Genomic variation within the maize stiff-stalk heterotic germplasm pool.

Nolan Bornowski,Kerrie Barry,C Robin Buell,Shujun Ou,Kathryn J Michel,Hope Hundley,Yuko Yoshinaga,Chris Plott,Jeremy Schmutz,Shawn M Kaeppler,Jayson Talag,Arun S Seetharam,Megan Kennedy,Chris Daum,Shengqiang Shu,Candice N Hirsch,Matthew B Hufford,Jerry Jenkins,John Hamilton ,Vasanth Singan ,Natalia De León

doi:10.1002/tpg2.20114

Abstract

The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13-2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.

Highlights

Maize (Zea mays L.) production is vital to American agriculture and the global food supply, and significant heterosis, or the superior performance of a hybrid progeny over its inbred parents, exists in maize
A high proportion of Whole-genome shotgun (WGS) reads aligned to their cognate assembly; >99.8% of WGS reads aligned to the non-B73 stiff-stalk genome assemblies, and 96.1% of B73 WGS reads aligned to the B73 v4 genome assembly (Supplemental Table S2)
The stiff-stalk population has been an important source of seed parent germplasm for maize breeders in the public and private sectors since the mid 20th century

Summary

Introduction

Maize (Zea mays L.) production is vital to American agriculture and the global food supply, and significant heterosis, or the superior performance of a hybrid progeny over its inbred parents, exists in maize. Using simple sequence repeat markers and multidimensional scaling, the author demonstrated that inbreds used in the “pre-heterotic” era do not cluster in a discernible pattern, while advanced inbreds classified as either stiff-stalk or non-stiff-stalk form two distinct groups (Duvick, 2005). This allelic diversity led to the great success of the heterotic pattern breeding method as alleles are fixed for contrasting allelic states between heterotic pools, contributing to additiveby-additive epistasis and repulsion phase linkages that create pseudo-overdominance (Graham et al, 1997; Larièpe et al, 2012)

Methods

Results

Conclusion