Phenotypic characterization of southeastern United States open-pollinated maize landraces
Data files
Oct 04, 2024 version files 928.43 KB
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Exp32_data.csv
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README.md
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SE_OPV_9ClusterTraitMeans.csv
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SE_OPV_data_cleaned.csv
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SE_OPV_Heritability_Pop_Means.csv
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SE_OPV_Observation_counts_per_trait.csv
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SE_OPV_Population_Cluster_Assign.csv
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SE_OPV_Population_Means.csv
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SE_OPV_PopulationMeans_ClusterAssign.csv
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SE_OPV_standardized_within_population_genetic_variances.csv
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SE_OPV_Table_2.csv
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SE_OPV_Trait_Correlations.csv
Abstract
Maize is the most important crop in the United States, but food production and niche uses such as distilling often rely on varieties that are not bred explicitly for these purposes. Farmers targeting niche food grain markets have expressed interest in historical open-pollinated varieties of maize, but few such populations are widely available, and even fewer are well-characterized. We planted field trials of a subset of 76 open-pollinated heirloom varieties available from catalogs and the USDA germplasm collection along with four F1 hybrid cultivars. We measured 24 traits across three years and three locations to characterize the selected varieties and measure their phenotypic relationships. We identified a subset of 19 traits useful for phenotypic analysis. Our results demonstrate that many historical accessions contain substantial genetic variation that should permit improvement from within-population selection. Variety name and origin are often not useful indicators of phenotypic relationships or potential crop value. Cluster analysis identifies nine morphologically distinct groups within the varieties tested, which are not fully in agreement with currently accepted landrace groupings, suggesting a need for genetic analysis of larger samples of USA open-pollinated populations to better define the natural classification of maize indigenous to the United States.
README: Characterization of Southeastern United States Open-Pollinated Maize Landraces
Maize (Zea mays L. subsp. mays) is the most important crop in the United States, but maize food and distillation products often rely on varieties that are not bred explicitly for these purposes. Farmers targeting niche food grain markets have expressed interest in historical open-pollinated varieties of maize, but few such populations are widely available, and even fewer are well-characterized. We planted field trials of 76 open-pollinated heirloom varieties available from seed catalogs and the USDA germplasm collection along with four F1 hybrid cultivars. We measured 24 traits across three years and three locations to characterize the selected varieties and measure their phenotypic relationships. We identified a subset of 19 traits with heritability > 0.5 and pairwise correlation coefficients not exceeding 0.9 for phenotypic analysis. Our results demonstrate that many historical accessions contain substantial genetic variation that should permit improvement from within-population selection. Variety name and origin are often not useful indicators of phenotypic relationships or potential crop value, although Hickory King varieties have maintained their identity even following global dispersion. Cluster analysis identifies nine morphologically distinct groups within the varieties tested, which are largely in agreement with previously proposed landrace groupings. Our results suggest a complex intermixing of Southern Dents with other maize types, rather than a clear distinction between Southern Dents and Derived Southern Dents, however. Genetic analysis of larger samples of USA open-pollinated populations will help better define the natural classification of maize indigenous to the United States.
