Segregation patterns of simple, hemi-, and homoeo-SNPs assayed using KASPar chemistry across tetraploid cotton species [G. hirsutum (AD1) and G. barbadense (AD2)] and their diploid progenitors [G. arboreum, G. herbaceum (A subgenome), and G. raimondii (D-subgenome)]. (a) Simple, or true SNP detects allelic variation between homologous loci of A subgenome of G. hirsutum (AD1) and G. barbadense (AD2). (b) Hemi-SNPs detect allelic variation in homozygous state in G. barbadense (AD2) and heterozygous state in G. hirsutum (AD1). (c) Homoeo-SNP detects homoelogous and/or paralogous loci both in A and D subgenomes, which are monomorphic between G. barbadense (AD2) and G. hirsutum (AD1). Allele calls depicted in blue, red, green, pink, and black represent alleles A, B, and AB, no amplification or missing locus, and no template control (NTC), respectively.
