
NSF Org: |
IOS Division Of Integrative Organismal Systems |
Recipient: |
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Initial Amendment Date: | August 9, 2016 |
Latest Amendment Date: | July 29, 2022 |
Award Number: | 1546890 |
Award Instrument: | Continuing Grant |
Program Manager: |
Gerald Schoenknecht
gschoenk@nsf.gov (703)292-5076 IOS Division Of Integrative Organismal Systems BIO Directorate for Biological Sciences |
Start Date: | August 15, 2016 |
End Date: | July 31, 2023 (Estimated) |
Total Intended Award Amount: | $2,165,997.00 |
Total Awarded Amount to Date: | $2,165,997.00 |
Funds Obligated to Date: |
FY 2018 = $1,035,539.00 |
History of Investigator: |
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Recipient Sponsored Research Office: |
506 S WRIGHT ST URBANA IL US 61801-3620 (217)333-2187 |
Sponsor Congressional District: |
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Primary Place of Performance: |
IL US 61820-5711 |
Primary Place of
Performance Congressional District: |
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Unique Entity Identifier (UEI): |
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Parent UEI: |
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NSF Program(s): | Plant Genome Research Project |
Primary Program Source: |
01001819DB NSF RESEARCH & RELATED ACTIVIT |
Program Reference Code(s): |
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Program Element Code(s): |
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Award Agency Code: | 4900 |
Fund Agency Code: | 4900 |
Assistance Listing Number(s): | 47.074 |
ABSTRACT
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
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PROJECT OUTCOMES REPORT
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This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.
Papaya is a major fruit crop in tropical and subtropical regions with an outstanding nutritional profile. It is one of the rare species with three sex types, male, female, and hermaphrodite. The sex is controlled by a pair of nascent sex chromosomes with XX for female, XY for male, and XYh for hermaphrodite. Any combination of the Y and Yh chromosomes, YY, YYh, and YhYh, are lethal. Papaya fruit production is mostly relied on hermaphrodite. Through population genomic analyses we discovered that hermaphrodite papaya was selected from a male population about 4,000 years ago, aligning with the emergence of Maya civilization. The YY lethality gene was identified, which has a disrupted allele in Y and Yh chromosome and a functional allele in the X chromosome. The lack of the X allele will lead to embryo abortion in 25 to 50 days after pollination. This YY lethality gene is a transcription factor that regulates the expression of a large number of genes, and encodes a chlorophyll localized ANK repeat protein. Transforming this gene into an autosome restored the fertility of YYh and YhYh papaya genotypes that do not exist in nature.
We have sequenced papaya SunUp and Sunset genomes to fill the gaps in the X and Y chromosomes. SunUp is a genetically modified variety in Hawaii, which is obtained by transforming its host Sunset with papaya ringspot virus (PRSV) coat protein gene to resist PRSV virus. Two high-quality papaya genomes of SunUp and its progenitor Sunset were assembled to 317Mb and 347Mb and anchored to 9 chromosomes, respectively. We identified a 1.64 Mb insertion containing three transgenic insertions in SunUp chromosome 5, consisting of 52 nuclear-plastid, 21 nuclear-mitochondrial, and one nuclear genomic fragments. A gapless 9.8 Mb hermaphrodite-specific region of the Yh chromosome (HSY) and 6.0 Mb X counterpart were assembled. Six female to male sex reversal mutants were generated using gamma ray irradiation of male pollens to identify the sex determination gene that suppress carpel development in male flowers. Sequencing the genomes of these six sex reversal mutants revealed large deletions in the HSY at about the same location. The shared region of these six deletions is about 1 Mb, redefining the sex determination region from 9.8 Mb to 1 Mb HSY sequences. Eight male specific genes were annotated and complementation test were done on four of the eight genes without changing the sex. The sex determination gene is among the four remaining candidate genes.
Our findings have provided a comprehensive understanding of the molecular mechanism controlling YY lethality in papaya, filled the gaps in the non-recombining region of the sex chromosomes, redefined the sex determination region from 9.8 Mb to 1 Mb region of the HSY, reduced the number of candidate genes to four, and improved our understanding of sex chromosome evolution in papaya. The gained knowledge can be applied to papaya improvement.
Last Modified: 08/03/2023
Modified by: Ray R Ming
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