Description of the data and file structure
Exp 32 was our local codename for this experiment, therefore it is used as a prefix in many of the file names.\
Exp32_data.csv is the primary plot-level data file. It contains 2922 records with 32 columns. Columns (and measurement units) are:
Year
Location: evaluation location, NC, MO, or SC
Rep: field complete block
Block: field incomplete block
Plot: randomized plot number
Sample: not used
Population: Name of variety or population
DTA: days from planting to 50% anthesis (days)
DTS: days from planting to 50% silking (days)
ASI: days between silking and anthesis (days)
Tillers: Number of tillers per plant (mean count)
Ears: Average number of ears per plant (mean count)
Lodging: percent of lodged plants (proportion)
Plant Height: height to uppermost node (cm)
Ear Height: height to primary ear node (cm)
Leaf Length: length of leaf above ear (cm)
Leaf Width: width of leaf above ear (cm)
Tassel Branches: number of primary branches per tassel (count)
Tassel MSL: Main stem length (MSL) was measured from lowest branch node to highest branch node (cm)
Tassel Length: distance from lowest branch node to tip of main spike (cm)
Tassel Spike: Tassel spike length was calculated as the difference between tassel length and tassel MSL (cm)
Tassel Internode: Tassel internode length was calculated as the count of branches divided by tassel MSL (cm)
Husk Color: binary score for presence of anthocyanins in husk leaves (0/1 score)
Husk Num: number of husk leaves (count)
Shank Length: length of lateral branch from main stem node to base of ear (cm)
Cob Length: length of cob from base to tip, excluding masculinized tips (cm)
Kernel Row Number: number of kernel rows per ear (count)
Ear Diam: diameter of ear, including seeds, at middle (cm)
Cob Color: color intensity score (1 - 5 score, white to dark red)
Cob Diam: diameter of shelled cob at middle (cm)
Weight100k: weight of 100 randomly selected kernels (g)
Kernel Width 1: first sample measure of kernel width (mm)
Kernel Width 2: 2nd sample measure of kernel width (mm)
Kernel Width 3: 3rd sample measure of kernel width (mm)
Kernel Width 4: 4th sample measure of kernel width (mm)
Ear Rot: percent of kernels with visible symptoms of fungal infection (proportion)
Missing values are recorded as "." or as NA
The following data summary files are generated by running the R scripts included on this initial data set:
SE_OPV_standardized_within_population_genetic_variances.csv
SE_OPV_9ClusterTraitMeans.csv
SE_OPV_data_cleaned.csv
SE_OPV_Heritability_Pop_Means.csv
SE_OPV_Observation_counts_per_trait.csv
SE_OPV_Population_Cluster_Assign.csv
SE_OPV_Population_Means.csv
SE_OPV_PopulationMeans_ClusterAssign.csv
SE_OPV_Trait_Correlations.csv
SE_OPV_Table_2.csv #Estimates of h2, ratio of within-genetic to among-population variances (Vw_g_Vp_ratio_mn), ratio of pop-by-env to among pop variances (Vpe_Vp_ratio_mn) for each trait
The following html files are knitted versions of the R markdown files, showing code, comments, and output together:
Step1_SE_OPV_raw_data_QC_cleaning_summary.html
Step2_SE_OPV_Pop_mean_heritability.html
Step3_SE_OPV_Population_variances.html
Step4_SE_OPV_cluster_and_PCA.html
Step5_Final_Tables.html
The following Word and csv files contain Supplemental Figures and Tables:
Southeastern_OPV_Maize_Supplemental_Figures.docx
Table_S1_Trait_Definitions.docx
Table_S2_SE_OPV_Trait_Correlations.csv
Table_S3_SE_OPV_PopulationMeans_ClusterAssign.csv
Table_S3_SE_OPV_standardized_within_population_genetic_variances.csv
Table_S5_SE_OPV_9ClusterTraitMeans.csv
Sharing/Access information
NA
Code/Software
The following R codes in R markdown format were used to analyze the data:
Step1_SE_OPV_raw_data_QC_cleaning_summary.Rmd
Step2_SE_OPV_Pop_mean_heritability.Rmd
Step3_SE_OPV_Population_variances.Rmd
Step4_SE_OPV_cluster_and_PCA.Rmd
Step5_Final_Tables.Rmd
Methods
In 2017, a single plot of each variety was planted at Clayton, NC. Each plot consisted of four 7.6-m rows of the same variety, seeded at a rate of 25 seeds per plot (100 seeds total per population). Seed was produced from each plot by bulking pollen within the plot each day and pollinating as many ears as possible by hand. Seed was bulked from each population and used as source seed for subsequent experiments. Check plots of T175 × T177 and T177 × T179 F1 hybrids were planted in three replicates distributed throughout the experiment field.
