Population Structure Of Core Inbred Lines And Allelic Diversity Of Rab17, A Candidate Gene For Drought Tolerance In Maize

Drought stress is one of the most important factors limiting maize production. Mining germplasm resources and discovering associated genes are fundamental approaches to enhancing drought tolerance in maize. There are much functional genetic variations for drought tolerance in maize germplasm. Identifying these functionally favorable alleles contributes to not only understanding molecular mechanism for drought-tolerance but also developing functional markers, and thus improving drought tolerance of maize new germplasm and hybrids by marker-assisted selection. Association analysis is a powerful approach for mining these alleles because its ability of identifying functional variations and association with phenotype.Analysis of genetics diversity and population structure were conducted by using maize inbred lines from the established core collection and some elite lines, in order to clarify population structure of these lines which is necessary for further association analysis and choose a mini core set with maximal diversity for evaluating sequence diversity and linkage disequilibrium (LD) of rab17, a candidate gene for drought tolerance. In addition, phenotypes related to drought tolerance were characterized for the set of materials. Finally, association test between rab17 polymorphisms with phenotype variation were performed in order to identify functional alleles that are responsible to phenotype variations with drought tolerance. The major results are as follows.1. Totally 288 maize inbred lines from the established core collection and some elite lines were assayed for genetic diversity at 49 Simple Sequence Repeat (SSR) loci. The results showed that total 262 alleles were identified, the average of alleles per locus was 5.3469, the average of PIC was 0.5057 and gene diversity for the SSRs was 0.5663. Analysis of population structure assessed the membership of the 288 lines in four clusters that corresponded to major germplasm sources (Tangsipingtou, Lancaster, Reid and P), respectively. Overall proportion of membership of the lines in each of the four germplasm sources was: 0.290 (Tangsipingtou), 0.267 (Lancaster), 0.260 (Reid) and 0.183 (P group). Taking allele number as major criterion, 94 lines were chosen as a mini core set from the 288 inbred lines. The mini core set captured 228 alleles, accounting for 87% of the total alleles in the 288 inbred lines.2. Sequence polymorphisms of rab17 were evaluated using lines of the mini core set. Totally 37 polymorphic sites were identified in 71 accessions, including 19 SNP (one per 87 bp) and 18 Indel (one per 92 bp). Among these polymorphic sites, 30 sites were in noncoding regions, accounting for 81%. The frequency of Indel occurring in noncoding regions were eight times higher than that occurring in coding regions. Higher nucleotide diversity were observed in the promoter region and the first exon region, and reduced rapidly in the downstream regions. Linkage disequilibrium decayed rapidly within 800 bp in the rabl7 region. There were 14 haplotypes in these accessions based on linkage disequilibrium in this region. Based on the sequence data of rabl7, analysis of phylogram tree showed that nine lines mostly deriving from P78599, an American maize hybrid, had the farthest geneticdistance from other lines.3. Six significant associations between polymorphisms and phenotypic traits were identified by structured association test. An Indel in the coding region showed significant association with abscisic acid (ABA) content in the leaves under well water and relative water content (RWC) in the leaves under water stress. At this polymorphic site, the allele contain inserts which led to frameshift mutation in the coding region had an effect on increasing relative water content under water stress. A Indel in 5'-UTR showed significant association with ASI under water stress, and the allele present in three lines (Weifeng322, Loll25 and Liao2204) led to a ASI increase of six days, compared with the other alleles. In addition, a haplotype, which consisted of eleven polymorphic sites, showed significant association with three yield related traits, and the allele present in nine lines (mostly deriving from P78599) had a positive effect on increasing the values of the three traits, implying that the allele had contribution to drought tolerance in maize and had the potential to be used in germplasm enhancement and breeding.