Quinoa is an important, highly nutritional grain crop in the Andean region of South America. DNA markers and linkage maps are important tools for the improvement of underdeveloped crops such as quinoa. The objectives of this study were to (i) develop a new set of SSR markers to augment the number of SSR markers available in quinoa, and (ii) construct a new genetic linkage map of quinoa based on SSRs using multiple recombinant-inbred line (RIL) populations. Here we report the development of 216 new polymorphic SSR markers from libraries enriched for GA, CAA, and AAT repeats, as well as 6 SSR markers developed from BAC-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranged from 0.12 to 0.90, with an average value of 0.56. These new SSR and BES-SSR markers were analyzed on two RIL mapping populations (designated Population 1 and Population 40), each obtained by crossing Altiplano and coastal ecotypes of quinoa. Additional markers, including AFLPs, two 11S seed storage protein loci, a SNP, and the nucleolar organizing region (NOR), were also analyzed on one or both populations. Linkage maps were constructed for both populations. The Population 1 map contains 275 markers, including 200 SSR and 70 AFLP markers, as well as five additional markers. The map consists of 41 linkage groups (LGs) covering 913 cM. The Population 40 map contains 68 markers, including 62 SSR and six BES-SSR markers, and consists of 20 LGs covering 353 cM. Thirty-nine anchor markers common between both maps were used to combine 15 Population 1 LGs with 13 Population 40 LGs. The resulting integrated map consists of 13 LGs containing 140 SSR, 48 AFLP, four BES-SSR, one SNP, and one NOR marker spanning a total of 606 cM. A high level of segregation distortion was observed in both populations, indicating possible chromosomal regions associated with gametophytic factors or QTLs conferring a selective advantage under the particular growing conditions. As these maps are based primarily on easily-transferable SSR markers, they are particularly suitable for applications in the underdeveloped Andean regions where quinoa is grown.



College and Department

Life Sciences; Plant and Wildlife Sciences



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Quinoa, SSR, genetic linkage map