Submitted to: The Plant Genome
Publication Type: Peer reviewed journal
Publication Acceptance Date: 11/15/2011
Publication Date: 2/1/2012
Citation: Mamidi, S., Chikara, S., Goos, R.J., Hyten, D.L., Moghaddam, S.M., Cregan, P.B., Mcclean, P.E. 2012. Genome-wide association analysis identifies candidate genes associated with iron deficiency chlorosis in soybean. The Plant Genome. 11:154-164. Interpretive Summary: Iron deficiency chlorosis (IDC) is a yield-limiting problem in the major soybean production areas of the North Central United States. The objective of this research was to use an approach called whole genome association mapping to find positions on the soybean chromosomes containing genes that are associated with IDC and which may contain genes that can be used to breed more IDC resistant soybean varieties. More than 140 soybean varieties and advanced breeding lines with varying levels of IDC resistance were grown in the field at five North Dakota locations in 2005 and four locations in 2006 and IDC symptoms were measured. The DNA of all lines was characterized with 1536 Single Nucleotide Polymorphism (SNP) DNA markers. A small subset of SNP DNA markers was identified that were associated with the severity of IDC. Seven different locations along the soybean chromosomes were significantly associated with IDC symptoms in both years. The DNA markers at these positions may be of use to soybean breeders and geneticists who are developing new IDC resistant soybean varieties.
Technical Abstract: Iron deficiency chlorosis (IDC) is a significant yield-limiting problem in some of the major soybean production regions in the United States. Soybean plants display a variety of symptoms, ranging from slight yellowing of the leaves to interveinal chlorosis and sometimes it is followed by stunted growth. In severe cases it may even lead to cell death. The objective was to employ whole genome association mapping approaches to uncover the genomic regions associated with IDC. The 2005 and 2006 populations from a multi-location, replicated IDC variety field testing program were evaluated. SNP genotyping identified 881 and 913 loci with a minor allele frequency > 10%, in 2005 and 2006, respectively. After controlling for population structure and individual relatedness, and selecting statistical models that minimized false positives, 42 and 88 loci were significant in 2005 and 2006, respectively. The loci accounted for 74.5% of the phenotypic variation in IDC symptoms in 2005 and 93.8% of the variation in 2006. Nine loci from seven genomic locations were significant in both years. These loci accounted for 43.7% of the variation in 2005 and 47.6% in 2006. A number of the loci discovered here mapped at or near previously discovered QTL loci. A total of 13 genes known to be involved in iron metabolism mapped in the vicinity of significant markers in one or both populations.