Additive and Over-dominant Effects Resulting from Epistatic Loci Are the Primary Genetic Basis of Heterosis in Rice

A set of 148 F9 recombinant inbred lines （RILs） was developed from the cross of an indica cultivar 93-11 and japonica cultivar DTI13, showing strong F1 heterosis. Subsequently, two backcross F1 （BCFI） populations were constructed by backcrossing these 148 RILs to two parents, 93-11 and DT713. These three related populations （281BCF1 lines, 148 RILs） were phenotyped for six yield-related traits in two locations. Significant inbreeding depression was detected in the population of RILS and a high level of heterosis was observed in the two BCF1 populations. A total of 42 main-effect quantitative trait loci （M-QTLs） and 109 epistatic effect QTL pairs （E-QTLs） were detected in the three related populations using the mixed model approach. By comparing the genetic effects of these QTLs detected in the RILs, BCF1 performance and mid-parental heterosis （HMp）, we found that, in both BCF1 populations, the QTLs detected could be classified into two predominant types： additive and over-dominant loci, which indicated that the additive and over-dominant effect were more important than complete or partially dominance for M-QTLs and E-QTLs. Further, we found that the E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both RILs and BCF1 populations. All of these results suggest that additive and over-dominance resulting from epistatic loci might be the primary genetic basis of heterosis in rice.

Molecular Evolution of the TACl Gene from Rice(Oryza sativa L.)

Tiller angle is a key feature of the architecture of cultivated rice （Oryza sativa）, since it determines planting density and influences rice yield. Our previous work identified Tiller Angle Control 1 （TACI） as a major quantitative trait locus that controls rice filler angle. To further clarify the evolutionary characterization of the TAC1 gene, we compared a TACl-containing 3164-bp genomic region among 113 cultivated varieties and 48 accessions of wild rice, including 43 accessions of O. rufipogon and five accessions of O. nivara. Only one single nucleotide polymorphism （SNP）, a synonymous substitution, was detected in TAC1 coding regions of the cultivated rice varieties, whereas one synonymous and one nonsynonymous SNP were detected among the TAC1 coding regions of wild rice accessions. These data indicate that little natural mutation and modification in the TAC1 coding region occurred within the cultivated rice and its progenitor during evolution. Nucleotide diversities in the TAC1 gene regions of O. sativa and O. rufipogon of 0.00116 and 0.00112, respectively, further indicate that TAC1 has been highly conserved during the course of rice domestication. A functional nucleotide polymorphism （FNP） of TAC1 was only found in the japonica rice group. A neutrality test revealed strong selection, especially in the 3＇-flanking region of the TAC1 coding region containing the FNP in the japonica rice group. However, no selection occurred in the indica and wild-rice groups. A phylogenetic tree derived from TAC1 sequence analysis suggests that the indica and japonica subspecies arose indepen- dently during the domestication of wild rice.