The home field advantage of modern plant breeding.

Since the mid-20th century, crop breeding has driven unprecedented yield gains. Breeders generally select for broadly- and reliably-performing varieties that display little genotype-by-environment interaction (GxE). In contrast, ecological theory predicts that across environments that vary spatially or temporally, the most productive population will be a mixture of narrowly adapted specialists. We quantified patterns of broad and narrow adaptation in modern, commercial maize (Zea mays L.) hybrids planted across 216 site-years, from 1999-2018, for the University of Illinois yield trials. We found that location was the dominant source of yield variation (44.5%), and yearly weather was the smallest (1.7%), which suggested a benefit for reliable performance in narrow biophysical environments. Varieties displayed a large "home field advantage" when growing in the location of best performance relative to other varieties. Home field advantage accounted for 19% of GxE and provided a yield increase of 1.01 ± 0.04 Mg ∙ ha-1 (7.6% relative to mean yield), yet was both smaller than predicted by a null model and unchanged across time. This counterfactual suggests that commercial breeding programs have missed an opportunity to further increase yields by leveraging local adaptation. Public breeding programs may pursue this opportunity by releasing specialist varieties that perform reliably in narrow environments. As seed sources are increasingly privatized and consolidated, this alternate strategy may compliment private breeding to support global food security.

A roadmap for functional structural variants in the soybean genome.

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits.

Comparative analyses identify the contributions of exotic donors to disease resistance in a barley experimental population.

Introgression of novel genetic variation into breeding populations is frequently required to facilitate response to new abiotic or biotic pressure. This is particularly true for the introduction of host pathogen resistance in plant breeding. However, the number and genomic location of loci contributed by donor parents are often unknown, complicating efforts to recover desired agronomic phenotypes. We examined allele frequency differentiation in an experimental barley breeding population subject to introgression and subsequent selection for Fusarium head blight resistance. Allele frequency differentiation between the experimental population and the base population identified three primary genomic regions putatively subject to selection for resistance. All three genomic regions have been previously identified by quantitative trait locus (QTL) and association mapping. Based on the degree of identity-by-state relative to donor parents, putative donors of resistance alleles were also identified. The successful application of comparative population genetic approaches in this barley breeding experiment suggests that the approach could be applied to other breeding populations that have undergone defined breeding and selection histories, with the potential to provide valuable information for genetic improvement.