Genetic Map and QTL Analysis of Agronomic Traits in a Diploid Potato Population using Single Nucleotide Polymorphism Markers

Genetic maps now can be constructed using thousands of genomewide single nucleotide polymorphisms (SNps) for identification of markers closely associated with agronomic traits. A diploid mapping population for potato (Solanum tuberosum L.) was developed from a pseudo-testcross between a homozygous line S. tuberosum Group phureja DM 1-3 516 r44 and a heterozygous outcrossing S. tuberosum Group Tuberosum clone, rH89-039-16. The population of 96 individuals was evaluated for seven traits in two consecutive years (2012 and 2013). Yield (total tuber yield [TTY], average tuber weight [ATW], and number of tubers per plant [TS]), food quality (specific gravity [SpGr]), and plant development traits (vigor, maturity [Mat], and tuber end rot [TEr]) were studied. Sixteen different quantitative trait loci (QTL) were identified. A QTL with major effects at 11.9 cM corresponding to 3.7 Mb on chromosome V of potato genome assembly explained between 20.3 and 75.7% of variance for TS, ATW, vigor, Mat, and TEr. For TTY, ATW and SpGr, the QTL was detected at 6.4 and 12.9 cM. The other 15 QTL were located on chromosomes I, II, III, IV, V, VI, IX, X, and XII. In general, the results confirmed QTL previously identified for yield, SpGr, and Mat in diploid and tetraploid populations. The Infinium 8303 potato Array provides an efficient means of scoring genomewide markers for constructing high-resolution genetic maps and thereby facilitates identification of genomic regions closely associated with genes coding for agronomic traits of interest. N.C. Manrique-Carpintero, J.J. Coombs, and D. Douches, Dep. of Plant, Molecular Plant Sciences Bldg., Michigan State Univ., 1066 Bogue St., Plant, Soil and Microbial Sciences Bldg., East Lansing, MI 48824; Y. Cui, Dep. of Statistics and Probability, Michigan State Univ., C-432 Wells Hall, East Lansing, MI 48824; R.E. Veilleux, Dep. of Horticulture, Virginia Polytechnic Institute and State Univ., 544 Latham Hall, 220 Ag Quad Ln., Blacksburg, VA 24061; and C.R. Buell, Dep. of Plant Biology, Michigan State Univ., 612 Wilson Road #S148, East Lansing, MI 48824. Received 30 Oct. 2014. Accepted 27 Mar. 2015. *Corresponding author ([email protected]). Abbreviations: ATW, average tuber weight; DH, doubled haploid; LOD, logarithm of odds; Mat, maturity; MIM, multiple interval mapping; MQM, multiple QTL models; QTL, quantitative trait locus or loci; REML, restricted maximum likelihood method; SNP, single nucleotide polymorphism; SPGR, specific gravity; TER, tuber end rot; TS, tubers per plant; TTY, total tuber yield. Published in Crop Sci. 55:2566–2579 (2015). doi: 10.2135/cropsci2014.10.0745 © 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 October 19, 2015