Multilocus interactions restrict gene introgression in interspecific populations of polyploid Gossypium (cotton)

Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from interspecific hyb ridization in nature. By applying a detailed restriction fragment length po lymorphism (RFLP) map to 3662 BC3F2 plants derived from 24 different BC1 in dividuals of a cross between Gossypium hirsutum and G. barbadense, large an d widespread deficiencies of donor (G. barbadense) chromatin were found, an d seven independent chromosomal regions were entirely absent. This skewed c hromatin transmission is best accounted for by multilocus epistatic interac tions affecting chromatin transmission. The observed frequencies of two-loc us genotypes were significantly different from Mendelian expectations about 26 times more often than could be explained by chance (P less than or equa l to 0.01). For identical pairs of loci, different two-locus genotypes occu rred in excess in different BC3 families, implying the existence of higher- order interlocus interactions beyond the resolution of these data. Some G. barbadense markers occurred more frequently than expected by chance, indica ting that genomic interactions do not always favor host chromatin. A prepon derance of interspecific allelic interactions involved one locus each in th e two different subgenomes of (allotetraploid) Gossypium, thus supporting s everal other lines of evidence suggesting that intersubgenomic interactions contribute to unique features that distinguish tetraploid cotton from its diploid ancestors.