Reproduced from Crop Science. Published by Crop Science Society of America. All copyrights reserved. 1098 WWW.CROPS.ORG CROP SCIENCE, VOL. 48, MAY– JUNE 2008 RESEARCH T he grain amaranths (A. hypochondriacus L., A. cruentus L., and A. caudatus L.) belong to the genus Amaranthus L., which includes 60 to 70 species (Sauer, 1976). The three grain amaranths are classifed along with their putative progenitor species (A. hybri- dus L., A. quitensis H.B.K., and A. powellii S. Wats.) in what is termed the A. hybridus complex and are thought to be paleo-allotetraploids (2n = 4x = 32), although chromosome counts of both 32 and 34 have been reported for A. cruentus (Pal et al., 1982; Greizerstein and Poggio, 1994, 1995). While the grain amaranths have been culti- vated for centuries in the Americas, they have been underutilized since the Spanish conquest, when they were replaced by Old World crops and their cultivation suppressed due to their deeply rooted use in indigenous religious practices (Sauer 1976, 1993; Iturbide and Gispert, 1994). In the last few decades, the grain amaranths have begun to reclaim some of their importance, largely because of the recognition of the nutritional value of their seed for human consumption (Bressani et al., 1992; Tucker, 1986). Amaranth grain is 50 to 60% starch, with higher fber (8%) and more fat (7–8%) than the grain of most cereals (Pedersen et Development and Characterization of Microsatellite Markers for the Grain Amaranths Melanie A. Mallory, Rozaura V. Hall, Andrea R. McNabb, Donald B. Pratt, Eric N. Jellen, and Peter J. Maughan* ABSTRACT The grain amaranths ( Amaranthus hypochon- driacus L., A. cruentus L., and A. caudatus L.) are important pseudo-cereals native to the Americas. The objective of this project was to produce and characterize a set of highly infor- mative, reproducible microsatellite markers for the grain amaranths. A total of 1457 clones were sequenced from three microsatellite-enriched libraries. Of these, 353 contained unique mic- rosatellites. An additional 29 microsatellite loci were identifed from 728 bacterial artifcial chro- mosome–end sequences. A total of 179 micro- satellites were polymorphic across accessions from the three grain amaranths. Among these polymorphic microsatellite loci, a total of 731 alleles were identifed with an average of four alleles per locus. Heterozygosity values ranged from 0.14 to 0.83, with a mean value of 0.62. Thirty-seven (21%) of the markers were polymor- phic between the parents of a segregating pop- ulation. Phylogenetic analysis using the marker data placed A. hybridus L. accessions into two of the three grain amaranth clades, suggesting the polyphyletic evolution of the three cultivated species from different A. hybridus ancestors. The transferability of these markers to A. hybri- dus, A. powellii S. Wats., and A. retroflexus L. is reported and suggests that these markers may be useful in studying other species within the genus Amaranthus, including several economi- cally important weeds and ornamentals. M.A. Mallory, R.V. Hall, A.R. McNabb, E.N. Jellen, and P.J. Maughan, Dep. of Plant and Animal Sci., Brigham Young University, Dep. of Plant & Animal Sciences, Provo, UT 84602. D.B. Pratt, Dep. of Biol- ogy, Stephen F. Austin State Univ., Nacogdoches, TX 75962. Received 16 Aug. 2007. *Corresponding author (Jef _Maughan@byu.edu). Abbreviations: AFLP, amplifed fragment length polymorphism; BAC, bacterial artifcial chromosome; BES, BAC-end sequence; H, heterozy- gosity; MAX, longest tandem repeat excluding half-repeats; ONA, observed number of alleles; PCR, polymerase chain reaction; SSR, sim- ple sequence repeat. Published in Crop Sci. 48:1098–1106 (2008). doi: 10.2135/cropsci2007.08.0457 © Crop Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. Published May, 2008