Dwarfing in rice has dramatically improved and stabilized rice yields worldwide, often controlled by a single dwarf gene, sd1. A novel semidwarf gene d60 complements the gametic lethal gene gal, such that the F1 between ‘Hokuriku 100’ (genotype d60d60GalGal, Gal: mutant non-lethal allele) and ‘Koshihikari’ (D60D60galgal, D60: tall allele) would show 25% sterility due to deterioration of gametes bearing both gal and d60. The F2 would segregate as one semidwarf (1 d60d60GalGal) : two tall and 25% sterile (2 D60d60Galgal) : six tall (2 D60d60GalGal : 1 D60D60GalGal : 2 D60D60Galgal : 1 D60D60galgal), skewed from a Mendelian segregation ratio of one semidwarf : three tall for a single recessive gene. To pyramid d60 and sd1, into the Japanese super-variety ‘Koshihikari’, the F1 (D60d60Galgal) of ‘Koshihikari’ × ‘Hokuriku 100’ was first backcrossed with ‘Koshihikari’, and the BCF1 segregated into a ratio of one tall and 25% sterile (D60d60Galgal) : two tall (1 D60D60Galgal : 1 D60D60galgal). Tall, 25% sterile BC1F1 plants (D60d60Galgal) were then selected for pollen sterility and backcrossed with ‘Koshihikari’ as the recurrent parent. It is unnecessary to grow out and select a semidwarf from the BCnF2 if a pollen parent with ∼70% pollen fertility is chosen from the BCnF1 to backcross with the recurrent parent. Semidwarfing genes d60 and sd1 were successfully pyramided into the ‘Koshihikari’ genome by crossing isogenic lines ‘Koshihikari d60’ and ‘Koshihikari sd1’, to produce ‘Minihikari’, a new parental source of both d60 and sd1. ‘Minihikari’ displayed super-short stature due to the combination of sd1 and d60, which are genetically and functionally independent.

Two sets of reciprocal introgression lines (ILs) and a population of recombinant inbred lines (RILs) derived from the cross between japonica cultivar Xiushui09 and indica breeding line IR2061-520-6-9 (abbreviated as IR2061) were used to identify QTL for heading date (HD). Phenotyping was conducted in Hainan Island for two winter seasons (2007 and 2009). Nine QTLs were detected in the ILs with Xiushui09 background (XS-ILs), and four of which were repeatedly mapped across 2 years. Five QTLs were identified in the ILs with IR2061 background (IR-ILs), and three of which were commonly detected in 2 years. All commonly detected QTL had the same direction of gene effect. Seven QTL for HD were identified in the RILs in 2009. Only three (25%) QTLs were commonly detected using all the three populations (XS-ILs, IR-ILs and RILs). The number of commonly identified QTLs among populations was related to degree of similarity of their genetic backgrounds, suggesting that the genetic background effect is important for detecting HD QTL. QHd7 and QHd10b stably expressed in different populations and across years thus would be exploited in rice breeding programme. Moreover, lines with both of QHd7 and QHd10b resulted in at least 3 days earlier than lines with only one of them QTL, showing evident pyramiding effect.

A major challenge in complex trait genetics is to unravel how multiple loci and environmental factors together cause phenotypic diversity. Both first (F1) and second (F2) generation hybrids often display phenotypes that deviate from what is expected under intermediate inheritance. We have here studied two chicken F2 populations generated by crossing divergent chicken lines to assess how epistatic loci, identified in earlier quantitative trait locus (QTL) studies, contribute to hybrid deviations from the mid-parent phenotype. Empirical evidence suggests that the average phenotypes of the intercross birds tend to be lower than the midpoint between the parental means in both crosses. Our results confirm that epistatic interactions, despite a relatively small contribution to the phenotypic variance, play an important role in the deviation of hybrid phenotypes from the mid-parent values (i.e. multi-locus hybrid genotypes lead to lower rather than higher body weights). To a lesser extent, dominance also appears to contribute to the mid-parent deviation, at least in one of the crosses. This observation coincides with the hypothesis that hybridization tends to break up co-adapted gene complexes, i.e. generate Bateson–Dobzhansky–Muller incompatibilities.

In previous analyses, the variation in actual, or realized, relationship has been derived as a function of map length of chromosomes and type of relationship, the variation being greater the shorter the total chromosome length and the coefficient of variation being greater the more distant the relationship. Here, the results are extended to allow for the relatives’ ancestor being inbred. Inbreeding of a parent reduces variation in actual relationship among its offspring, by an amount that depends on the inbreeding level and the type of mating that led to that level. For descendants of full-sibs, the variation is reduced in later generations, but for descendants of half-sibs, it is increased.

FST, a measurement of the genetic differentiation among subpopulations, is a fundamental parameter in population genetics, with many valuable applications in molecular biology, evolutionary biology, conservation and forensics. One of its close relatives, GST, has been widely used to measure differentiation from highly polymorphic markers such as microsatellites. However, because of the high mutation rate of such markers, GST may underestimate the genomic differentiation due to demographic causes such as migration rate and subpopulation size. A new statistic proposed recently, Jost's D, was claimed to have better properties than GST and was advocated to replace GST as a measure of differentiation. This paper shows that D is not a proper measure of differentiation because it fails to meet some fundamental requirements as a differentiation statistic, and is hardly estimable without bias in practice. D is highly dependent on the gene diversity of a marker and on the unknown parameter of the number of subpopulations, is highly sensitive to how alleles and loci are defined and how data are analysed, does not increase monotonically with either divergence time or drift, and does not always have a maximal value of 1. The maximal D value can be zero or close to zero, depending on the number of alleles at a locus relative to the number of subpopulations. I suggest continuing the use of GST, with caution in its interpretation when highly polymorphic markers are used, before a better estimator of FST that explicitly accounts for mutations is developed.