Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population

Abstract

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 1930’s. Flowering time and plant height are critical characteristics for both inbred parents and their test crossed hybrid progeny. To study these traits, a six parent multiparent advanced generation intercross (MAGIC) 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 two field replicates in 2016 and 2017, and a subset of 689 and 561 doubled haploid lines were crossed to two testers, respectively, and evaluated as hybrids in two 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 two 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 to 0.63), and indirect models trained using per se data to predict hybrid traits had slightly lower predictive abilities (0.49 to 0.55). Overall, this finding is consistent with the overlapping and non-overlapping significant QTL 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.

A practical method to improve the efficiency of pollination in maize breeding and genetics research

“…From routine utilization within our maize breeding program, we have not observed any limitations in the method due to the choice of inbred line during hybrid seed generation. As an example, in one seed production nursery in Verona, WI in 2022, we used this method to collect pollen across 30 unique inbred lines that included both expired plant variety protection inbred lines, current commercial inbred lines, and publicly developed double haploids from the WI‐SS‐MAGIC population (Michel et al., 2022). Collecting pollen across this diverse germplasm led to the generation of over 230 hybrids when mixed pollen was directly applied to plants with receptive silks or stored for 24 h prior to application.…”

“…T A B L E 6 Analysis of variance (ANOVA) describing the effect of inbred line and days of storage on average grain fill when pollen was collected from 24 different inbred lines and immediately used to pollinate LH244 or stored for 24 h prior to pollination. double haploids from the WI-SS-MAGIC population (Michel et al, 2022). Collecting pollen across this diverse germplasm led to the generation of over 230 hybrids when mixed pollen was directly applied to plants with receptive silks or stored for 24 h prior to application.…”

2020-2021 Field Seasons of Maize G x E Project within Maize Genomes to Fields Initiative

“…A set of 1184 publicly available hybrids were evaluated in the 2020 and 2021 seasons across 30 different locations. The main group of hybrids was produced by the cross of doubled-haploid (DH) inbred lines from the Wisconsin Stiff Stalk MAGIC population (WI-SS-MAGIC), crossed with three ex-PVP inbred testers, PHZ51, PHP02, and PHK76 [1]. The WI-SS-MAGIC population involves the inbreds B73, B84, NKH8431, LH145, PHB47, and PHJ40 as parents in the initial crosses, and a detailed description of the population creation and DH production is in Michel et al (2022) [1].…”

“…The main group of hybrids was produced by the cross of doubled-haploid (DH) inbred lines from the Wisconsin Stiff Stalk MAGIC population (WI-SS-MAGIC), crossed with three ex-PVP inbred testers, PHZ51, PHP02, and PHK76 [1]. The WI-SS-MAGIC population involves the inbreds B73, B84, NKH8431, LH145, PHB47, and PHJ40 as parents in the initial crosses, and a detailed description of the population creation and DH production is in Michel et al (2022) [1]. The testers were selected to allow adaptation of materials to the wide array of maturities sampled across the project.…”

Statistical models and tools for QTL mapping in multi-parent populations

“…MPPs, as an intermediate between BPPs and diversity panels, increase genetic diversity by using multiple parents and balancing population structure through experimental crossing schemes (Scott et al 2020;Arrones et al 2020). Genetic studies using MPPs have recently been applied to a wide range of crops and vegetables, such as rice (Kitony et al 2021;Zheng et al 2022;Liang et al 2022), maize (Swarts et al 2021;Odell et al 2022;Michel et al 2022), potato (Amadeu et al 2021), wheat (Rollar et al 2021a;Hu et al 2022), barley (Dang et al 2020;Hautsalo et al 2021;Grieco et al 2022), cowpea (Ravelombola et al 2021(Ravelombola et al , 2022, chickpea (Thudi et al 2014), tomato (Diouf et al 2018;Campanelli et al 2019), eggplant (Gramazio et al 2019).…”