Candidate gene based SSR and SNP markers for gynoecy in bitter gourd (Momordica charantia L.)

Background Even though the bitter gourd hybrids are shown to have significant heterosis for many of the economic traits, processes such as manual bagging and hand pollination make the hybrid seed production labour-intensive. Use of gynoecious line as female parent makes hybrid seed production more economical. This work was performed with the objective to identify the candidate gene based molecular markers for gynoecy in bitter gourd. Methods and results Seven putative genes for flowering and sex expression, isolated from the monoecious (MC-136) and gynoecious (KAU-MCGy-101) bitter gourd accessions, were sequence characterized. MADS-box transcription factor genes AG6 and McAG2 had nucleotide polymorphisms at five sites each and were potential candidates for marker development. An In/Del polymorphism of 48 bp ([TC](24)) in AG6 gene was used to develop an SSR marker and a transition mutation of [A/G] in this gene was used to develop a set of SNP markers. These markers have developed distinct polymorphism between the monoecious and gynoecious genotypes and were found suited for the marker assisted selection. Conclusions MADS box transcription factor genes AG6 and McAG2 are identified as candidates for sex expression in bitter gourd. Based on the InDels and transition in the intronic region of AG6, SSR marker BGAG6 and an SNP marker set segregating with the sex forms were developed. The markers have been validated using four other monoecious lines and are routinely used in our bitter gourd hybrid seed production programmes.