Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance inGlycine soja, the Wild Progenitor of Cultivated Soybeans

Abstract

Natural populations across a species range demonstrate population structure owing to neutral processes such as localized origins of mutations and migration limitations. Selection also acts on a subset of loci, contributing to local adaptation. An understanding of the genetic basis of adaptation to local environmental conditions is a fundamental goal in basic biological research. When applied to crop wild relatives, this same research provides the opportunity to identify adaptive genetic variation that may be used to breed for crops better adapted to novel or changing environments. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses. The identification of potentially adaptive variants in this ex situ collection may permit a more targeted use of germplasm collections.

Detecting the genetic basis of local adaptation in loblolly pine (Pinus taeda L.) using whole exome‐wide genotyping and an integrative landscape genomics analysis approach

“…We applied the multivariate approach RDA to examine the relationship between climate/geographic variables and genetic variation of the outlier SNPs. alleles detected by environmental association and SNPs outliers detected by the outlier methods is consistent with previous studies on loblolly pines and other species (Anderson, Kono, Stupar, Kantar, & Morrell, 2016;Eckert et al, 2013). However, the joint effect of climate and geography due to collinearity comprised 47% of the SNP outliers' variance, and the strong pattern of collinearity may skew the results (Rellstab et al, 2015).…”

Relationships between soil and leaf mineral composition are element‐specific, environment‐dependent and geographically structured in the emerging model Arabidopsis halleri

“…A comparative evaluation of the edaphic range of A. halleri will only become possible once similar datasets are available for other plant species (van der Ent et al ., ). Soil composition is thought to be patchy (Kruckeberg, ; Baxter & Dilkes, ; Condit et al ., ), and our results stress this empirically, thus supporting the exemplary sampling design employed here, rather than the use of existing data available only at coarse resolution (Anderson et al ., ; Pease et al ., ).…”

Past and Future Use of Wild Relatives in Crop Breeding

“…Landscape genomics and environmental association analysis are also ways to detect putatively valuable alleles in CWR (Anderson et al, 2016). Genomics may thus be able to support the collecting and conservation of CWR, as well as their use.…”

“…4). Linking collection location information with genomic data to map allelic variation and predict the usefulness of specific wild populations, or even alleles, is a novel approach (Thormann et al, 2014;Anderson et al, 2016;Russell et al, 2016). Much critical information is lacking for a lot of this material.…”