Abstract
Iron deficiency chlorosis (IDC) is a yield limiting problem in soybean (Glycine max (L.) Merr) production regions with calcareous soils. Genome-wide association study (GWAS) was performed using a high density SNP map to discover significant markers, QTL and candidate genes associated with IDC trait variation. A stepwise regression model included eight markers after considering LD between markers, and identified seven major effect QTL on seven chromosomes. Twelve candidate genes known to be associated with iron metabolism mapped near these QTL supporting the polygenic nature of IDC. A non-synonymous substitution with the highest significance in a major QTL region suggests soybean orthologs of FRE1 on Gm03 is a major gene responsible for trait variation. NAS3, a gene that encodes the enzyme nicotianamine synthase which synthesizes the iron chelator nicotianamine also maps to the same QTL region. Disease resistant genes also map to the major QTL, supporting the hypothesis that pathogens compete with the plant for Fe and increase iron deficiency. The markers and the allelic combinations identified here can be further used for marker assisted selection.
Highlights
Iron (Fe) is an essential element for multiple plant functions including photosynthesis, respiration, chlorophyll biosynthesis, and redox reactions in plants, and is a structural component in heme, the Fe-sulfur cluster, and Fe-binding sites
The objective of this study was to identify quantitative trait loci (QTL) and genes involved in Iron deficiency chlorosis (IDC) of soybean using a Genome-wide association study (GWAS) population and a new high density SNP map obtained through genotype-by-sequencing (GBS)
We used a high density GBS data set with a large plant GWAS population to map genes/QTL involved in IDC of soybean
Summary
Iron (Fe) is an essential element for multiple plant functions including photosynthesis, respiration, chlorophyll biosynthesis, and redox reactions in plants, and is a structural component in heme, the Fe-sulfur cluster, and Fe-binding sites. Iron deficiency chlorosis (IDC) is an important yield-limiting factor for soybeans (G. max) grown on calcareous soils that have a high percentage of calcium carbonate and soluble salts. This soil type is common in the northcentral regions of the United States [4] where soybean is widely grown. In these soils, interactions of high pH, carbonate and high field moisture content at planting leads to early IDC symptoms that effect yield. It is estimated that the current revenue losses due to IDC in soybean are $260 million [5]
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