| As an important part of yield,the growth and development of ears and kernels can directly affect the yield of maize.Yield traits such as ears and kernels in maize are important agronomic traits,and the traits are restricted and linked to each other,regulated by multiple genes,and affected by the environment.Ear traits mainly include ear length,ear perimeter,ear rows number,and kernel number per row,and kernel traits mainly include kernel length,kernel width,kernel thickness,kernel area,and 100-kernel weight.To clarify the effect of each trait on yield and the correlation between them,and then to mine more related candidate genes,identify whether there is genetic overlap between the traits.Therefore,in this study,the Northeast core association panel with extensive natural variation was used as the research material,and genotyping and SNPs quality control were carried out.Candidate genes were searched for each 50kb attenuation distance upstream and downstream,and related candidate genes were analyzed through gene function annotation and tissue expression specificity,which provided theoretical help for molecular breeding of ear and kernel-related traits.The main results are as follows:（1）Correlation analysis of maize ear and kernel traitsThe correlations between the traits are mainly concentrated in the ear and the kernel,among which the ear traits are mainly concentrated in the kernel number per row,ear length,and ear perimeter,and there is a very significant positive correlation,which is related to the correlation between ear traits in a single environment.Basically the same,kernel traits were mainly concentrated in kernel length,kernel width,and kernel area,which showed a very significant positive correlation.Except for 100-kernel weight,the correlations were the same as those of single environment kernel traits.For the correlation between ear and kernel traits,there was a very significant positive correlation between ear length,ear perimeter,and100-kernel weight,which was consistent with the correlation in a single environment.（2）Phenotypic variation of maize ear and kernel traitsThe phenotypic variation analysis of the four traits of ear rows number,kernel number per row,ear length,and ear perimeter showed that there was extensive phenotypic variation in the four ear traits and the distribution was normal.Genetic variation analysis showed that genotype had a very significant effect on all ear traits.In addition,the broad-sense heritability analysis showed that different traits ranged from medium to high,which were the ear rows number>the kernel number per row>the ear perimeter>the ear length,and the distribution range of heritability was 0.45（ear length）～0.81（ear rows number）,in which the ear rows number in a panicle has a high heritability,while the kernel number per row,ear length and ear perimeter have medium heritability.Genetic variation analysis showed that genotypes had extremely significant effects on all kernel traits.The phenotypic variation analysis of five traits including kernel length,kernel width,kernel thickness,kernel area,and 100-kernel weight of maize showed that there were extensive phenotypic variations in all five traits,and all of them showed a normal distribution.Genetic variation analysis showed that the genotypes of all kernel traits showed extremely significant differences.In addition,the broad-sense heritability analysis showed that its distribution from high to low was 100-kernel weight>kernel width>kernel thickness>kernel length>kernel area,and its heritability distribution ranged from 0.41（kernel area）to 0.89（100-kernel weight）of which 100-kernel weight showed high heritability,while kernel width and kernel thickness showed medium heritability,and kernel length and kernel area showed low heritability.It indicated that its panicle traits had a complex genetic structure.（3）Genome-wide association analysis identified SNPs related to ear and kernel traitsAssociation analysis by the BLINK model showed that a total of 28 significant SNPs loci were detected for ear traits,which were higher than the threshold line P=1.02×10-5,and all SNPs loci were distributed on chromosomes 1,2,3,4,6,8,10,the phenotypic contribution rate（R2）explained by a single significant SNP ranged from 4.4%to 13.4%,and two significantly related SNPs were found to have an R2 value greater than 10%.In addition,a total of 35 significant SNPs loci were detected for kernel traits,which were higher than the threshold line P=1.02×10-5,and all SNPs loci were distributed on chromosomes 1,2,3,4,5,6,7,8,and 10,in which the interpretable phenotypic contribution rate（R2）ranged from 1.9%to15.3%,and three significantly associated SNPs were found with R2 values greater than 10%.These results indicated that ear and kernel traits were complex quantitatively inherited traits,controlled by major genes and minor polygenes.