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ARS Home » Southeast Area » Raleigh, North Carolina » Soybean and Nitrogen Fixation Research » Research » Publications at this Location » Publication #300207

Research Project: Increasing the Competitiveness of U.S. Soybeans in Global Markets through Genetic Diversity, Genomics, and Plant Breeding

Location: Soybean and Nitrogen Fixation Research

Title: Quantitative trait loci controlling aluminum tolerance in soybean: candidate gene and SNP marker discovery

item ABDEL-HALEEM, HUSSEIN - University Of Georgia
item Carter Jr, Thomas
item RUFTY, THOMAS - North Carolina State University
item BOERMA, ROGER - University Of Georgia
item LI, ZENGLU - University Of Georgia

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/22/2013
Publication Date: 4/1/2014
Citation: Abdel-Haleem, H., Carter Jr, T.E., Rufty, T., Boerma, R., Li, Z. 2014. Quantitative trait loci controlling aluminum tolerance in soybean: candidate gene and SNP marker discovery. Molecular Breeding. 33, pp. 851-862.

Interpretive Summary: Acid soils comprise about 50% of the productive agricultural land throughout the world and are commonly derived from Al-rich parent material such as granite. Aluminum-rich acidic subsoils are a potent agricultural problem, leading to major reductions in crop productivity in drought stressed environments by curtailing deep rooting and limiting access to subsoil moisture. An environmentally friendly solution to the problem is to develop tolerant cultivars which have deeper rooting in the presence of Al. Previous research reported exotic soybean PI 416937 was resistant to Al toxicity while standard cultivar Young was susceptible. Genetic studies identified four genomic segments associated with Al tolerance. In this study, the genomic segments were investigated in more detail, to identify robust genetic markers that can be used in applied breeding programs. The research team added additional genetic markers to the genetic population used previously, refined the genetic map regions genetic map regions responsible for Al tolerance, and identified underlying genes which may control Al tolerance. This refinement of genomic technology lends itself well to applied breeding programs aimed at development of Aluminum tolerant cultivars.

Technical Abstract: Aluminum (Al) toxicity is an important abiotic stress that affects soybean production in acidic soils. Development of Al-tolerant cultivars is an efficient and environmentally friendly solution to the problem. Effective selection of Al-tolerant genotypes in applied breeding requires an understanding of the inheritance of Al tolerance and availability of robust markers at identified quantitative trait loci QTL for marker assisted selection. A previous report identified QTL for Al tolerance inherited from PI 416937, using RFLP markers, in a population of ‘Young’ x PI 416937. The population was genotyped with 162 SSR to enhance the power of QTL detection and enable the selection of candidate genes for functional marker development. Using the enhanced set of DNA markers, a QTL was refined on chromosomes (chr) 8 that explained 54% of the phenotypic variation in root extension under Al stress conditions (HIAL). This QTL from PI 416937 explained 45 phenotypic variation in. A candidate gene approach was used to identify a SNP marker associated with Al tolerance for MAS. Six homologues for citrate synthase genes (CS) were found in the soybean genome sequence at chr 2, 8, 14, 15, and 18. The CS homologue on chr 8 was then sequenced in both Young and PI 416937 and 16 SNPs were identified. A SimpleProbe (melting curve method) assay was developed for the major QTL on chr 8 for the Al tolerance. The SNP identified from this region could be used for MAS of Al tolerance.