RESEARCH-PGR: Genomic mechanisms of domesticating a Y chromosome in papaya

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Many plants have male and female floral parts housed on the same plant. Papaya plants, on the other hand, are gender-distinct: papaya plants may be male or female or so-called hermadrodites, which are plants that both male and female parts in the same flowers. Wild papayas are male and female only, and cultivated papayas are mostly hermaphrodite, which was selected from sex reversed male papaya about 4,000 years ago in Central America. Understanding how this rare gender biology is controlled, and whether hermaphroditism could be harnessed for control of flowering, would greatly benefit agriculture of papaya. It is currently known that the difference among these trees is due to different Y chromosomes: females have two X chromosomes, males have an X and Y and hermaphrodites an X and modified Yh. There is also evidence that hermaphrodite chromosome may have evolved during the earliest days of domestication of papaya in Central America. The project will identify what factors and genome-wide changes are occurring in the plants with varying chromosome types. Once identified, plants could be engineered to produce hermaphrodites with no X chromosome, hence no segregation of types. This material will expedite the identification of the factors that control the formation of male flowers, the target for sex reversal from male back to hermaphrodite. Undergraduate students will be trained to gain hands-on research experience while working with this important crop and developing breeding tools. The project will display information for growers on informative videos about papaya biology and ways to control flowering. Papaya sex chromosomes are the first trio (Y, Yh, and X) to be sequenced. The unique set of three sex chromosomes and abundant genomic and biological resources allow us to investigate the reversion from male to hermaphrodite, a rare event during the early stage of sex chromosome evolution. Our goal is to understand the genomic and evolutionary mechanisms governing the domestication of the Yh chromosome. The first aim is to establish the molecular basis for papaya YY lethality gene and restore fertility of YhYh hermaphrodite and YhY male genotypes for functional analysis of Yh-specific genes. A strong candidate gene has been identified and is being tested for function by being transformed into hermaphrodite plants. Once viable YhYh hermaphrodites are generated, the 40 mutations on Y chromosome affecting flower morphology and pollen fertility will be identified through fine mapping. The second aim is to identify the sex determination gene suppressing carpel development in male flowers and the mutation event leading to the sex reversal from male back to hermaphrodite. The project is focusing on 12 sex reversal mutants generated for identification of the sex determination gene suppressing carpel development in male flowers, and will conduct map based gene cloning once the YYh fertility is restored. Comparative analysis of gene expression between YY and Yh Yh genotypes will reveal differentially expressed genes and gene networks controlled by the sex determination gene. The target genes and genomic resources generated will lead to selection of new papaya varieties without segregation of sex types and with improved productivity