Association Analysis Between Drought Tolerance Candidate Gene Dhn2 And Related Phenotypic Traits In Maize

Association analysis is an important way which can indentify favorable alleles associating with drought tolerance in corn germplasm resources, providing technical support to benefit germplasm enhancement and genetic improvement to reduce the negative effect of drought on corn production. A maize association mapping population which is consisted of 95 maize inbred lines was used for evaluating sequence diversity and linkage disequilibrium (LD) of dhn2, a candidate gene of drought tolerance in the study. Phenotypes related to drought tolerance were also characterized. Moreover, based on the consideration of influence of population structure, association analysis of dhn2 polymorphism and drought tolerance phenotypes was conducted, hoping to identify functional alleles of dhn2 gene. Main results are as follows.1. Sequence polymorphism of dhn2 was evaluated using 75 inbred lines of the association panel. Totally 37 polymorphic sites were identified in the coding region of 75 sequences obtained, including 20 SNPs (one per 48 bp) and 15 Indels (one per 64 bp). Among these polymorphic sites, two sites were in the first intron region, only accounting for 5.4%. Higher nucleotide diversity was observed in the exon regions, and reduced rapidly in other regions. Linkage disequilibrium decayed rapidly within 500 bp in the dhn2 region, and there existed linkage disequilibrium among multi-polymorphic sites.2. Correlation analysis showed that a number of traits including kernel length, ear length, ear diameter, ear dry-weight, kernel number per row and 100-kernel weight could influence yield, especially ear dry-weight (Pearson correlation coefficients is 0.96861, P<0.0001). And 100-kernel weight showed significant correlation with ear diameter and ear dry-weight. Therefore, the choice of inbred lines with longer ear and kernel, thicker ear, more kernel number per row, higher ear dry-weight and higher 100-kernel weight are optimal to gain a higher yield.3. Seven significant associations between polymorphism and phenotypic traits were identified by association analysis. All three SNP were C/G mutation. Under drought conditions, one SNP mutation from C to G associated with the increase of chlorophyll content. The other two alleles associated with the increase of ear length, ear length, ear diameter, ear dry-weight or kernel yield. Meanwhile, two InDel alleles including 3-bp insertion associated with the increase of tassel length, and one InDel with 1-bp insertion associated with the increase of ear diameter, and one InDel with 9-bp deletion associated with the increase of kernel length.