Identification of candidate gene-based markers (SNPs and SSRs) in the zinc and iron transporter sequences of maize (Zea mays L.)

Molecular marker systems such as SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms) derived from candidate genes are proving extremely useful in the genetic improvement of crop plants. The availability of maize genome sequence has opened up the possibility of identifying candidate genes involved in zinc and iron accumulation in grains. Scanning of maize genome sequence consisting of 153,370 contigs resulted in the identification of 48 candidate genes predicted to be involved in iron and zinc transport in maize. Thirteen genes belonging to the ZIP (zinc-regulated transporter/iron-regulated transporter proteins) family, 16 to the NRAMP (natural resistance associated macrophage protein) family, 17 to the YS (yellow stripe) family, 1 to the CE (cation efflux) family and 1 to the ferritin family were identified based on the presence of characteristic signature sequences in the respective gene families. Thirty-four SSRs of di-, tri- and tetranucleotide repeats were identified in exons, introns, 3'UTRs and 5'UTRs of 28 candidate genes for zinc and iron transporters of maize. SSRs of di- and trinucleotide repeats are more prevalent in the candidate genes identified in this study. Amplification of candidate gene SSRs on a set of 124 maize inbreds, which are part of the maize biofortification programme of Department of Biotechnology, Govt of India, resulted in varying allelic diversities. SNPs were detected in exons of candidate genes ZmZIP7, ZmZIP11 and ZmNRAMP11. The SNPs showed restriction site differences for Msp1 in the exon of ZmZIP11 and for Dpn1 in ZmNRAMP11. A total of 14 markers out of which seven were from introns of ZmZIP1, ZmZIP2, ZmZIP3, ZmNRAMP1, ZmNRAMP3, ZmNRAMP5 and ZmYS14 genes, three from 3'UTRs of ZmZIP3, ZmZIP10 and ZmYS2 genes, three from SSRs in ZmYS1, ZmFer1 and ZmYS3 genes and one SNP in the ZmNRAMP11 gene showed size polymorphism among 124 maize inbreds. Allelic frequencies varied from 0.8 to 86.3% for SSR markers, 4 to 91.94% in intron-size markers and 5.6 to 89.52% in 3'UTR size markers.