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

Abstract

To understand the types of gene action controlling seven quantitative traits in rice, we carried out quantitative trait locus (QTL) mapping in order to distinguish between the main-effect QTLs (M-QTLs) and digenic epistatic QTLs (E-QTLs) responsible for the trait performance of 254 recombinant inbred lines (RILs) from rice varieties Lemont/Teqing and two backcross hybrid (BCF1) populations derived from these RILs. We identified 44 M-QTL and 95 E-QTL pairs in the RI and BCF1 populations as having significant effects on the mean values and mid-parental heterosis of heading date, plant height, flag leaf length, flag leaf width, panicle length, spikelet number and spikelet fertility. The E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both the RI and BCF1 populations. In both BCF1 populations, over-dominant (or under-dominant) loci were more important than additive and complete or partially dominant loci for M-QTLs and E-QTL pairs, thereby supporting prior findings that overdominance resulting from epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice.

Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design

“…The additive QTL do not contribute to heterosis, while the non-additive QTL, including dominant, overdominant, and epistatic do contribute [12,15,19,22,24,25,28]. The second one is to use the measurements of heterosis as the data input to perform QTL analysis [13][14][15][24][25][26]30,43]. QTL effects for Z 1 and Z 2 in the RIL-based NCIII design provide estimates of the augmented effects a*, which measures the net contribution of the QTL to the parental difference, and d*, which measures the net contribution of the QTL to midparent heterosis [14].…”

“…Another modification of the NCIII design is to use recombinant inbred lines (RIL) as the base population. The results showed that the primary genetic basis of heterosis is dominance in the interval mapping by Xiao et al [22], and epistasis and overdominance in the mixed model analysis [23] by Li et al [24], Luo et al [25] and Mei et al [26]. It should be noted that repulsion linkage might lead to pseudo-overdominance.…”

“…The reasons are as follows. First, RIL is a permanent segregating population, so it can be shared between research groups, and testcross progeny can be repeatedly generated and phenotyped as needed [14,15,26,29]. Second, RIL allows more recombinational segregation of tightly linked QTL than the other populations, and this offers a higher mapping resolution [15,22,29].…”

Field level evaluation of rice introgression lines for heat tolerance and validation of markers linked to spikelet fertility

“…RM235 was associated with spikelet fertility QTL qHt12 on chromosome 12 with 10 % phenotypic variance in heat stress treatment during flowering stage . This marker was also linked to leaf width in RIL population of cross Lemont × Teqing and two backcross hybrid populations derived from these RILs (Mei et al 2005). Jagadish et al (2010a) reported qtl_2.3 for spikelet fertility in control conditions and the allele was contributed by Azucena, a susceptible parent.…”

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).…”