Genetic Dissection of an Elite Rice Hybrid Revealed That Heterozygotes Are Not Always Advantageous for Performance

Abstract

We introduced an experimental design that produced an “immortalized F2” population allowing for complete dissection of genetic components underlying quantitative traits. Data for yield and three component traits of the immortalized F2 were collected from replicated field trials over 2 years. Using 231 marker loci, we resolved the genetic effects into individual components and assessed relative performance of all the genotypes at both single- and two-locus levels. Single-locus analysis detected 40 QTL for the four traits. Dominance effects for about one-half of the QTL were negative, resulting in little “net” positive dominance effect. Correlation between genotype heterozygosity and trait performance was low. Large numbers of digenic interactions, including AA, AD, and DD, were detected for all the traits, with AA as the most prevalent interaction. Complementary two-locus homozygotes frequently performed the best among the nine genotypes of many two-locus combinations. While cumulative small advantages over two-locus combinations may partly explain the genetic basis of heterosis of the hybrid as double heterozygotes frequently demonstrated marginal advantages, double heterozygotes were never the best genotypes in any of the two-locus combinations. It was concluded that heterozygotes were not necessarily advantageous for trait performance even among genotypes derived from such a highly heterotic hybrid.

Molecular Genetic Diversity and Combining Ability for Some Physiological and Agronomic Traits in Rice under Well-Watered and Water-Deficit Conditions

“…The non-significant correlation recorded between SSR-based GD, hybrid performance, heterosis (mid or better parent) and SCA effects for all the studied traits could be a result of using a relatively small number of markers. Analogous findings were reported by Xiao et al [ 26 ], Hua et al [ 35 ], Gramaje et al [ 22 ], and Zhang et al [ 88 ]. However, Xangsayasane et al [ 31 ] and Singh et al [ 33 ] reported a significant association between GD, heterosis and hybrid performance.…”

“…Microsatellites or simple sequence repeats (SSR) are valuable markers due to their co-dominant transmission, multi-allelic nature, relative abundance, genome coverage, informativeness, and low DNA requirement [ 30 ]. Numerous published reports have revealed a significant relationship between GD-based molecular markers with F 1 hybrid performance and heterosis [ 31 , 32 , 33 ], although other studies have detected no significant correlation [ 22 , 26 , 34 , 35 ]. We hypothesized that crossing diverse exotic and local rice genotypes with different levels of tolerance to water deficit would provide promising high-yielding and tolerant F 1 hybrids.…”

Estimating genetic variance contributed by a quantitative trait locus: A random model approach

“…An IMF2 (immortalized F 2 ) population of rice with n = 278 hybrids was used as an example for illustration [ 54 ]. The trait is the 1000-grain weight (KGW).…”

“…A normalized kinship matrix has a property of tr( K ) = n , i.e., the trace of K equals the sample size. The data were originally published by Hua et al [ 54 ] and later by Xu et al [ 55 ]. We illustrated the analysis of a single marker (Bin725) as an example.…”

QTL Mapping and Candidate Gene Analysis for Seed Germination Response to Low Temperature in Rice

“…Among them, two QTLs were overlapped on chromosome 6 in the same marker interval RM528-RM20632 in both the repeated experiments. Li et al and Hua et al characterized qGP3-1 and qGP-6, respectively, associated with grain number per panicle [32,33]. It is also reported that the GA biosynthesis gene (OsGA20ox1) is located in qGP3 for the number of grains per panicle [34].…”