（4）Related candidate genes regulating ear and kernel traitsAccording to the genome information of the maize B73 V4 version,a total of 70 genes were detected within the 50kb（confidence interval）attenuation distance upstream and downstream of the marker loci of maize ear trait-related SNPs,of which 44 genes were in Arabidopsis/rice homologous genes annotated.A total of 13 candidate genes related to the growth and development pathways of maize ear traits were identified.Zm00001d011297 is involved in transcriptional regulatory pathways.Analysis of the candidate gene Zm00001d029721 identified for ear rows number indicated that it encodes a receptor protein kinase and is involved in regulating meristem size during inflorescence development.The candidate gene Zm00001d050211 identified by the number of kernel number per row regulates the content of auxin by encoding amino acid/auxin permease,thereby affecting the development of the whole ear.In addition,the candidate gene is also located at significant SNP loci co-located by 21SY kernel number per row and 21SY kernel thickness.In addition,a total of 88 genes were detected at a 50 kb decay distance before and after the marker loci of maize kernel trait-related SNPs,of which 44 genes were annotated in Arabidopsis/rice homologous genes.According to the annotation information,a total of 11 candidate genes related to the growth and development of maize kernel traits were identified.Among them,Zm00001d043694 is involved in the cell transport pathway,Zm00001d033287 is involved in RNA editing,Zm00001d034387 is involved in an oxidation-reduction reaction,Zm00001d018494,Zm00001d044691,Zm00001d016106,Zm00001d013466 participates in a transcriptional regulation pathway,Zm00001d022473,Zm00001d033286,Zm00001d033288are involved in the metabolic pathway,Zm00001d018474 is involved in regulating the secretion pathway.Analysis of the candidate gene Zm00001d033287 identified for the kernel thickness trait suggests that it may affect the size of maize kernel and thus maize yield by regulating the formation of G proteinγsubunits.The candidate gene Zm00001d022473identified by the kernel width trait participates in the synthesis of auxin by regulating amide synthase,thereby affecting the size and development of the kernel.Another candidate gene,Zm00001d033288,identified for the kernel width,can affect the size of the kernel and the development of embryo and endosperm by encoding the pentapeptide repeat PPR family protein.（5）Co-localization analysis of ear and kernel traitsIn the 20SY environment,a SNP marker locus chr1.S 182385855 was identified which was significantly correlated with the ear rows number and the ear perimeter.This locus is located at 182385855bp of chromosome 1,the minimum P-value of this marker locus is 5.20E-11,and the maximum phenotype contribution rate is 8.3%.In addition,by comparing the correlations between the ear rows number and ear perimeter under the 20SY environment,it was found that there was a very significant positive correlation between the traits.In the 21SY environment,a SNP marker locus chr4.S 73769620 was identified which was significantly correlated with the kernel number per row and the kernel thickness.This locus is located at73769620bp of chromosome 4,the minimum P-value of the marker locus is 0.00000515,and the maximum phenotype contribution rate is 13.4%.In addition,by comparing the correlation between the kernel number per row and the kernel thickness in the 21SY environment,it was found that there was a very significant negative correlation between the traits.Furthermore,both marker loci fall on the introns of the genes.These results suggest that different traits may be regulated by the same gene,which in turn affects maize yield.（5）Co-localization analysis of maize ear and kernel traitsIn the 20SY environment,an identical SNP marker locus chr1.S 182385855 was identified which was significantly associated with both ERN and EP.This locus is located at182385855bp of chromosome 1,the minimum P value of this marker is 5.20E-11,and the maximum phenotype contribution rate is 8.3%.In addition,by comparing the correlation between ERN and EP traits in 20SY environment,it was found that there was a very significant positive correlation between their traits.In the 21SY environment,an identical SNP marker locus chr4.S 73769620 was identified,which was significantly associated with both KNR and KT.This locus is located at 73769620bp of chromosome 4,the minimum P value of this marker is 0.00000515,and the maximum phenotype contribution rate is 13.4%.In addition,by comparing the correlations between KNR and KT traits in the 21SY environment,it was found that there was a very significant negative correlation between their traits.Furthermore,both of these sites fall on introns of genes.These results suggest that different traits may be regulated by the same gene,which in turn affects maize yield. |
