Genomic variation within the maize stiff-stalk heterotic germplasm pool

Area of Science:

• Plant Genomics
• Maize Breeding
• Crop Genetics

Background:

• The stiff-stalk heterotic group is crucial for U.S. commercial maize hybrid production, with founder inbreds like B14, B37, B73, and B84 appearing in many commercial seed parent pedigrees.
• Understanding the genetic diversity within these historically significant inbred lines is essential for ongoing crop improvement.

Purpose of the Study:

• To generate high-quality genome assemblies for five important stiff-stalk maize inbred lines: B84, LH145 (representing B14), NKH8431, PHB47 (representing B37), and PHJ40.
• To analyze the genetic variation, synteny, and transposable element content within these inbreds compared to the reference B73.
• To assess the representation of the original Iowa Stiff Stalk Synthetic breeding population within these released inbred lines.

Main Methods:

• Long-read sequencing was employed to create highly contiguous genome assemblies (2.13-2.18 Gbp) with N50 scaffold lengths exceeding 200 Mbp.
• Inbred-specific gene annotations were generated using a five-tissue gene expression atlas, and transposable element (TE) annotation utilized de novo and homology-directed approaches.
• Comparative synteny analyses were performed against the B73 reference genome to identify conserved and unique genomic regions.

Main Results:

• Highly contiguous genome assemblies were successfully generated for the five stiff-stalk inbred lines.
• Synteny analyses revealed extensive collinearity among the five genomes, alongside the detection of unique components within the maize pangenome.
• Comparison with the original breeding population indicated that the analyzed inbreds represent a subset of the original variation, featuring highly conserved haplotypes.

Conclusions:

• Despite a reduction in variation compared to the original stiff-stalk pool, substantial genetic and genomic variation exists within these key inbred lines.
• The generated genome assemblies provide valuable genomic resources for the stiff-stalk maize breeding pool.
• These findings offer insights into the maize pangenome and support the potential for continued breeding success within this important heterotic group.