Construction of Papaya Male and Female BAC Libraries and Application in Physical Mapping of the Sex Chromosomes

Gschwend, Andrea R.; Yu, Qingyi; Moore, Paul H.; Saski, Christopher; Chen, Cuixia; Wang, Jianping; Na, Jong-Kuk; Ming, Ray

doi:10.1155/2011/929472

Cited by 14 publications

(9 citation statements)

References 26 publications

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“…A physical map of the papaya MSY was constructed from the AU9 male BAC library, using probes from BACs in the HSY physical map (Gschwend et al 2011). Candidate BACs were confirmed by a combination of PCR and BAC end sequencing, and gaps in the physical map were filled using chromosome walking (see Methods).…”

Section: Sequencing and Analysis Of A Papaya Msymentioning

confidence: 99%

Origin and domestication of papaya Y^h chromosome

et al. 2015

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Sex in papaya is controlled by a pair of nascent sex chromosomes. Females are XX, and two slightly different Y chromosomes distinguish males (XY) and hermaphrodites (XY h ). The hermaphrodite-specific region of the Y h chromosome (HSY) and its X chromosome counterpart were sequenced and analyzed previously. We now report the sequence of the entire male-specific region of the Y (MSY). We used a BAC-by-BAC approach to sequence the MSY and resequence the Y regions of 24 wild males and the Y h regions of 12 cultivated hermaphrodites. The MSY and HSY regions have highly similar gene content and structure, and only 0.4% sequence divergence. The MSY sequences from wild males include three distinct haplotypes, associated with the populations' geographic locations, but gene flow is detected for other genomic regions. The Y h sequence is highly similar to one Y haplotype (MSY3) found only in wild dioecious populations from the north Pacific region of Costa Rica. The low MSY3-Y h divergence supports the hypothesis that hermaphrodite papaya is a product of human domestication. We estimate that Y h arose only ∼4000 yr ago, well after crop plant domestication in Mesoamerica >6200 yr ago but coinciding with the rise of the Maya civilization. The Y h chromosome has lower nucleotide diversity than the Y, or the genome regions that are not fully sex-linked, consistent with a domestication bottleneck. The identification of the ancestral MSY3 haplotype will expedite investigation of the mutation leading to the domestication of the hermaphrodite Y h chromosome. In turn, this mutation should identify the gene that was affected by the carpel-suppressing mutation that was involved in the evolution of males.

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Section: Sequencing and Analysis Of A Papaya Msymentioning

confidence: 99%

Origin and domestication of papaya Y^h chromosome

et al. 2015

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“…A large-insert library is important because the number of clones required for adequate coverage of the genome is reduced, and it consequently simplifies the screening and generation of BAC contigs as demonstrated by the BAC screening in this study. Larger inserts can span larger gaps, covering more space with less overlap and reducing the costs of sequencing as reported for several BAC libraries such as in tomato (Budiman et al 2000), common bean (Liu et al 2010) and papaya (Gschwend et al 2011). Analysis of BAC clones through digestion with NotI followed by electrophoresis demonstrated that most clones contained one fragment.…”

Section: Discussionmentioning

confidence: 85%

Construction and characterization of a BAC library from the Coffea arabica genotype Timor Hybrid CIFC 832/2

et al. 2013

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Most of the world's coffee production originates from Coffea arabica, an allotetraploid species with low genetic diversity and for which few genomic resources are available. Genomic libraries with large DNA fragment inserts are useful tools for the study of plant genomes, including the production of physical maps, integration studies of physical and genetic maps, genome structure analysis and gene isolation by positional cloning. Here, we report the construction and characterization of a Bacterial Artificial Chromosome (BAC) library from C. arabica Timor Hybrid CIFC 832/2, a parental genotype for several modern coffee cultivars. The BAC library consists of 56,832 clones with an average insert size of 118 kb, which represents a dihaploid genome coverage of five to sixfold. The content of organellar DNA was estimated at 1.04 and 0.5 % for chloroplast and mitochondrial DNA, respectively. The BAC library was screened for the NADPH-dependent mannose-6-phosphate reductase gene (CaM6PR) with markers positioned on four linkage groups of a partial C. arabica genetic map. A mixed approach using PCR and membrane hybridization of BAC pools allowed for the discovery of nine BAC clones with the CaM6PR gene and 53 BAC clones that were anchored to the genetic map with simple sequence repeat markers. This library will be a useful tool for future studies on comparative genomics and the identification of genes and regulatory elements controlling major traits in this economically important crop species.

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“…Cloning and characterization of the papaya sexdetermining and sex-related genes have profound applications in papaya production. Recently Ming and coworkers (Gschwend et al, 2011) constructed two bacterial artificial chromosome (BAC) libraries from papaya male and female genomic DNA. Papaya Y chromosome has a male-specific region, which has undergone severe recombination suppression and DNA sequence degeneration Ming et al, 2007).…”

Section: Papaya Sex-linked Dna Markers and Traits Genes For Sex-determentioning

confidence: 99%