The IM analysis requires sequence data from individual loci that show variation within or between two populations, under the assumption that recombination is negligible.
To understand its interaction with another identified locus and possibly additional loci, we performed crosses within and between two populations separated by 2000 km, phenotyped the progeny and sequenced candidate markers at both sex-determining loci.
Also the corrected numbers of MPD between populations were determined, i.e. the MPD between two populations minus the mean number of MPD contained within these two populations.
If hybrids are formed between two populations that are barely differentiated, they may remain undetected, since their features may fall within the range of variability of one or both of the populations.
Reciprocal crosses between three population pairs [ 59], and within-population breeding experiments with half-sib (NCII) designs in a subset of four of the present populations (K. Räsänen and A. Laurila, unpubl. data), find evidence for direct genetic effects, negligible maternal effects and moderate to high heritability (h 2 up to 0.6) in larval traits.
Sexual behavior indicators varied greatly between the two populations and between genders within each population.
In order to confirm the low nucleotide diversity of Hd6 gene within or between the two populations of O. sativa and O. rufipogon, additional analysis was performed using the above 398 bp (122-bp in exon 2, 80-bp in intron between the exon 2 and exon 3, 195-bp in exon 3) sequences from the world collections of rice varieties and wild rice accessions (Supplementary Table 1).
We then examined whether the distribution of the sums was similar at each position within and between the two populations (i.e., the distribution of the light and dark orange [BT] and the light and dark blue [USW] bar heights).
