Genetic variation and population structure in China summer maize germplasm

Area of Science:

• Plant genetics and breeding
• Genomics and bioinformatics
• Agricultural science

Background:

• Maize (Zea mays L.) germplasm in China Summer maize (CSM) region is diverse but lacks systematic molecular characterization.
• Understanding genetic variation and population structure is crucial for optimizing breeding strategies.

Purpose of the Study:

• To systematically characterize the genetic variation, genome diversity, linkage disequilibrium, population structure, and heterotic groups of CSM maize inbred lines.
• To develop and validate a method for assigning inbred lines to heterotic groups using genomic data.

Main Methods:

• Genotyping-By-Sequencing (GBS) to obtain 525,141 Single Nucleotide Polymorphisms (SNPs) from 490 inbred lines.
• Analysis of genetic variation, genome diversity, linkage disequilibrium (LD), and population structure using SNPs and ADMIXTURE software.
• Development and validation of a heterotic grouping procedure based on genomic data and tagSNPs.

Main Results:

• High genetic diversity (66.05% lines with near-zero kinship) was observed in the CSM germplasm.
• Inbred lines were classified into 3 supergroups, 6 groups, and 10 subgroups based on SNP data.
• Significant genome differentiation (Fst) and genetic diversity (GD) were found among subgroups.
• North American germplasm contributes significantly to 54% of the collection, with increasing prevalence.
• Two main heterotic patterns identified: M-Reid × TSPT and X subgroup × Local subgroups.

Conclusions:

• The CSM maize breeding germplasm exhibits substantial genetic diversity and complex population structure.
• A robust genomic-based method for heterotic grouping was established and validated.
• Understanding these patterns is vital for optimizing hybrid breeding and improving maize production in the CSM region.