Dominance, Overdominance and Epistasis Condition the Heterosis in Two Heterotic Rice Hybrids

Abstract

Two recombinant inbred (RI) populations having 194 and 222 lines each, derived, respectively, from a highly heterotic inter-(IJ ) and intrasubspecific (II ) hybrid, were backcrossed to their respective parents. The RI and two backcross populations along with F 1 and its two parents of each hybrid were evaluated for nine important traits, including grain yield and eight other yield-related traits. A total of 76 quantitative trait loci (QTL) for the IJ hybrid and 41 QTL for the II hybrid were detected in the RI population, midparent heterosis of two backcross populations, and two independent sets of data by summation (L 1 1 L 2 ) and by subtraction (L 1 À L 2 ) of two backcross populations (L 1 and L 2 ). The variance explained by each QTL ranged from 2.6 to 58.3%. In the IJ hybrid, 42% (32) of the QTL showed an additive effect, 32% (24) a partial-tocomplete dominant effect, and 26% (20) an overdominant effect. In the II hybrid, 32% (13) of the QTL demonstrated an additive effect, 29% (12) a partial-to-complete dominant effect, and 39% (16) an overdominant effect. There were 195 digenic interactions detected in the IJ hybrid and 328 in the II hybrid. The variance explained by each digenic interaction ranged from 2.0 to 14.9%. These results suggest that the heterosis in these two hybrids is attributable to the orchestrated outcome of partial-to-complete dominance, overdominance, and epistasis. H ETEROSIS, a term to describe the superiority of heterozygous genotypes over their corresponding parental genotypes (Shull 1908), has been under investigation for $100 years, but no consensus exists about the genetic basis underlying this very important phenomenon. Two contending hypotheses, the dominance hypothesis and the overdominance hypothesis, were proposed to explain this phenomenon about one century ago. The dominance hypothesis attributes heterosis to canceling of deleterious or inferior recessive alleles contributed by one parent, by beneficial or superior dominant alleles contributed by the other parent in the heterozygous genotypes at different loci (Davenport 1908;Bruce 1910;Jones 1917). The overdominance hypothesis attributes heterosis to the superior fitness of heterozygous genotypes over homozygous genotypes at a single locus (East 1908;Shull 1908).Molecular markers and their linkage maps have greatly facilitated the identification of individual loci conditioning heterosis and the estimation of gene action of underlying loci. Quantitative trait locus (QTL) mapping studies aiming at understanding the genetic basis of heterosis have been conducted in rice and other crops (Xiao et al. 1995;Li et al. 1997Li et al. , 2001Yu et al. 1997;Luo et al. 2001;Hua et al. 2002Hua et al. , 2003Semel et al. 2006;Frascaroli et al. 2007; Melchinger et al. 2007a,b). Evidence from such studies suggests that heterosis may be attributable to dominance (Xiao et al. 1995;Cockerham and Zeng 1996), overdominance (Stuber et al. 1992;Li et al. 2001;Luo et al. 2001), pseudooverdominance due to tightly linked loci with beneficial ...

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

“…The two dimensional scanning methods, which consider both main and epistatic effects of pair QTL simultaneously with genetic background controlling, such as the mixed model approach of Wang et al [23] and inclusive composite interval mapping (ICIM) of Li et al [42], are alternative methods. However, the genetic design matrix should be reconstructed (Table 1) and the genetic parameter should be correctly explained [14][15][16]24,30,41]. Although the multiple interval mapping in Garcia et al [16] can estimate the augmented main and epistatic effects simultaneously, it differs from our method in two aspects.…”

“…Heterosis represents one of the most revolutionary advancements in crop improvement, i.e., maize [8] and rice [4]. In the genetic dissection of heterosis, NCIII design, proposed by Comstock and Robinson [9,10], is one of the most powerful and widely used mating schemes [11][12][13][14][15][16][17]. Therefore, the importance of heterosis necessitates an in-depth study of the NCIII design.…”

“…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].…”

“…Second, RIL allows more recombinational segregation of tightly linked QTL than the other populations, and this offers a higher mapping resolution [15,22,29]. Finally, the use of homozygous RIL can gain the highest statistical power for QTL detection [15,17,29]. Therefore, further exploration of the RIL-based NCIII design is warranted.…”

“…Li et al [15] studied heterosis by QTL analysis in the RIL-based NCIII design. QTL analysis was performed separately for the RIL, MPH of two backcross populations and the SUM (L 1 +L 2 ) and DIFF (L 1 −L 2 ) data of two backcross populations (L 1 and L 2 ).…”