Development, Characterization, and Linkage Mapping of Single Nucleotide Polymorphisms in the Grain Amaranths (Amaranthus sp.)

• Published in: The plant genome Vol. 4; no. 1; pp. 92 - 101
• Main Authors: Maughan, P.J., Smith, S.M., Fairbanks, D.J., Jellen, E.N.
• Format: Journal Article
• Language: English
• Published: Crop Science Society of America 01.03.2011; Wiley
• ISSN: 1940-3372; 1940-3372
• DOI: 10.3835/plantgenome2010.12.0027

The grain amaranths (Amaranthus sp.) are important pseudo‐cereals native to the New World. During the last decade they have garnered increased international attention for their nutritional quality, tolerance to abiotic stress, and importance as a symbol of indigenous cultures. We describe the development of the first single nucleotide polymorphism (SNP) assays for amaranth. In addition, we report the characterization of the first complete genetic linkage map in the genus. The SNP assays are based on KASPar genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen of 41 accessions of the cultivated amaranth species and their putative ancestor species (Amaranth hybridus L.) showed that the minor allele frequency (MAF) of these markers ranged from 0.05 to 0.5 with an average MAF of 0.27 per SNP locus. One hundred and forty‐one of the SNP loci were considered highly polymorphic (MAF ≥ 0.3). Linkage mapping placed all 411 markers into 16 linkage groups, presumably corresponding to each of the 16 amaranth haploid chromosomes. The map spans 1288 cM with an average marker density of 3.1 cM per marker. The work reported here represents the initial first steps toward the genetic dissection of agronomically important characteristics in amaranth.