Studies on the Relationship between DNA Sequence Variation in Waxy Gene and Kernel Quality of Inbrids and Hybrids in Maize

In order to understand the association between DNA sequence variation of waxy genes, and kernel appearance traits related to starch composition of maize hybrids grown in Taiwan, two white corns, four waxy corns, four sweet corns, four feed corns and 10 waxy inbreds with various whiteness were used as materials. In this study, extension of electrophoresis time, designation of SNP-specific primer, and TA-cloning of PCR product were used to identify the alleles of hybrid F1. The result indicates that the TA-cloning is the most efficient way to identify hybrid alleles. To determine the kernel appearance traits, total starch content, amylose content, whiteness and L, a, b value were investigated. It was found that sweet corns had the least starch content and waxy corns had the least amylase content, but the most starch and amylose content were produced in the kernel of white corns and feed corns. Results from whiteness and color scale determination showed that high amylose lines had lower whiteness, and the L, a, b values were highly correlated with the pericarp. After comparing and analyzing the DNA sequences and kernel phenotypes, 18 variation sites in exon region, and 64 variation sites in intron region were observed. The sequence variation proportion is approximately 3.5 times higher in intron than in exon, and the down-stream region of exon 12 has the highest rate of variation. Four functional sequence variations, including 30 bp deletion in exon 7, SNPs on 4380 bp(G/A), 4387 bp(G/C) and 4472 bp(G/A), which caused amino acid substitution or deletion in waxy protein, were identified. The waxy gene sequences from 6 monocot species (including maize, barley, rice, millet and sorghum), and 6 dicot species (including potato, cassava, sweet potato and pea) extracted from NCBI database were aligned and analyzed. Only three conserved segments in waxy DNA sequences were identified because of the highly difference among the surveyed sequences. However, conserved regions in monocot crops are larger than in dicot ones. These results revealed the slower evolution rate in waxy genes of monocot species. The result in this study involved in the relationship between DNA sequence variation of waxy allele and kernel starch composition have application potential for breeding corns with different utilizations.