Sequence Polymorphisms Analysis Of Inflorescence Development-Related Genes TD1 And FEA2 And Their Associations With Yield-Related Traits In Mazie(Zea Mays L.)

Maize is not only one of the three largest crops but also a dominant crop for food,feed and fuel throught the world.The yield-related traits of maize are controlled by a large number of minor genes with complex genetic mechanism.At present,identification of favorable allels and introduction of these beneficial allels into breeding materials by pyramiding breeding have become important approaches for the improvement of maize yield.TD1 and FEA2 are key genes in the maize inflorescence development,and directly related to yield-related traits,yet little is know about sequence variation and favorable allels of TD1 and FEA2 locus in commonly used maize inbred lines.In this study,the genomic sequences of TD1 and FEA2 genes in 323 maize inbred lines representing broad genetic diversity were obtained and resequenced.The nucleotide polymorphisms,neutral evolution of variable sites and haplotypes were analyzed.In addition,the data of 15 yield-related traits measured in 3 environments were used to mine favorable allels significantly associated with maize yield based on candidate gene association.The major results are as follows:1.4726 bp and 4074 bp of sequence were obtained and resequenced in TD1 and FEA2 gene among 323 maize inbred lines.Sequence polymorphism analysis of TD1 and FEA2 showed that,184 SNP and 57 InDel were identified in TD1 gene and nucleotide diversity（π）was 0.0088;and 132 SNP and 20 InDel were detected within FEA2 gene and nucleotide diversity was 0.0052.In comparison with the other gene region,nucleotide diversity of promotor region was highest,while nucleotide diversity was lowest in coding region.In addotion,the SNPs in the coding region of genes TD1 and FEA2 classified these genes into 47 and 20 haplotypes,respectively,and significant difference in phenotype were found between majoy haplotypes.Furthermore,all maize germplasm were divided into 3 groups by using distance-based cluster method based on resequenced genes of TD1 and FEA2.2.Statistic analysis of yield-related traits revealed that extremely significant difference（p<0.01）were found among 15 yield traits in 323 maize inbred lines,and the broad-sense heritability of eight traits was above 50%.Tassel branch number was hightest and grain thickness was smallest in terms of the coefficient of variant.Addotionally,population structure was divided into 3 groups by using distance-based cluster and model-based cluster methods based on 187,126 high quality SNPs in maize genome.3.Results of candidate gene-based association analysis indicated that a total of 13 sequence variants were significantly associated with phenotypic variantions.One nonsynonymous SNP₅47 and two InDel（InDel₄6 and InDel₅53）resulting amino acid variations in coding region of TD1 gene were significantly associated with ear length,ear diameter,cob diameter and tassel length,respectively.Specially,InDel₅53 could explain 5.23%of ear length variation.An InDel₅73 of promotor region in TD1gene was significantly associated with ear length and kernel number per row with contribution of 4.34%and 4.01%,respectively.Moreover,one nonsynonymous SNP₁693 resulting amino acid variations（L/F）in coding region of FEA2 gene was significantly associated with ear diameter.An InDel₅73 in the promotor region of FEA2 was significantly associated with kernel row number,cob diameter and ear diameter,with contribution of 8.72%,4.90%and B.B2%,respectively.Results from this research will provide a better understanding about sequence polymorphism of genes TD1 and FEA2 in commonly used maize inbred lines,and beneficial alleles in maize TD2 and FEA2 locus could be used in molecular marker-assisted selection to aid maize breeding for enhanced yield.