| Maize is a high yield crop,and an important source of feedstuff and bioenergy raw materials.It plays a key role in promoting national economic development and ensuring food security.MADS-box is a large number of gene family,and the earliest studies on the gene function of MADS-box family genes were mainly on floral organs.In recent years,it has been found that a large number of MADS-box genes are related to fruit development and ripening,and fruit is an important food source for human survival and development,so it is of great significance to study the effect of MADS-box gene on fruit.In this study,MADS-box genes were sequenced using targeted sequence capture technology in 32 teosintes,68 landraces,and 285 maize inbred lines to analyze the sequence polymorphisms of MADS-box genes in three populations and the patterns of evolution during the domestication process.In addition,a total of 15 maize yields related traits were measured in three environments.The candidate gene association analysis method was used to mine the favorable alleles significantly associated with agronomic traits.The main results are as follows:1.Totally,ten members of the maize MADS-box gene family were successfully captured in 385 lines and analyzed their sequence variation.It was found that the nucleotide polymorphism of MADS-box genes in upstream,intron,and downstream region was high,while the code region was relatively low.During the domestication process,the nucleotide polymorphism in each region of MADS-box genes was decreased.The LD pattern analysis showed that the four genes of mads41,zmm2 7,zapl and zmm31 may be significantly selected.2.Sequence polymorphism analysis showed that among 285 maize inbred lines,the number of variations in MADS-box gene zmm31 was the most(221 SNPS and 418 InDel)and the number of variations in mads55 were the least(323 SNPS and 17 InDel).The highest frequencies of variations were found in mads55,with an average of one variation per 7.63 bp.The frequency of variation in zap1 was the lowest,with an average of one variation per 28.76 bp.3.The results of candidate gene association analysis showed that 9 MADS-box genes were significantly correlated with yield-related traits.The genetic variations of mads65,mads41 and IDP1944 were significantly correlated with the number of tassel branches,the genetic variations of zmm2 7 were significantly correlated with the number of tassel rows,and the genetic variations of mads73 were significantly correlated with the tassel length.Seven significant loci were located in mads65,among which,SNP1943 caused the synonymous mutation of proline,InDel-1127 explained 4.2%of the phenotypic variation,and there was a significant difference in tassel branch number between different alleles of InDel-1127,Ten significant loci were located in mads41,among which,the tassel branch number of different alleles of SNP-2898 had the largest difference with a contribution rate of 4.44%,and the tassel branch number of different alleles of SNP-2627 had a significant difference with a contribution rate of 4.49%.In IDP1944,17 significant loci were identified,among which,SNP1812 resulted in the synonymous mutation of threonine,and the SNP1927 resulted in the non-synonymous mutation of amino acids.A total of 15 significant loci were located in zmm27,among which,the SNP-667 was located in the promoter region,with a significant difference in the number of panicle rows between different alleles,the ear rows of different alleles of InDel8891 had the largest difference with a contribution rate of 5.25%.Six significant loci were located in mads73,among which,SNP4024 and InDel5868 had the significant differences in spike length between different alleles with contribution rate of 4.71%and 4.27%,respectively.This study will provide a better understanding about sequence variation and genetic evolution of the MADS-box genes during maize domestication.The identified favorable alleles can be used through molecular marker-assisted selection of germplasm improvement. |
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