Open Access Open Badges Research article

Construction of physical maps for the sex-specific regions of papaya sex chromosomes

Jong-Kuk Na16, Jianping Wang17, Jan E Murray18, Andrea R Gschwend1, Wenli Zhang3, Qingyi Yu2, Rafael Navajas‒ Pérez48, F Alex Feltus4, Cuixia Chen19, Zdenek Kubat110, Paul H Moore5, Jiming Jiang3, Andrew H Paterson4 and Ray Ming1*

Author affiliations

1 Department of Plant Biology, University of Illinois at Urbana Champaign, Urbana, IL, 61801, USA

2 Texas AgriLife Research Center, Weslaco, TX, 78596, USA

3 Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA

4 Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30606, USA

5 Hawaii Agriculture Research Center, Kunia, HI, 96759, USA

6 Department of Agricultural Bio-resources, National Academy of Agricultural Science, RDA, Suwon, 441-701, Republic of Korea

7 Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA

8 Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada Campus de Fuentenueva s/n, 18071, Spain

9 Shandong Agricultural University, Tai’an, Shandong, 271018, China

10 Laboratory of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, Brno, CZ-612 65, Czech Republic

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Citation and License

BMC Genomics 2012, 13:176  doi:10.1186/1471-2164-13-176

Published: 8 May 2012



Papaya is a major fruit crop in tropical and subtropical regions worldwide. It is trioecious with three sex forms: male, female, and hermaphrodite. Sex determination is controlled by a pair of nascent sex chromosomes with two slightly different Y chromosomes, Y for male and Yh for hermaphrodite. The sex chromosome genotypes are XY (male), XYh (hermaphrodite), and XX (female). The papaya hermaphrodite-specific Yh chromosome region (HSY) is pericentromeric and heterochromatic. Physical mapping of HSY and its X counterpart is essential for sequencing these regions and uncovering the early events of sex chromosome evolution and to identify the sex determination genes for crop improvement.


A reiterate chromosome walking strategy was applied to construct the two physical maps with three bacterial artificial chromosome (BAC) libraries. The HSY physical map consists of 68 overlapped BACs on the minimum tiling path, and covers all four HSY-specific Knobs. One gap remained in the region of Knob 1, the only knob structure shared between HSY and X, due to the lack of HSY-specific sequences. This gap was filled on the physical map of the HSY corresponding region in the X chromosome. The X physical map consists of 44 BACs on the minimum tiling path with one gap remaining in the middle, due to the nature of highly repetitive sequences. This gap was filled on the HSY physical map. The borders of the non-recombining HSY were defined genetically by fine mapping using 1460 F2 individuals. The genetically defined HSY spanned approximately 8.5 Mb, whereas its X counterpart extended about 5.4 Mb including a 900 Kb region containing the Knob 1 shared by the HSY and X. The 8.5 Mb HSY corresponds to 4.5 Mb of its X counterpart, showing 4 Mb (89%) DNA sequence expansion.


The 89% increase of DNA sequence in HSY indicates rapid expansion of the Yh chromosome after genetic recombination was suppressed 2–3 million years ago. The genetically defined borders coincide with the common BACs on the minimum tiling paths of HSY and X. The minimum tiling paths of HSY and its X counterpart are being used for sequencing these X and Yh-specific regions.

Bacterial artificial chromosome (BAC); Carica papaya; Sex chromosomes; Sex determination; Suppression of recombination