Genetic composition of yield heterosis in an elite rice hybrid

Abstract

Heterosis refers to the superior performance of hybrids relative to the parents. Utilization of heterosis has contributed tremendously to the increased productivity in many crops for decades. Although there have been a range of studies on various aspects of heterosis, the key to understanding the biological mechanisms of heterotic performance in crop hybrids is the genetic basis, much of which is still uncharacterized. In this study, we dissected the genetic composition of yield and yield component traits using data of replicated field trials of an "immortalized F(2)" population derived from an elite rice hybrid. On the basis of an ultrahigh-density SNP bin map constructed with population sequencing, we calculated single-locus and epistatic genetic effects in the whole genome and identified components pertaining to heterosis of the hybrid. The results showed that the relative contributions of the genetic components varied with traits. Overdominance/pseudo-overdominance is the most important contributor to heterosis of yield, number of grains per panicle, and grain weight. Dominance × dominance interaction is important for heterosis of tillers per plant and grain weight and has roles in yield and grain number. Single-locus dominance has relatively small contributions in all of the traits. The results suggest that cumulative effects of these components may adequately explain the genetic basis of heterosis in the hybrid.

Fig. 1.

Profiles of additive and dominance effects in the entire genome for yield and yield component traits. AE1998, DE1999, etc. indicate additive and dominance effects detected in the data of 1998 and 1999, respectively. AD score refers to the absolute amounts of additive and dominance effects of the trait. Green triangles indicate the centromere positions on the chromosomes.

Fig. 2.

Dominance and overdominance in the entire genome for yield and yield component traits. The effects were identified using an h test confirmed by permutation. The adjacent bins that are clustered are separated by columns. The height of the columns shows the dominance values. Red indicates overdominance, and orange indicates partial to full dominance. Black represents statistically insignificant effects. Green triangles indicate the centromere positions on the chromosomes.

Fig. 3.

(A–D) Relative contributions of dominance, overdominance, and epistasis to heterosis. Numbers indicated the percentage contribution of each effect. ND, negative dominance; NDD, negative digenic dominance; NO, negative overdominance; PD, positive dominance; PDD, positive digenic dominance; PO, positive overdominance.