Deconstructing the genetic architecture of iron deficiency chlorosis in soybean using genome-wide approaches

Abstract

Background: Iron (Fe) is an essential micronutrient for plant growth and development. Iron deficiency chlorosis (IDC), caused by calcareous soils or high soil pH, can limit iron availability, negatively affecting soybean (Glycine max) yield. This study leverages genome-wide association study (GWAS) and a genome-wide epistatic study (GWES) with previous gene expression studies to identify regions of the soybean genome important in iron deficiency tolerance. Results: A GWAS and a GWES were performed using 460 diverse soybean PI lines from 27 countries, in field and hydroponic iron stress conditions, using more than 36,000 single nucleotide polymorphism (SNP) markers. Combining this approach with available RNA-sequencing data identified significant markers, genomic regions, and novel genes associated with or responding to iron deficiency. Sixty-nine genomic regions associated with IDC tolerance were identified across 19 chromosomes via the GWAS, including the major-effect quantitative trait locus (QTL) on chromosome Gm03. Cluster analysis of significant SNPs in this region deconstructed this historically prominent QTL into four distinct linkage blocks, enabling the identification of multiple candidate genes for iron chlorosis tolerance. The complementary GWES identified SNPs in this region interacting with nine other genomic regions, providing the first evidence of epistatic interactions impacting iron deficiency tolerance. Conclusions: This study demonstrates that integrating cutting edge genome wide association (GWA), genome wide epistasis (GWE), and gene expression studies is a powerful strategy to identify novel iron tolerance QTL and candidate loci from diverse germplasm. Crops, unlike model species, have undergone selection for thousands of years, constraining and/or enhancing stress responses. Leveraging genomics-enabled approaches to study these adaptations is essential for future crop improvement.

Meta-GWAS for quantitative trait loci identification in soybean

“…A peak on chromosome 3 at 34.24–35.18 Mb was found to be significantly associated with iron deficiency chlorosis tolerance and Pythium irregulare resistance. This region has previously been investigated as the source of IDC tolerance in “Isoclark” ( Stec et al 2013 ; Assefa et al . 2020 ).…”

Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean

“…Glyma.03G130400 is homologous to the Arabidopsis bHLH038, and resides within the major IDC QTL on soybean chromosome 3. In Arabidopsis, bHLH038 plays a major role in the -Fe stress response [18,25,85]. Also involved in the iron deficiency stress response is Glyma.07G128000, homologous to the Arabidopsis ACS7, which is involved in IDC induced ethylene biosynthesis [86].…”

“…For example, Peiffer et al [ 7 ] fine mapped the major iron deficiency chlorosis quantitative trait locus (QTL) on soybean chromosome three and identified two candidate basic helix-loop-helix (bHLH) transcription factors with homology to AtbHLH38 in Arabidopsis . AtbHLH38 interacts with AtFIT to regulate iron uptake [ 25 ]. However, silencing the two candidate genes in soybean had no phenotypic affect [ 26 ].…”

Novel Genes and Genetic Loci Associated With Root Morphological Traits, Phosphorus-Acquisition Efficiency and Phosphorus-Use Efficiency in Chickpea

“…In chickpea, association mapping between SNP markers and seed copper (Cu), P, and potassium (K) concentrations identified eight SNPs associated with variation in three nutrients in more than two environments (Ozkuru et al, 2018). Similarly, seed mineral concentration in pea (Pisum sativum L.; Gali et al, 2019), Fe chlorosis in soybean; Mamidi et al, 2014;Assefa et al, 2020), and Fe bioavailability in cooked dry beans (Phaseolus vulgaris L.; Katuuramu et al, 2018) have been mapped. Novel genes involved in the accumulation of P in Lotus japonicas have been reported using GWAS analysis (Giovannetti et al, 2019).…”