In 2018 and 2019 an 8×10 alpha-lattice design with three full replications was planted in each of three locations: Clayton, NC; Pendleton, SC; and Columbia, MO. Experimental units were single 7.6-m rows sown with 25 seeds of each variety. Experimental fields were irrigated as needed with overhead irrigation at Columbia and Clayton and drip irrigation at Pendleton. At Clayton, fields received nitrogen at 53.2 kg ha-1 pre-planting, and then 190.5 kg ha-1 in a split application during the growing season. At Columbia, fields received 134.5 kg ha-1 N pre-planting, then 11.2 kg ha-1 in a single application during the growing season. At Pendleton, fields received 44.8 kg ha-1 N pre-planting.
We collected data on a subset of the morphological traits previously recommended for maize racial classification by Sánchez G. et al. (1993) from each of the four rows of the seed increase plots in 2017 and from each experimental plot in 2018 and 2019 (Table S1). Days to anthesis (DTA), days to silking (DTS), anthesis-silk interval, mean numbers of ears and tillers per plant, and lodging percentage were measured on a plot-basis. DTA and DTS were the first dates on which half or more of the plants in a plot were shedding pollen or silking, respectively. Anthesis-silking interval (ASI) was calculated as the difference between DTS and DTA. Mean numbers of ears and tillers per plant were measured as the total count of ears or tillers per plot, divided by number of plants per plot. The end plants in each plot were not included in counts of ears or tillers or in the total count of plants per plot. Lodging percentage was the proportion of plants within a plot that exhibited root lodging (stalks leaning from base of the plant by more than 30° from upright) or stalk lodging (stalks broken below the primary ear or dropped primary ear).
Other traits were measured on one randomly selected individual plant per row in 2017 and on two plants per row in 2018 and 2019. Plant and ear heights were measured approximately two weeks after pollination. Plant height was measured from base to node of the leaf subtending the tassel; ear height was measured from base to the primary ear node. Ear position, the ear height relative to plant height, was calculated as (Ear height/Plant height)*100. Leaf length was measured along the midrib from ligule to tip on the leaf above the primary ear. Leaf width was measured at the widest point on the same leaf. Tassels were detached from the plant and measured in the field. The number of primary branches per tassel were counted. Tassel length was measured from lowest branch node to tip of main spike.
In year 2017, one sib-pollinated ear was selected from each row to measure ear and kernel traits. In years 2018 and 2019, two plants per plot were randomly chosen for self- or sib-pollination, and at maturity, two self-pollinated ears from each plot were collected, along with two open-pollinated ears from other plants in the plot (not including the end plants) for ear and trait measurements. Sib- or self-pollinated ears were used to measure husk and shank traits, and the range of kernel colors among all sibbed/selfed ears per population were noted (Table 1). Open-pollinated ears generally had more complete pollination and remained healthier during maturation, and thus were used to measure other ear and kernel traits in 2018 and 2019.
Husk color was recorded as a binary trait for presence or absence of anthocyanin in the outer husk leaves. Husk number was the number of husk leaves covering each ear. Shank length was measured with a Fowler Xtra-Valu caliper (54-101-300-1; Newton, MA). Ear diameter was measured by caliper at the middle of the ear with seeds attached to the cob. Kernel row number was counted at the middle of the ear. Each ear was assigned a percentage ear rot score based on the proportion of the ear exhibiting signs of rot diseases incited by Fusarium, Aspergillus, or Diplodia fungi. Ears were dried in a forced-air drier for two weeks and kernels were removed from ears to permit cob and kernel measurements. Cob length was measured with a caliper from the base of the ear to the tip after removal of staminate tips (where present). Cob color was noted on a 5-point scale from 1 (white cob, no pigment) through 5 (dark red; Figure S1). Cob diameter was measured at the middle of the cob with a caliper. Kernel width was estimated as the mean of four individual kernel values measured with calipers per ear. A sample of 100 kernels was randomly selected from each ear to measure 100-kernel weight.
Usage notes
R, Rstudio. ASReml-R used for some analyses, this is commercial software requiring a license. Echidna is a free software that could be used as an alternative to ASReml-R