B73-Mo17 near-isogenic lines demonstrate dispersed structural variation in maize

Area of Science:

• Plant genetics and genomics
• Maize (Zea mays ssp. mays) breeding
• Quantitative trait loci (QTL) analysis

Background:

• Recombinant inbred lines from B73 and Mo17 maize are crucial for QTL discovery and genetic mapping.
• Near-isogenic lines (NILs) with introgressed regions were developed from B73 and Mo17 backgrounds.
• A novel array-based genotyping platform was employed for high-throughput genetic analysis.

Purpose of the Study:

• To develop and characterize a comprehensive set of maize near-isogenic lines (NILs).
• To assess the utility of these NILs for quantitative trait loci (QTL) discovery and validation.
• To investigate patterns of residual heterozygosity and copy number variants in the NIL population.

Main Methods:

• Genotyping of over 7,000 loci in 150 NILs using a novel array-based platform.
• Analysis of residual heterozygosity and its distribution in relation to recombination rates.
• Identification and characterization of copy number variants (CNVs) differentiating the parental lines.

Main Results:

• The NIL population, with introgressions covering most of the maize genome, exhibited excess residual heterozygosity.
• This excess heterozygosity was particularly enriched in low-recombination centromeric regions.
• Numerous Mo17-specific duplications (copy number variants) were identified across the genome.

Conclusions:

• The developed maize NILs represent a valuable resource for high-resolution genetic mapping and QTL studies.
• The observed heterozygosity patterns provide insights into genome structure and recombination in maize.
• This population facilitates the discovery and validation of genes controlling complex traits like plant height.