A genome-wide survey of reproductive barriers in an intraspecific hybrid

Genetic study of the reproductive barriers between related species plays an essential role in understanding the process of speciation. We developed a new method for mapping all possible factors causing deviations from expecte d Mendelian segregation ratios in F-2 progeny, which substantially contribu te to reproductive isolation. A multiresponse nonlinear regression analysis of the allele frequencies of the markers covering an entire genome in the F, population was performed to estimate the map position and intensity of t he reproductive barriers on each chromosome. In F, plants from a cross betw een a Japonica variety of rice, Nipponbare, and an Indica variety, Kasalath , the deviations of allele frequencies were well explained by 33 reproducti ve barriers. Of these, 25 reproductive barriers affected the allele transmi ssion rate through the gametophyte and in 9 of these 25 cases, an Indica al lele was transmitted at a higher frequency than a Japonica allele. The othe r 18 reproductive barriers altered the viability of the zygote via its geno type. Two zygotic reproductive barriers showed overdominance and 5 showed u nderdominance. The most pronounced reproductive barrier, mapped at 62.3 +/- 0.4 cM on chromosome 3, transmitted the Indica allele by 94% through the m ale gametophyte. The accuracy of the barrier position in the regression ana lysis was confirmed by progeny analysis. The regression analysis proved to be a powerful tool for detecting and characterizing every reproductive barr ier, irrespective of whether it acted on the male or female gametophyte or the zygote.