Originally published as Genetics Published Articles Ahead of Print on October 18, 2007.

Genetics, Vol. 177, 2481-2491, December 2007, Copyright © 2007
doi:10.1534/genetics.107.081463

Construction of a Sequence-Tagged High-Density Genetic Map of Papaya for Comparative Structural and Evolutionary Genomics in Brassicales

Cuixia Chen^*, Qingyi Yu, Shaobin Hou, Yingjun Li^*, Moriah Eustice, Rachel L. Skelton, Olivia Veatch^,, Rachel E. Herdes^*, Lauren Diebold^*, Jimmy Saw, Yun Feng^**, Wubin Qian^**, Lee Bynum, Lei Wang^**, Paul H. Moore, Robert E. Paull, Maqsudul Alam and Ray Ming^*,1

^* Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Hawaii Agriculture Research Center, Aiea, Hawaii 96701, Center for Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, Department of Molecular Bioscience and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, ^** TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area (TEDA), Tianjin 300457, China, Tianjin Research Center for Functional Genomics and Biochip, Tianjin Economic-Technological Development Area (TEDA), Tianjin 300457, China, W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, Hawaii 96720 and Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii 96822

¹ Corresponding author: Department of Plant Biology, 148 ERML, MC-051, 1201 W. Gregory Dr., University of Illinois at Urbana-Champaign, Urbana, IL 61801.
E-mail: rming{at}life.uiuc.edu

A high-density genetic map of papaya (Carica papaya L.) was constructed using microsatellite markers derived from BAC end sequences and whole-genome shot gun sequences. Fifty-four F₂ plants derived from varieties AU9 and SunUp were used for linkage mapping. A total of 707 markers, including 706 microsatellite loci and the morphological marker fruit flesh color, were mapped into nine major and three minor linkage groups. The resulting map spanned 1069.9 cM with an average distance of 1.5 cM between adjacent markers. This sequence-based microsatellite map resolved the very large linkage group 2 (LG 2) of the previous high-density map using amplified fragment length polymorphism markers. The nine major LGs of our map represent papaya's haploid nine chromosomes with LG 1 of the sex chromosome being the largest. This map validates the suppression of recombination at the male-specific region of the Y chromosome (MSY) mapped on LG 1 and at potential centromeric regions of other LGs. Segregation distortion was detected in a large region on LG 1 surrounding the MSY region due to the abortion of the YY genotype and in a region of LG6 due to an unknown cause. This high-density sequence-tagged genetic map is being used to integrate genetic and physical maps and to assign genome sequence scaffolds to papaya chromosomes. It provides a framework for comparative structural and evolutional genomic research in the order Brassicales.

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