A genetic linkage map of quinoa (Chenopodium quinoa) based on AFLP, RAPD, and SSR markers

Abstract

Quinoa ( Chenopodium quinoa Willd.) is an important seed crop for human consumption in the Andean region of South America. It is the primary staple in areas too arid or saline for the major cereal crops. The objective of this project was to build the first genetic linkage map of quinoa. Selection of the mapping population was based on a preliminary genetic similarity analysis of four potential mapping parents. Breeding lines 'Ku-2' and '0654', a Chilean lowland type and a Peruvian Altiplano type, respectively, showed a low similarity coefficient of 0.31 and were selected to form an F(2) mapping population. The genetic map is based on 80 F(2) individuals from this population and consists of 230 amplified length polymorphism (AFLP), 19 simple-sequence repeat (SSR), and six randomly amplified polymorphic DNA markers. The map spans 1,020 cM and contains 35 linkage groups with an average marker density of 4.0 cM per marker. Clustering of AFLP markers was not observed. Additionally, we report the primer sequences and map locations for 19 SSR markers that will be valuable tools for future quinoa genome analysis. This map provides a key starting point for genetic dissection of agronomically important characteristics of quinoa, including seed saponin content, grain yield, maturity, and resistance to disease, frost, and drought. Current efforts are geared towards the generation of more than 200 mapped SSR markers and the development of several recombinant-inbred mapping populations.

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

“…Quinoa (Chenopodium quinoa Willd) is an allotetraploid (2n = 4x = 36) that shows disomic inheritance for most qualitative traits (Simmonds 1971;Risi and Galwey 1984;Ward 2000;Maughan et al 2004). Its small seed has an excellent carbohydrate, fat, and protein content balance (Risi and Galwey 1984;Coulter and Lorenz 1990;Chauhan et al 1999) and a seed protein content substantially higher than that of the major cereal grains, varying between 7.5% and 22.1% (Tapia et al 1979).…”

Characterisation of quinoa (Chenopodium quinoa Willd.) accessions for the saponin content in Mediterranean environment

“…Nevertheless, high levels of saponin are considered a major impediment to the diffusion of the crop (Bhargava et al, 2006) because they can affect the absorption and digestibility of nutrients (Maughan et al, 2004). Consequently, the development of varieties with low or no saponin is one of the important breeding objectives for quinoa (Spehar and Rocha, 2010).…”

IDENTIFICATION OF NEW POLISH LINES OF Chenopodium quinoa (Willd.) BY SPECTRAL ANALYSIS OF PIGMENTS AND A CONFIRMATION OF GENETIC STABILITY WITH SCoT AND RAPD MARKERS

“…The only variation detected with the genetic markers was observed in plants representing original cultivars. RAPD markers were successfully used in the genetic linkage map creation for quinoa [Maughan et al 2004], although among 60 primers screened only 6 gave polymorphic bands in the plants tested, and the authors pointed to a lower efficiency of this technique than AFLP or SSR markers. The technique has been successfully applied in the genetic diversity and stability studies on chrysanthemum, Pittosporum ericarpum, Cleome gynandra and more [Rathore et al 2014, Feng et al 2016, Thakur et al 2016.…”

“…The Random Amplified Polymorphic DNA marker (RAPD), first proposed by Welsh and McClelland [1990] and Williams et al [1990] is often applied in the studies of genetic identity as well as variation of crops and it was used, side by side with AFLP and SSR markers, by Maughan et al [2004] to create the genetic linkage map of quinoa. The Start Codon Targeted Polymorphism (SCoT) molecular markers technique was proposed by Collard and Mackill [2009] and has not been yet applied for quinoa examination.…”