Development, Characterization, and Linkage Mapping of Single Nucleotide Polymorphisms in the Grain Amaranths (Amaranthus sp.)
By P. Maughan, S. Smith, D. Fairbanks, E. Jellen. 2011
86 citations recorded by the source corpus.
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.
Subfields: Food Science, Plant Science
View Paper: https://www.semanticscholar.org/paper/6a13dc0650e4b5654e869bf30cb118cb0352dc51
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Citations in the corpus
- Introgression of crop alleles into wild or weedy populations (2013, background): “Direct SNP genotyping as well as single molecule sequencing are advancing rapidly, and cheaper flexible genotyping methods are becoming available (Maughan et al. 2011).”
- Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement (2013, background): “…that were previously ignored by the genomics community, a sampling of which include cassava, common bean, pea, sunflower, cowpea, and grain amaranth (Bachlava et al. 2012; Ferguson et al. 2011; Hyten et al. 2010; Maughan et al. 2011; Smýkal et al. 2012; Varshney et al. 2009; Varshney et al. 2010).”
- Current knowledge on Amaranthus spp.: research avenues for improved nutritional value and yield in leafy amaranths in sub-Saharan Africa (2014, background): “…studies using biochemical (Das 2012; Drzewiecki 2001; Juan et al. 2007) and molecular markers (Costea et al. 2006; Lymanskaya 2012; Maughan et al. 2011; Ranade et al. 1997; Ray and Roy 2009; Wassom and Tranel 2005; Xu and Sun 2001) were conducted to analyze the genetic variability…”