| Foxtail millet(Setaria italica(L.)Beauv.)is one of the most important miscellaneous crops in China,and the growth and development at seedling stage plays a vital role for its production.In this study,the relative chlorophyll content,plant height,leaf length,above ground fresh weight and dry weight of 360 germplasm accessions from the Chinese foxtail millet core germplasm resources were determined at the seedling stage.Genome-wide association analysis(GWAS)and haplotype analysis were performed by combining the re-sequencing data of the accessions and phenotypic data.The bioinformatics analysis was performed on the gene families related to the candidate genes from GWAS.The results of the study were as follows:1.Analysis of characteristics and related traits at seedling stage of foxtail millet The coefficients of variation for the five traits at the seedling stage were all relatively high,especially for the above-ground dry weight,which was over 40%.Correlation analysis revealed that the correlation coefficients between leaf length,plant height and above-ground fresh weight were high,over 0.70.The correlation coefficient of plant height and leaf length was the highest,reaching 0.93.2.The genome-wide association analysis of the traits at seedling stage in foxtail milletGenome-wide association analysis was performed on the traits related to the seedling in foxtail millet.The results showed that a total of 33 SNPs were detected from the association analysis on relative chlorophyll content,plant height and leaf length.The genome-wide association analysis on above ground fresh and dry weight showed many significant SNP sites,and only a few SNPs were analyzed in the following haplotype analysis.3.Haplotype analysis and candidate genes predictionHaplotype analysis of the genes within the 50 Kb regions upstream and downstream of the SNP loci above showed that there were 131 genes with significant differences among the haplotypes of the related seedling traits,and the functional annotations for these genes were predicted.Twelve candidate genes were determined based on the annotations and their relevance to the traits.Among them,Si3g00020,Si3g00010,Si8g00010 were related to relative chlorophyll content;Si3g00030 was related to plant height and yield;Eight genes,Si7g00010,Si7g00020,Si7g00030,Si7g00040,Si1g00010,Si5g00010,Si5g00020,Si9g00010,were related to not only plant height,but also leaf length.4.Analysis of NDPK gene family in foxtail milletAs the genes in other plants homologous to Si3g00020 are closely related to the chlorophyll content,confirming to certain extent the reliability of the GWAS results,so the NDPK gene family in foxtail millet were identified and analyzed.The results showed that there were 7 NDPK family genes in foxtail millet;phylogenetic analysis showed that the NDPK family of foxtail millet was more closely related to the that of setaria viridis;the cis-elements in the promoter sequences of NDPK gene family members in foxtail millet were mainly related to auxin,gibberellin and light responses.It was found that the expression of NDPK family members was tissue-specific through the heat map analysis.Si9g31470 was predominantly expressed in the late grain filling(S5)stage,and Si2g32240 was highly expressed in S1 and S3 stages.Si3g12070 is specifically expressed in seeds 3 days after germination,and Si3g00020 was highly expressed in seeds 30 and 60 days after maturation.In summary,this study determined the seedling related traits in foxtail millet,carried out genome-wide association analysis with these traits and related haplotype analysis.Preliminary predictions on candidate genes related to the relative chlorophyll content,plant height and leaf length at the seedling stage were made.The identification and bioinformatics analysis of the members of the NDPK gene family provided a theoretical basis for further study on the NDPK genes in foxtail millet. |
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