Marker-assisted selection for low phytic acid (lpa1-1) with single nucleotide polymorphism marker and amplified fragment length polymorphisms for background selection in a maize backcross breeding programme

The level of phytic acid is difficult to assess in a maize breeding programme, therefore a co-dominant single nucleotide polymorphism (SNP) marker was used to detect the single recessive low phytic acid (lpa1-1) gene in a BC2F1 population developed from a locally adapted tropical normal inbred line (P 16) and CM 32 (lpa1-1 donor). High-resolution melt analysis of the lpa1-1 SNP marker was able to identify 11 homozygous recessive and 17 heterozygote genotypes for the lpa1-1 mutation. The SNP R ² values for the heterozygotes were higher (90.95?C99.59%) than the lpa1-1 recessives (82.81?C99.58%). The selected BC2F1 lines were fingerprinted with six amplified fragment length polymorphism (AFLP) EcoRI/MseI primer combinations to determine the amount of recurrent parent genome present. The 277 AFLP markers were clearly able to differentiate all the BC2F1 lines from each other and the parental controls with a similarity range from 62.12 to 92.15%. It is expected in the BC2 generation to find 87.5% similarity to the recurrent parent, however in this study higher levels of similarity in 13 BC2F1 lines (six heterozygotes and seven homozygous recessive) with 92.15?C83.33% similarity were observed. The use of marker-assisted selection for foreground and background selection greatly increased the efficiency of detection of the homozygous recessive (99.58%) and heterozygous (99.59%) genotypes as well as improving the recovery of the recurrent parent (92.15%) in the BC2F1 generation of the maize backcross breeding programme.