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The Stiff Stalk heterotic pool is a foundation of US maize seed parent germplasm and has been heavily utilized by both public and private maize breeders since its inception in the 1930s. Flowering time and plant height are critical characteristics for both inbred parents and their test crossed hybrid progeny. To study these traits, a 6-parent multiparent advanced generation intercross population was developed including maize inbred lines B73, B84, PHB47 (B37 type), LH145 (B14 type), PHJ40 (novel early Stiff Stalk), and NKH8431 (B73/B14 type). A set of 779 doubled haploid lines were evaluated for flowering time and plant height in 2 field replicates in 2016 and 2017, and a subset of 689 and 561 doubled haploid lines were crossed to 2 testers, respectively, and evaluated as hybrids in 2 locations in 2018 and 2019 using an incomplete block design. Markers were derived from a practical haplotype graph built from the founder whole genome assemblies and genotype-by-sequencing and exome capture-based sequencing of the population. Genetic mapping utilizing an update to R/qtl2 revealed differing profiles of significant loci for both traits between 635 of the DH lines and 2 sets of 570 and 471 derived hybrids. Genomic prediction was used to test the feasibility of predicting hybrid phenotypes based on the per se data. Predictive abilities were highest on direct models trained using the data they would predict (0.55-0.63), and indirect models trained using per se data to predict hybrid traits had slightly lower predictive abilities (0.49-0.55). Overall, this finding is consistent with the overlapping and nonoverlapping significant quantitative trait loci found within the per se and hybrid populations and suggests that selections for phenology traits can be made effectively on doubled haploid lines before hybrid data is available.

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.

BackgroundMaize stover is an important source of crop residues and a promising sustainable energy source in the United States. Stalk is the main component of stover, representing about half of stover dry weight. Characterization of genetic determinants of stalk traits provide a foundation to optimize maize stover as a biofuel feedstock. We investigated maize natural genetic variation in genome-wide association studies (GWAS) to detect candidate genes associated with traits related to stalk biomass (stalk diameter and plant height) and stalk anatomy (rind thickness, vascular bundle density and area).ResultsUsing a panel of 942 diverse inbred lines, 899,784 RNA-Seq derived single nucleotide polymorphism (SNP) markers were identified. Stalk traits were measured on 800 members of the panel in replicated field trials across years. GWAS revealed 16 candidate genes associated with four stalk traits. Most of the detected candidate genes were involved in fundamental cellular functions, such as regulation of gene expression and cell cycle progression. Two of the regulatory genes (Zmm22 and an ortholog of Fpa) that were associated with plant height were previously shown to be involved in regulating the vegetative to floral transition. The association of Zmm22 with plant height was confirmed using a transgenic approach. Transgenic lines with increased expression of Zmm22 showed a significant decrease in plant height as well as tassel branch number, indicating a pleiotropic effect of Zmm22.ConclusionSubstantial heritable variation was observed in the association panel for stalk traits, indicating a large potential for improving useful stalk traits in breeding programs. Genome-wide association analyses detected several candidate genes associated with multiple traits, suggesting common regulatory elements underlie various stalk traits. Results of this study provide insights into the genetic control of maize stalk anatomy and biomass.

Maize (Zea mays L.) grown in the US Midwest contains only a small fraction of the genetic diversity present in the species. Maize populations from other parts of the world may contain genetic variation that could be used to improve or increase the diversity of US germplasm. This study was conducted to assess the performance and phenotypic stability of hybrids containing diverse exotic introgressions across North American environments. Doubled haploid (DH) lines were created by the Germplasm Enhancement of Maize project from backcross 1 families that used 27 open‐pollinated populations from Latin America as donor parents and PHZ51, a non‐Stiff Stalk inbred developed in Iowa, as the recurrent parent. DH lines were testcrossed with LH195, a Stiff Stalk inbred developed in Iowa, and hybrid field trials were performed at 24 environments in the United States and Canada. Experimental hybrids had variable flowering time, plant and ear height, and test weight, but none had significantly greater yield than the PHZ51 × LH195 hybrid. The slopes of linear reaction norm models were significantly lower for the experimental hybrids than the US‐adapted reference hybrids for three traits: yield, growing degree units (GDU) to anthesis, and GDU to silking. The results suggest that unfavorable alleles and phenotypic stability should be considered when exotic open‐pollinated populations are used in US maize breeding. Core Ideas: Open‐pollinated maize populations are diverse and contain haplotypes that are rare or absent in US germplasm.Hybrids with exotic introgressions had variation in flowering time, plant height, and ear height.None of the hybrids with introgressions had significantly greater yield than the recurrent parent hybrid.Exotic‐derived hybrids and US hybrids had significantly different phenotypic stability for some traits. [ABSTRACT FROM AUTHOR]

Delayed silking relative to pollen shed, measured as the anthesis–silking interval (ASI, the period between pollen shed and silking), is a good indicator of response to abiotic stresses in maize (Zea mays L.). This research was conducted to investigate how ASI is affected by nitrogen (N) and water availability and to assess the utility of ASI to indirectly predict grain yield (GY) under contrasting water and N treatments. Two experiments were conducted in Hancock, WI, in 2018 and 2019. One experiment (Diverse hybrids) included 302 hybrids resulting from the cross of diverse inbred lines by a single tester evaluated at four different treatment levels resulting from combining nonlimited and low N with nonlimited and low water treatments. The second experiment (NSS FAC) included a set of 408 hybrids derived from the cross of biparental doubled‐haploid lines from 13 factorial populations and evaluated under nonlimited and low N treatments. Anthesis and silk time in growing degree days, and GY (Mg ha−1) were measured. Genomic prediction was assessed using a genomic best linear unbiased prediction model, and predictive ability was calculated as the correlation between genomic predictions and adjusted means in the different treatments. Predictive ability ranged from.15 to.49 for NSS FAC and from.06 to.51 for Diverse hybrids across traits and treatments. The ASI was a good indicator of stress and showed higher heritability than GY in the limited treatments for both experiments; however, it did not improve yield predictability. Core Ideas: ASI is more heritable than GY under limited conditions but did not improve prediction in a combined model.The ASI is a good indicator of water and N stress.The top hybrids were tolerant to both water and N limited conditions. [ABSTRACT FROM AUTHOR]