Development and validation of gene‐based markers for shrunken2‐Reference allele and their utilization in marker‐assisted sweet corn (Zea mays Sachharata) breeding programme

The recessive shrunken2‐Reference (sh2‐Ref) allele is traditionally used in sweet corn cultivar development worldwide. However, non‐availability of suitable gene‐based marker(s) for sh2‐Ref has considerably delayed its utilization in molecular breeding. Here, 7,320 bp sequence of Sh2 gene among five wild‐ and six sh2‐Ref‐based inbreds was analysed by employing 13 overlapping primers. SNP583 (A in wild and G in mutant) and SNP755 (T in wild and C in mutant) in 5’UTR, and SNP5112 (C in wild and T in mutant) in intron‐12 clearly differentiated dominant (Sh2) and recessive (sh2‐Ref) allele. These SNPs were used to develop four gene‐based PCR markers. The newly developed markers were validated in six F2 populations segregating for sh2‐Ref allele, and 230 diverse inbreds of normal and sweet corn types. These markers were further used in genotyping of BC1F1 populations leading to successful selection of sh2‐Ref allele in the marker‐assisted breeding. Globally, this assumes great significance in molecular breeding of sweet corn.