Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

Abstract

Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.

Development and validation of SSR markers for Coffea arabica L.

“…It was previously reported that the frequency, distribution and abundance of SSRs can vary strongly among different organisms, mainly due to the different search criteria, origin of the sequences, and the size of the sampled genome . Dinucleotide repeats were also the most frequent class of SSR derived from genomic DNA of quinoa (Jarvis et al 2008), peanut (Cuc et al 2008), melon (Ritschel et al 2004), orange tree (Novelli et al 2006), bean (Benchimol et al 2007) and sugarcane (Cordeiro et al 2000). Analyzing ESTs for the Coffea species Aggarwal et al (2007) found 46% of dinucleotides and 26% of trinucleotides.…”

Genetic structure in cultivated quinoa (Chenopodium quinoa Willd.), a reflection of landscape structure in Northwest Argentina

“…From the primers developed by Mason et al (2005) and Jarvis et al (2008), 35 and 4 SSR primers pairs, respectively, were selected according to the values of Heterozygosity (which ranged from 0.44 to 0.87), the Observed Number of Alleles reported (which ranged from 2 to 11), the chromosomal location and simple pattern amplification. Amplification reactions were carried out in a 7 ll reaction mixture.…”

Reliability and comparison of the polymorphism revealed in amaranth by amplified fragment length polymorphisms (AFLPs) and inters simple sequence repeats (ISSRs)

“…Simple sequence repeats (SSR's) are one of the frequently used molecular markers for genotyping crops (Tautz, 1989). A number of research studies have demonstrated the use of SSRs and ISSRs to detect polymorphism and diversity in amaranth Xu and Sun, 2001;Ray and Roy, 2007), and quinoa (Mason et al, 2005;Jarvis et al, 2008;Fuentes et al, 2009). However, inter-simple sequence repeat (ISSR) markers are simpler to use than SSR technique (Ray and Roy, 2007;Nolan et al, 2010).…”