DOI: 10.5061/dryad.tb2rbp04c
title: Data for: Evaluation of pollination traits important for hybrid wheat development in Great Plains germplasm

description: Hybrid wheat (Triticum aestivum L.) offers potential yield advantages over
 conventional inbred cultivars. For hybrid wheat to be a commercial
 success, the cost to produce the hybrid seed needs to be minimized.
 Although wheat is naturally self-pollinated, hybrid wheat seed production
 can be improved by increasing the amount and availability of pollen for
 cross-pollination. This research examined 19 pollination traits using the
 Hard Winter Wheat Association Mapping Panel for three years. Anther
 extrusion, pollen 50 date (date at which a genotype has 50% of spikes
 pollinating), plant height, and pollination duration (last spike pollen 50
 date minus first spike pollen 50 date) were identified as the most
 important traits for hybrid seed production. Anther extrusion, plant
 height, and pollen 50 date varied widely among genotypes, while
 pollination duration had significant genotypic differences in one year of
 testing. These traits also had significant genotype x year interactions,
 but better and poorer performers were consistent among years. Anther
 extrusion was weakly, negatively correlated with plant height, and high
 anther extrusion semi-dwarf genotypes were identified. Pollination
 duration was reduced in a high temperature (&gt;30ºC) environment, and
 genotypic differences in pollination duration were identified only in a
 milder temperature (24ºC) environment. Hierarchical clustering suggested
 that excellent pollinator genotypes with high anther extrusion and longer
 pollination duration tended to pollinate early and were of short to
 moderate stature. Pollination traits were higher when temperatures were
 mild, which benefited early genotypes because they pollinated before
 higher temperatures limited their pollination duration.
description: The Hard Winter Wheat Association Mapping Panel (HWWAMP) consists
 of 299 historic, experimental (pre-2010), and released genotypes from both
 public and private institutions is a valuable genetic resource for
 studying marker trait associations in Great Plains genetic backgrounds
 (Guttieri et al., 2017).  The HWWAMP was grown at the University of
 Nebraska Lincoln Agronomy Farm (40º51’23.3”N, 96º36’23.8”W) in 2016, 2018,
 and 2019.  Genotypes were planted in 1m long plots with 30 cm row spacing:
 as single rows in 2016 (harvest year with the planting being in the
 previous fall) and in two-row plots in 2018 and 2019 using a Wintersteiger
 Rowseed Planter (Salt Lake City, U.S.A.).  Planting population was 2.5
 million seeds per hectare, based on the recommended seeding rates for the
 area.  Each trial was intensively managed so as to remove the effect of
 disease and was treated with
 [2-[[[1-(4-chloropheny)-1H-pyrazol-3-yl]oxy]methyl]phenyl]methoxy-, methyl
 ester), metconazole,
 5-[(4-chlorophenyl)methyl]-2,2-dimethyl-1-(1H-1,2,4-triazol-1-ylmethyl)
 cyclopentanol Metconazole plus pyraclostrobin (TwinLine®, BASF Crop
 Protection, Research Triangle Park, NC) at Zadok’s 45 and
 5-[(4-chlorophenyl)methyl]-2,2-dimethyl-1-(1H-1,2,4-triazol-1-ylmethyl)
 cyclopentanol Metconazole (Caramba®, BASF Crop Protection, Research
 Triangle Park, NC) at Zadok’s 50 to control fungal diseases.  Fungal
 diseases were controlled as commercial hybrid seed production would be
 optimized to have the highest grain yields possible.  A modified augmented
 experimental design was used with an incomplete block size of 24 genotypes
 and three repeated check genotypes (‘Camelot’, Baenziger et al., 2009;
 ‘TAM 107’, Porter et al., 1987; and ‘NE06545’, Baenziger et al., 2014),
 per incomplete block. Two full replicates were planted in 2016 and 2018
 and one full replicate was planted in 2019.
