PHACEclimate_database_final_forSD

Annual site-specific climate data for years 2007-2011, Cheyenne WY

PHACEphenology_summary_final_forSD

Mean timing of life cycle events (in DOY) for all species in all treatments in all years. Treatment designation are as follows: ct are the ambient CO2, ambient temperature treatments (i.e. control); cT are the ambient CO2, warmed treatments; Ct are the CO2 enriched, ambient temperature treatments; and CT are the CO2 enriched, warmed treatments. Marked (*) cells designate those species that initiated leaf emergence and flower production earliest, and seed maturation and senescence latest in the season within a treatment within a year. Standard errors (SE) are included in parenthesis where applicable. Where SE is blank, there was no variation in induction dates for that particular species or the sample size was not more than one individual per treatment per year. Number of plots (n) where species did occur per treatment is also included (maximum possible n is 5)

PHACEswc_database_final_forSD

Volumetric soil water content data from primary rooting depth (5-25cm) in a mixed-grass prairie exposed to CO2 enrichment and warming, years 2007-2011, Cheyenne WY

Allelic Variation in Developmental Genes and Effects on Winter Wheat Heading Date in the U.S. Great Plains

<div><p>Heading date in wheat (<i>Triticum aestivum</i> L.) and other small grain cereals is affected by the vernalization and photoperiod pathways. The reduced-height loci also have an effect on growth and development. Heading date, which occurs just prior to anthesis, was evaluated in a population of 299 hard winter wheat entries representative of the U.S. Great Plains region, grown in nine environments during 2011–2012 and 2012–2013. The germplasm was evaluated for candidate genes at vernalization (<i>Vrn-A1</i>, <i>Vrn-B1</i>, and <i>Vrn-D1</i>), photoperiod (<i>Ppd-A1</i>, <i>Ppd-B1</i> and <i>Ppd-D1</i>), and reduced-height (<i>Rht-B1</i> and <i>Rht-D1</i>) loci using polymerase chain reaction (PCR) and Kompetitive Allele Specific PCR (KASP) assays. Our objectives were to determine allelic variants known to affect flowering time, assess the effect of allelic variants on heading date, and investigate changes in the geographic and temporal distribution of alleles and haplotypes. Our analyses enhanced understanding of the roles developmental genes have on the timing of heading date in wheat under varying environmental conditions, which could be used by breeding programs to improve breeding strategies under current and future climate scenarios. The significant main effects and two-way interactions between the candidate genes explained an average of 44% of variability in heading date at each environment. Among the loci we evaluated, most of the variation in heading date was explained by <i>Ppd-D1</i>, <i>Ppd-B1</i>, and their interaction. The prevalence of the photoperiod sensitive alleles <i>Ppd-A1b</i>, <i>Ppd-B1b</i>, and <i>Ppd-D1b</i> has gradually decreased in U.S. Great Plains germplasm over the past century. There is also geographic variation for photoperiod sensitive and reduced-height alleles, with germplasm from breeding programs in the northern Great Plains having greater incidences of the photoperiod sensitive alleles and lower incidence of the semi-dwarf alleles than germplasm from breeding programs in the central or southern plains.</p></div

Box plot of number of days from 1 January to heading of 299 hard winter wheat entries varying for photoperiod insensitive (<i>Ppd-B1a</i>, <i>Ppd-D1a</i>) and sensitive alleles (<i>Ppd-B1b</i>, <i>Ppd-D1b</i>), evaluated in four Colorado environments.

<p>The box describes the minimum, lower quartile (25th percentile), median (50th percentile), upper quartile (75th percentile) values. The notch displays the 95% confidence interval around the median value, and if the notches don’t overlap between two boxes on the same plot, there is strong evidence their median values differ. The interquartile range is described as the upper quartile minus the lower quartile. The whiskers extend to the most extreme data point that is up to 1.5 times the interquartile range from the median value. Outlying points that fall outside of this range are represented as dots. The environments are (A) partial irrigation at Greeley, CO in 2012 (Gr12P), (B) full irrigation at Greeley, CO in 2012 (Gr12F), and (C) Fort Collins, CO in 2013 (Fo13).</p

Allelic effects (number of days) of gene-based terms included in the best-fit model for winter wheat heading date in each of nine environments, and the proportion of variability (<i>R</i>^<i>2</i>) in heading date explained by all terms in each model.

<p>The environments are described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152852#pone.0152852.t001" target="_blank">Table 1</a>. The model terms were fit separately for each environment. The intercept (Int) describes the number of days from 1 January to heading in each environment before the allelic effects are applied. The allelic effect (number of days) at each locus is added to the Int value.</p

Description of environments where field trials were grown.

<p>Environment abbreviation, location, moisture treatment, latitude and longitude, and planting and harvest dates.</p

ANOVA table for two-gene model estimating the effects of <i>Rht-B1</i> and <i>Rht-D1</i> on heading date in a combined analysis across nine environments.

<p>A total of 285 entries with homozygous calls at both loci were included in the analysis.</p

Number of entries (n) derived during four different time periods, and the proportion of entries in each group with the photoperiod sensitive allele at <i>Ppd-A1</i>, <i>Ppd-B1</i>, or <i>Ppd-D1</i>.

<p>All 285 entries had complete genotypic data at all three loci.</p

Frequency of photoperiod and reduced-height alleles in wheat entries from three regions of the U.S. Great Plains.

<p>Map shapefiles are open source and freely available from Natural Earth < <a href="http://www.naturalearthdata.com/" target="_blank">http://www.naturalearthdata.com</a>>. (A) Geographic distribution of 263 winter wheat entries that originated from the northern (Montana, North Dakota, South Dakota, n = 39 entries), central (Nebraska, Colorado, Kansas, n = 119), or southern (Oklahoma, Texas, n = 105) U.S. Great Plains. (B) Proportion of wheat entries from each U.S. Great Plains sub-region, or combined across all three sub-regions, with the photoperiod insensitive alleles <i>Ppd-A1a</i>, <i>Ppd-B1a</i>, and <i>Ppd-D1a</i>, and semi-dwarf alleles <i>Rht-B1b</i>, <i>Rht-D1b</i>.</p