTLs and E-QTLs affecting seven traits, including heading date (HD), plant height (PH), flag leaf length (FLL), flag leaf width (FLW), panicle length (PL), spikelet number per panicle (SN) and spikelet fertility (SF), were identified and could be classified into two predominant groups, additive QTLs detected primarily in the RILs, and overdominant QTLs identified exclusively in the TC populations. There is little overlap between QTLs identified in the RILs and in the TC populations. This result implied that additive gene action is largely independent from non-additive gene action in the genetic control of quantitative traits of rice. The detected E-QTLs collectively explained a much greater portion of the total phenotypic variation than the M-QTLs, supporting prior findings that epistasis has played an important role in the genetic control of quantitative traits in rice. The implications of these results to the development of inbred and hybrid cultivars were discussed.

Identification of Quantitative Trait Loci Across Recombinant Inbred Lines and Testcross Populations for Traits of Agronomic Importance in Rice

“…For the seven QTL with strongest main effect (i.e., ph1, ppp2, spp1, gpp1, gw1, gypp1, and hd6a), we explored the publicly available QTL database (http://www.gramene.org) to search their alignment QTL identified in the same chromosome region in previous studies. For ph1, the same QTL associated with plant height has been reported in six populations: CNHZAU Zh97/Ming63 RI (Cui et al 2002), Cornell 9024/LH422 RI (Xiao et al 1996), Cornell Jef/Oruf BC (Thomson et al 2003), IRRI Mor/CO39 (Huang et al 1996), IRRI IR64/Azu DH (Venuprasad et al 2002), and IRRI Lem/Teq RI QTL (Mei et al 2003). In the vicinity of ph1, two genes associated with plant height have been identified and isolated: one is the gibberellin biosynthetic gene OsGA3ox2 (Itoh et al 2001) and the other is the brassinosteroid biosynthetic gene D2 (Hong et al 2003).…”

“…One allele of the gene (Hd3a) has been cloned, which encodes a protein closely related to Arabidopsis FT (Kojima et al 2002). For five yield-related QTL (i.e., ppp2, spp1, gpp1, gw1, and gypp1), the same QTL have been reported in the corresponding chromosome regions in 5, 9, 3, 3, and 4 populations, respectively, among total 13 populations: CNHZAU Zh97/Ming63 RI (Cui et al 2002;Hua et al 2002Hua et al , 2003, CNHZAU Zhe97/Wuy2 (Jiang et al 2004), CNRRI Tes/CB (Zhuang et al 1997), CNRRI Zh97B/ Mil46 RI (Zhuang et al 2001(Zhuang et al , 2002, Cornell 9024/ LH422 RI (Xiao et al 1996), Cornell IR64/IRG105 (Septiningsih et al 2003), Cornell Jef/Oruf BC (Thomson et al 2003), HNAES MIL23/Aki RI (Yagi et al 2001), IGCAS ZYQ8/JX17 F 2 (Xu et al 1995), IRRI Lem/Teq RI (Mei et al 2003), IRRI Mil23/Aki RI (Nagata et al 2002;Kobayashi et al 2003), JRGP Nip/Kas F 2 (Yamaya et al 2002), and NIAS Kosh/Kas near isogenic lines (Obara et al 2004). Recently, the gene Gn1a, which produces more grains per panicle near the QTL gpp1 and encodes a cytokinin oxidase, has been cloned (Ashikari et al 2005).…”

Genetic Analysis of Heterosis for Yield and Yield Components in Rapeseed (Brassica napus L.) by Quantitative Trait Locus Mapping

“…Nevertheless in rapeseed 3 of 4 loci for grain yield showed overdominance. High levels of overdominance for reproductive traits were also reported in rice Luo et al 2001;Mei et al 2003Mei et al , 2005 and tomato (Semel et al 2006), leading Semel et al to the hypothesis that an association of overdominant QTL for traits determining higher reproductive fitness was selected for in evolution. On the other hand, analyzing five biomass-related traits Kusterer et al (2007b) mapped 6 QTL with significant dominance effects.…”

“…No overdominance and epistasis was detected. These results are in disagreement with a series of studies on heterosis in rice by Yu et al (1997), Li et al (2001), Luo et al (2001), and Mei et al (2003Mei et al ( , 2005. Plant height, grain yield, and yield components were analyzed by QTL mapping in recombinant inbred line populations, in the correspond-1 ing testcross populations with an independent tester, and in backcross populations.…”

Mixed linear model approaches in mapping QTLs with epistatic effects by a simulation study

“…Hence, genetic models for QTL mapping assuming no epistasis can lead to a biased estimation of QTL parameters (Bocianowski 2013). A large number of epistatic effects have recently been detected in rice (Oryza sativa L.) using polymorphic markers in the whole genome (Hua et al 2002;Mei et al 2003Mei et al , 2005. Epistatic effects have been found to be important in the expression of dough rheological properties in a wheat DH population (Ma et al 2005).…”