A Unified Single Nucleotide Polymorphism Map of Sunflower ( Helianthus annuus L.) Derived from Current Genomic Resources

Dense genetic maps are critical tools for plant breeders and geneticists. While many maps have been developed for sunflower in the last few decades, most have been based on lowthroughput technologies and include marker numbers in the hundreds. However, two maps with reasonably dense coverage of about 5000 and 9000 single nucleotide polymorphism (SNP) loci each have recently been produced using high-throughput genotyping methods. Unfortunately, no mapping population is common between the two maps, making the development of a joint map a challenge. With genome sequencing and resequencing of mapping populations currently in progress, there will be opportunities in the near future to develop much more informative resources. In the meantime, there is much demand from the sunflower community, particularly plant breeders, to combine these two maps to develop a denser map for immediate needs. In this paper, we used an in silico approach to join the two SNP maps by placing our existing marker sequences on draft genome scaffolds. Genetic map positions of the markers were determined from a resequenced mapping population aligned to the same draft genome scaffolds. In this way, we were able to directly place 10,247 SNP and insertion-deletion (Indel) loci on a common linkage map, and also provide the ability to infer genetic position of a further 6724 SNP loci from both previously published maps. These results will allow researchers to compare previous genetics research conducted on the separate maps, and facilitate collaborative work on marker-assisted breeding approaches in sunflower. B.S. Hulke and L.L. Qi, Sunflower and Plant Biology Research Unit, Northern Crop Science Lab. , 1605 Albrecht Blvd. N. , Fargo, ND 58102-2765; C.J. Grassa and L.H. Rieseberg, Univ. of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4; J.E. Bowers and J.M. Burke, Univ. of Georgia, Dep. of Plant Biology, Miller Plant Sciences Bldg. , Athens, GA 30602; and Z.I. Talukder, Dep. of Plant Sciences, North Dakota State Univ., P.O. Box 6050, Fargo, ND 581086050. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. Received 5 Nov. 2014. Accepted 18 Mar. 2015. *Corresponding author (brent.hulke@ars.usda.gov). Abbreviations: cM, centiMorgan; ESTs, expressed sequence tags; Indel, insertion-deletion; LG, linkage group; RAD, restriction site associated DNA; RIL, recombinant inbred line; SSRs, simple sequence repeats; SNP, single nucleotide polymorphism; WGS, whole-genome shotgun. Published in Crop Sci. 55:1696–1702 (2015). doi: 10.2135/cropsci2014.11. 0752 © Crop Science Society of America | 5585 Guilford 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 August 10, 2015