Phylogenetic relationship and genetic differentiation of maize landraces revealed by genome-wide SNP developed by genotyping-by-sequencing in Daliangshan Mountain area,China
Maize landraces are important source of maize breeding germplasm,with diverse types and outstanding field performance for some traits,often containing excellent resistance genes that can be utilized in breeding.Due to the unique geographical location and light-thermal resources of Daliangshan Mountain area,many maize landraces with distinctive characteristics had been accumulated here in maize production.However,the lack of systematic ge-netic research on these varieties had resulted in slow progress in maize breeding and utilization in this region.In this study,the genotyping-by-sequencing(GBS)technique was used to conduct phylogenetic and genetic differentiation analyses on 360 maize landraces collected from different regions of Daliangshan Mountain area.Through high-throughput sequencing analysis,250.99 GB of effective data was generated,with a total of 1 659 033 712 clean reads from all samples,with an average read count of 4 608 427 and an average raw base of 0.70 GB and clean base of 0.67 GB.The average Q20 value of all samples was greater than or equal to 94.57%,the average Q30 value was greater than or equal to 87.14%,and the average GC content was 48.20%.After SNP calling and filtering,124 342 single nucleotide polymorphism(SNP)loci and 32 063 insertion-deletion(InDel)loci(including 15 738 insertion loci and 16 325 deletion loci)were obtained.The neighbor-joining method was used to construct a phylogenetic tree,which clearly divided the 360 maize landraces into 2 major groups,A and B,supporting the two-group theory of maize heterosis.Principal component analysis also showed that the 2 groups were distantly related and presented ge-netic differentiation.Further population structure analysis divided the 2 major groups into 9 subgroups.The F-statis-tics(Fst)value between group A and group B was 0.462 2,and the nucleotide diversity(π)of group A was higher than that of group B.In the selective sweep analysis,96 genomic regions were identified,and 418 genes were further filtrated from the top 5%of the selective regions.Gene ontology enrichment analysis showed that the candidate genes enriched in the selective regions were related to stress response,such as cold response genes,drought response genes,and pathogen response genes.The results of the study provided a reference for the conservation and genetic improvement of maize landraces in Daliangshan Mountain area.
万方数据
维普
