Association Mapping Across a Multitude of Traits Collected in Diverse Environments Identifies Pleiotropic Loci in Maize

Abstract

Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data -- 18M markers -- from two partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least seven US states and scored for 162 distinct trait datasets enabled the identification of of 2,154 suggestive marker-trait associations and 697 confident associations in the maize genome using a resampling-based genome-wide association strategy. The precision of individual marker-trait associations was estimated to be three genes based a reference set of genes with known phenotypes. Examples were observed of both genetic loci associated with variation in diverse traits (e.g. above-ground and below-ground traits), as well as individual loci associated with the same or similar traits across diverse environments. Many significant signals are located near genes whose functions were previously entirely unknown or estimated purely via functional data on homologs. This study demonstrates the potential of mining community association panel data using new higher density genetic marker sets combined with resampling-based genome-wide association tests to develop testable hypotheses about gene functions, identify potential pleiotropic effects of natural genetic variants, and study genotype by environment interaction.

Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel

“…(B). Comparison of the distribution of repeatability values – defined here as the proportion of variance attributed to differences between replicates of the same genotype in a single environment – for the reflectance of 2,151 individual one nanometer wide wavelengths and for a set of 30 hand measured traits scored from maize plants in the same field experiment Mural et al . (2022).…”

“…Rows were 7.5 feet long, with 30 - inch row spacing and 2.5 feet alley ways between sequential plots. Published plant-level phenotypes for the same experiment were taken from Mural et al . (2022).…”

Elucidating the patterns of pleiotropy and its biological relevance in maize

“…Zm00001d040920 is a tRNA methyltransferase pleiotropic within NAM field and GAP expression data. Lastly, we searched for overlap in our top twenty highly pleiotropic genes within a prior large-scale maize pleiotropy study [17]. We found one shared sphingomyelin synthetase family protein ( Zm00001d034600 ), in GAP field traits that impacted two tassel traits, and a G2-like1 gene ( Zm00001d044785 ) in GAP mass features that impacted six root traits (Mural et al 2022) .…”

“…However, few maize genes have shown true biological or mediated pleiotropy. Some pleiotropy is present between phenotypes of the same trait type, like the architecture of tassels, ears, leaves, or flowering time; however, very few single nucleotide polymorphisms (SNPs) are shared between different trait types [16,17]. Some evidence of pleiotropy between root, leaf, and flowering traits has been shown but requires additional testing and validation [17].…”

“…Some pleiotropy is present between phenotypes of the same trait type, like the architecture of tassels, ears, leaves, or flowering time; however, very few single nucleotide polymorphisms (SNPs) are shared between different trait types [16,17]. Some evidence of pleiotropy between root, leaf, and flowering traits has been shown but requires additional testing and validation [17]. A similar maize study showed evidence of pleiotropy but within inflorescence traits, such as kernel row number with thousand kernel weight and tassel standing, tassel length, and tassel spike length [18].…”