Development and Use of Microsatellite Markers for Germplasm Characterization in Quinoa (Chenopodium quinoa Willd.)

Abstract

an ideal balance of all 20 essential amino acids (Ruas et al., 1999). Quinoa (Chenopodium quinoa Willd.) is a widely consumed foodQuinoa is especially important as a source of protein crop and a primary protein source for many of the indigenous inhabitants of the Andean region of South America. The objective of this for subsistence farmers on the Altiplano of Bolivia and study was to develop a collection of reproducible and highly informa- Peru (Wilson, 1988), an area that covers 255 000 km 2 at tive microsatellite markers for quinoa. A total of 1276 clones were an elevation of 3500 to 3850 m above sea level and is sequenced from three microsatellite-enriched (CA, ATT, ATG) ligenerally characterized as cold and arid. Quinoa is one braries. Four hundred fifty-seven (36%) of the clones contained of only a few crop plants adapted to the extreme condiunique microsatellites. The most common repeated motifs, other than tions that characterize much of this region (Cusack, CA, AAT, and ATG, were GA and CAA. Flanking primers were 1984; Risi and Galwey, 1984; Prado et al., 2000; Vacher, designed for 397 microsatellite loci and screened using a panel of 1998). Although increasing quinoa productivity is a pridiverse quinoa accessions and one accession of C. berlandieri Moq., a mary food-security issue in the Andean region, limited wild relative of quinoa. Two hundred eight (52%) of the microsatellite research on quinoa genetics and plant breeding has been markers were polymorphic among the quinoa accessions. An additional 25 of the microsatellite markers (6%) were polymorphic when conducted (see reviews by Fleming and Galwey, 1995; the C. berlandieri accession was included in the analysis. Only in rare Risi and Galwey, 1984). Fortunately, a new awareness instances (nine) did a microsatellite amplify in quinoa and not in C. of the importance of quinoa, as well as a growing health berlandieri. The number of observed alleles ranged from 2 to 13, with food export market for quinoa, has led to the establishan average of four alleles detected per locus. Heterozygosity values ment of several new quinoa breeding programs throughranged from 0.20 to 0.90 with a mean value of 0.57. Sixty-seven markers out the Andean region of South America. In addition (32%) were highly polymorphic (H Ն 0.70). These microsatellites to germplasm management, principal objectives of these markers are an ideal resource for use in managing quinoa germplasm,programs include enhancing grain yield, disease resistrait mapping and marker-assisted breeding strategies. The wide crosstance, drought tolerance, and modulating saponin conspecies transportability of these markers may extend their value to tent (Ochoa et al., 1999). These programs recognize that research involving other Chenopodium species.the development and use of molecular markers are critical to meeting these objectives (A. Gandarillas, personal communication).

Assessment of genetic diversity patterns in Chilean quinoa (Chenopodium quinoa Willd.) germplasm using multiplex fluorescent microsatellite markers

“…Twenty di-or tri-nucleotide microsatellites reported by Mason et al (2005), and Jarvis (unpublished data), were selected based on high heterozygosity values (Mason et al 2005), reproducibility, and clear amplification of a single amplicon. The primer sequences were synthesized by ABI (Applied Biosystems, Foster City, CA) with blue (6FAM), green (VIC) and yellow (NED) fluorophores ( Table 2).…”

Transcriptome Analysis of Drought Induced Stress in <i>Chenopodium quinoa</i>

“…In this study, we compared the response to different water treatments approximating drought-like conditions in two quinoa varieties, specifically "Ingapirca", derived from a valley ecotype native to Ecuador, and "Ollague", derived from a Salares ecotype native to Chile [28]. We used RNA sequencing (RNA-Seq) technology to identify putative gene products that are differentially expressed during progressive water stress.…”

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).…”