Sequence Variation Analysis Of Height-related Gene Dwarf3 And Dwarf9 And Their Association With Grain Yield Related Traits In Maize (Zea Mays L.)

In this study, a diverse natural population with 81 maize inbred lines was selected to study the sequence variation of two height-related genes Dwarf9 and Dwarf3. Based on the target sequence capture platform technology of NimbleGen, the target sequence of gene Dwarf3 and Dwarf9 were re-sequenced and its nucleotide polymorphisms and haplotype diversity were further identified. Further, candidate gene association study was conducted using 13 yield related traits to detect the favorable allelic variations. The results are as follows:1?Sequence polymorphism analysis showed that, a total of 308 sequence variants, including 219 SNPs and 88 Indels were identified within Dwarf3 gene, and there are 39 SNPs in gene coding sequence.82 SNPs and 25 InDels were identified in Dwarf9 gene among 87 maize elite inbred lines, including 52 SNPs in gene coding sequence. LD analysis showed that some SNPs were in strong LD but some SNPs show weak LD with others, the different LD pattern suggested that these genes ?Dwarf3, Dwarf9? maybe undergone different selection during the breeding process.2?According to the results of the association analysis, eight SNPs in Dwarf3 gene were significantly associated with yield related traits in two environments. Of them, SNP₂820?T/G? was significantly associated with plant height, which explained 7.44% of phenotypic variations. It is a nonsynonymous site, which can lead to coding protein sequence changes?T/P?. Eight SNP sites in Dwarf9 gene were significantly associated with yield related traits, SNP₁569 ?A/C? was significantly associated with plant height, which explained 6.38% of phenotypic variations. SNP₁569?A/C? was a nonsynonymous site, which could result amino acid varation. One nonsynonymous site SNP₉75 is associated with the ear length and the length of bare tip, it can explain 7.85% and 6.93% phenotypic variation. These results suggested that the polymorphisms in maize Dwarf3 and Dwarf9 locus could be used in molecular marker-assisted selection to modify the plant height in maize breeding programs.