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Predicting pollen compatibility in ryegrass using genomic sequences of self-incompatibility genes
Self-incompatibility (SI): SI is a reproductive mechanism preventing self-pollination, shared by more than half of the angiosperms and many forage grasses.
The outcrossing nature of perennial ryegrass (_Lolium perenne_ L.) is caused by **self-incompatibility (SI)**. SI is a reproductive mechanism preventing self-pollination, shared by more than half of the angiosperms and many forage grasses. We have recently identified and published the putative genes governing this trait.
SI represents a constraint for **plant breeding** as it prevents self-pollination and therefore the creation of homozygous parental inbred lines. But SI can also create biases in traditional polycrosses in plant breeding, depending on the allelic diversity of the SI genes. Being able to predict pollen compatibility of two or multiple parents is important to optimize crossing schemes for efficient plant breeding.
The outcrossing nature of perennial ryegrass (_Lolium perenne_ L.) is caused by **self-incompatibility (SI)**. SI is a reproductive mechanism preventing self-pollination, shared by more than half of the angiosperms and many forage grasses. We have recently identified and published the putative genes governing this trait. SI represents a constraint for **plant breeding** as it prevents self-pollination and therefore the creation of homozygous parental inbred lines. But SI can also create biases in traditional polycrosses in plant breeding, depending on the allelic diversity of the SI genes. Being able to predict pollen compatibility of two or multiple parents is important to optimize crossing schemes for efficient plant breeding.
This master thesis’ objectives are 1) to predict the pollen compatibility between different individual plants based on the allelic sequence of the SI genes and 2) to test if the predictions are correct by phenotyping the crosses.
This master thesis’ objectives are 1) to predict the pollen compatibility between different individual plants based on the allelic sequence of the SI genes and 2) to test if the predictions are correct by phenotyping the crosses.
Under the supervision of a postdoctoral researcher as well as a senior scientist, the student will predict the compatibility of a large set of crosses, based on SI genes sequences. Prior to the start of this project, the SI genes will be sequenced. This work will require sequence assembly, alignments, and protein prediction. The predicted compatibility based on the different alleles will then be tested by _in-vitro_ pollination of the plant set. The SI phenotypes are rated using a microscopy assay that allows to visualize pollen tube growth (see figure). Depending on the phenotypes of the different crosses, the prediction model will be adjusted.
Under the supervision of a postdoctoral researcher as well as a senior scientist, the student will predict the compatibility of a large set of crosses, based on SI genes sequences. Prior to the start of this project, the SI genes will be sequenced. This work will require sequence assembly, alignments, and protein prediction. The predicted compatibility based on the different alleles will then be tested by _in-vitro_ pollination of the plant set. The SI phenotypes are rated using a microscopy assay that allows to visualize pollen tube growth (see figure). Depending on the phenotypes of the different crosses, the prediction model will be adjusted.
The student will learn skills in **bioinformatics, microscopy, experimental design and statistical analysis**. He/she will also learn to **work in a group** of researchers and to **plan a project** with time constrains. Finally, the student will learn how to **analyse** and **interpret** his/her results and to present them to other researchers.
The student will learn skills in **bioinformatics, microscopy, experimental design and statistical analysis**. He/she will also learn to **work in a group** of researchers and to **plan a project** with time constrains. Finally, the student will learn how to **analyse** and **interpret** his/her results and to present them to other researchers.
This project is suitable for a Master student with basic laboratory and microscopy skills, bioinformatics skills (sequence assembly and alignment...), and interest in genetics and plant breeding. The student must be available between April and end of July. The work will take place at **ETH Zurich Zentrum** and at **Eschikon Lindau**, where the plants are located.
This project is suitable for a Master student with basic laboratory and microscopy skills, bioinformatics skills (sequence assembly and alignment...), and interest in genetics and plant breeding. The student must be available between April and end of July. The work will take place at **ETH Zurich Zentrum** and at **Eschikon Lindau**, where the plants are located.
For more details, please contact Chloé Manzanares (chloe.manzanares@usys.ethz.ch)
For more details, please contact Chloé Manzanares (chloe.manzanares@usys.ethz.ch)