 <strong>Description of Traits
 Measured</strong> In total, 19 traits (anther
 extrusion, first spike heading date, heading date, last spike heading
 date, first spike pollen 50 date, pollen 50 date (syn. anthesis date, when
 50% of the spike in a plot were pollinating), growing degree days
 accumulated, day length at pollen 50 date, photothermal accumulated units,
 last spike pollen 50 date, spike emergence duration, first spike heading
 date to heading date, heading date to last spike heading date, pollination
 duration, first spike pollen 50 date to pollen 50 date, pollen 50 date to
 last spike pollen 50 date, heading date to pollen 50 date, and total
 flowering period) were measured or calculated (Supplemental Table 1,
 Supplemental Figure 1). These traits are a comprehensive set with the idea
 that we wanted to measure many traits and then, based upon our results,
 determine which traits had no genetic variation or were correlated such
 that collecting data on one trait effectively meant we did not need to
 collect data on the correlated trait. Our goal was to develop reduced list
 of important traits for hybrid wheat male parent selection. We did not
 want to assume a trait was important or unimportant until we had results
 to support this conclusion. Anther extrusion (visually scored where 1 was
 no anthers extruded and 9 was where all the anthers are extruded was
 measured shortly after the pollen 50 date when the majority of plants
 would have extruded anthers), plant height, pollen 50 date, growing degree
 days accumulated (GDD), day length, and photothermal accumulated units
 were measured in all three years.  The remaining traits were measured or
 calculated in 2018 and 2019 (Supplemental Table 1, Supplemental Figure 1).
 First spike heading (syn. head emergence) date and last spike heading date
 were recorded when the spike emerged from the boot, and the spikes were
 marked with scientific tape. Those marked spikes were then used to
 estimate when primary and later tillers pollinated to determine first
 spike pollen 50 date and last spike pollen 50 date. However, we observed
 that the specific spikes to emerge first/last were not always the
 first/last to pollinate. Growing degree days accumulated were calculated
 with temperatures retrieved from nearby weather stations on a given
 genotype’s pollen 50 date, with a start date of January 1, and Tbase
 (growing degree day base temperature)  of 0ºC (McMaster and Wilhelm,
 1997). Day lengths were retrieved from https://timeanddate.com (verified Dec. 8, 2021).  Photothermal accumulation was calculated by multiplying the GDD accumulated by day length when the genotype reached pollen 50 (Li et al., 2018). <em>Statistical Analysis</em> ASREML 4 for R was used to calculate mean-adjusted Best Linear Unbiased Predictions (BLUPs) for each trait (Butler et al., 2018). All traits were run through a model selection pipeline in R to evaluate and correct for spatial variability (Supplemental Materials 1) using standard mixed linear models and mixed linear models with various variance-covariance structures (Belamkar et al., 2018). The best model was then selected based on Akaike information criterion (AIC), Bayesian information criterion (BIC), and visual diagnostics of residual plots for each trait/year combination, and a best overall model was also selected for trait x year (e.g. environment) testing (Belamkar et al., 2018). Trait x year testing was conducted using a cross-classified model as fitting an unstructured or factor analytic model yielded similar results (Isik et al., 2017; Supplemental Materials 2). The selected models were then used to generate mean adjusted BLUPs for each individual trait x year combination and an overall mean adjusted BLUP for each trait. Likelihood ratio tests were used to determine both genotype x year (within cross-classified model) and genotype significance (within the best overall model) by removing either the genotype x year term or the genotype term and testing if the models differed significantly using the lr function from asremlPlus R package (Brien, 2019). Repeatability (individual year) or broad sense heritability (multiple years) was estimated with the two equations given in the associated article. <strong>Multivariate Analysis</strong> Multivariate analyses were conducted using the mean-adjusted BLUPs in R 3.5.2 calculated above (Belamkar et al., 2015; RStudio Team, 2019). A description of R functions and packages used for multivariate analyses can be found in Supplemental Materials 3. Spearman rank correlations using the original BLUPs were calculated to examine trait x year interactions to determine if phenotypic ranks changed. The phenotypic diversity of the HWWAMP along with the presence of sub-groups based on phenotype were investigated through hierarchical cluster analysis and principal component analysis (PCA). Both analyses were conducted using data standardized to mean = 0, standard deviation = 1.  The Euclidean distance matrix was generated using the standardized dataset with the intercluster distance estimated using Ward’s linkage method with the grouping cutoff set at 100 (Ward, 1963).  Genetic correlations were calculated using BLUPs for each genotype and trait on standardized data (mean=0, standard deviation =1) after accounting for effects of year and experimental design using SAS v9.4 (SAS Institute, Cary, NC, Supplemental Materials 4). The phenotypic diversity of the HWWAMP along with the presence of sub-groups based on phenotype were investigated through hierarchical cluster analysis (Ward’s method) and principal component analysis (PCA). Both analyses were conducted using BLUPs from standardized data (mean = 0, standard deviation = 1) for the 11 traits with statistically significant genetic variance. A two-dimensional PCA plot comparing Principal Component (PC) 1 vs PC2 was used to investigate phenotypic diversity and the traits that contribute to the phenotypic diversity while also validating the findings from the hierarchical clustering
description: ASREML, SAS, JMP