INTRODUCTION, SCIENTIFIC CONTEXT:
Characterizing the mechanisms that underlie reproductive isolation between diverging lineages is central in understanding the speciation process. As populations evolve, they gradually develop reproductive isolation by passing through intermediate steps, often referred to as the “grey zone of speciation” [1]. The establishment of reproductive isolation manifests by the occurrence of genomic regions that act as barriers reducing local gene flow in comparison to the rest of the genome. Population genomic approaches for the detection of barrier loci hence involves identifying outlier loci with specific signatures. However, other processes can create similar signatures, making barrier detection a challenging task. We recently developed a tool, RIDGE – Reproductive Isolation Detection using Genomic Polymorphisms, which is tailored to identify genomic regions potentially involved in reproductive isolation [2].
We are now aiming to apply this tool in wild and domestic plants, using plant domestication as a model to explore the mechanisms of reproductive isolation and its underlying molecular determinants. Domestication has resulted in drastic morphological changes between wild and cultivated forms,
collectively known as the domestication syndrome. One important trait, though often overlooked, is reproductive isolation, which has been crucial in preserving the integrity of these forms despite gene flow [3]. Given their recent divergence, wild/domestic systems provide an opportunity to study reproductive barriers at the early stages of their formation [4].
During this internship, our focus will be on the genus Zea, which includes maize (Zea mays ssp. mays) and its wild relatives, collectively known as teosintes. These species cover varying degrees of divergence with maize. Divergences ranges from 9,000 generations between maize and its most closely related relative, the annual teosinte Z. mays ssp. parviglumis (from which maize was domesticated) to 68,000 generations with a more distant wild relative Z. mays ssp huehuetenangensis; up to more distantly related species from the Luxuriantes section, such as the perennial diploid Zea diploperennis and the annual diploid Zea luxurians, that diverged around 120,000 generations ago from maize [5].
Barriers to cross-fertilization have been identified between some of these taxa, as well as within taxa among different genetic group [6]. For example, incompatibilities with maize vary between the Chalco and Central Plateau races of Z. mays ssp. mexicana, each controlled by different genetic mechanisms [7]. Three well-characterized loci that prevent maize pollen from fertilizing Z. mays ssp. mexicana are Ga1, Tcb1, and Ga2 [7,8,9]. A simulation study suggests that those barrier loci experience rapid turnover due to parental conflicts [10]. Another system, Teosinte Pollen Drive (TPD), involving three interacting loci, affects pollen fertility of hybrids derived from maize pollinating Z. mays ssp. mexicana. Active TPD has also been found in Z. luxurians and Z. perennis [11]. Thus, these genes have a much older history than domestication, and their role in the evolutionary history within the genus Zea, and during domestication remains to be elucidated.
RESEARCH PROPOSAL/OBJECTIVES:
The internship will involve: (1) running RIDGE between all pairs of taxa considering independently each genetic group within taxa to discover barrier loci; (2) characterize the genomic distribution of barrier loci; (3) test the hypothesis of the accumulation of barriers with divergence time, and assess the impact of domestication on their accumulation. Results interpretations will also be guided by available genome annotations and the well-characterized barrier loci described above.
DESCRIPTION OF DATA :
Sequencing data are available for seven diploid (sub)species: four from the Zea section — Zea mays ssp. mays, ssp. parviglumis, ssp. mexicana and ssp. huehuetenangensis — as well as three from the Luxuriantes section — Zea luxurians, Zea perennis, Zea diploperennis, Zea nicaraguensis) [8]. The identification of polymorphisms (SNPs) will be completed before the start of the internship by a team in ECOBIO (Rennes).
METHODOLOGIES:
The student will use RIDGE to discover barrier loci, and analyze the outcomes including the underlying demographic models, the point estimates of the parameters, and the distributions of a number of summary statistics obtained for barrier loci in comparison with the rest of the genome. He/She will handle genomic visualization tools to study the distribution of barrier loci and rely on genome annotations to carry functional analysis. The internship, conducted at UMR GQE-Le Moulon, will be co-advised between Maud Tenaillon and a second year PhD student, A. Wojcik; but also in close collaboration with Sylvain Glémin’s team located at UMR ECOBIO in Rennes.
REFERENCES:
[1] Roux C, Fraïsse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic divergence. PLOS Biology. 2016;14: e2000234. doi:10.1371/journal.pbio.2000234
[2] Burban E., Tenaillon M.I., Glémin S. 2024. RIDGE, a tool tailored to detect gene flow barriers across species pairs. Molecular Ecology Resources. doi: 10.1111/1755-0998.13944.
[3] Dempewolf H, Baute G, Anderson J, Kilian B, Smith C, Guarino L. 2017. Past and Future Use of Wild Relatives in Crop Breeding. Crop Science 57: 1070-1082. doi.org/10.2135/cropsci2016.10.0885
[4] Tenaillon M.I., Burban E., Huynh S., Wojcik A., Thuillet A-C, Manicacci D., Gérard P. R., Alix K., Belcram H., Cornille A., Brault M., Stevens R., Lagnel J., Dogimont C., Vigouroux Y., Glémin S. 2023. Crop
domestication as a step toward reproductive isolation. American Journal of Botany. doi: 10.1002/ajb2.16173.
[5] Lu et al. 2022. Genome sequencing reveals evidence of adaptive variation in the genus Zea. Nature Genetics. doi: 10.1038/s41588-022-01184-y.
[6] Kermicle, J. 1997. Cross compatibility within the genus Zea. Gene Flow Among Maize Landraces, Improved Maize Varieties, and Teosinte: Implications for Transgenic Maize. JA Serratos, MC Willcox, F. Castillo (eds). CIMMYT, México, D. F. pp, 40-43. [7] Evans, M., Kermicle, J. Teosinte crossing barrier1, a locus governing hybridization of teosinte with maize. Theor Appl Genet 103, 259–265 (2001). https://doi.org/10.1007/s001220100549
[8] Chen, Z., Zhang, Z., Zhang, H. et al. A pair of non-Mendelian genes at the Ga2 locus confer unilateral cross-incompatibility in maize. Nat Commun 13, 1993 (2022). https://doi.org/10.1038/s41467-022-29729-z
[9] Wang, Y., Li, W., Wang, L. et al. Three types of genes underlying the Gametophyte factor1 locus cause unilateral cross incompatibility in maize. Nat Commun 13, 4498 (2022). https://doi.org/10.1038/s41467- 022-32180-9
[10] Rushworth, C. A., Wardlaw, A. M., Ross-Ibarra, J., & Brandvain, Y. 2022. Conflict over fertilization underlies the transient evolution of reinforcement. PLoS biology, 20(10), e3001814.
[11] Berube B, Ernst E, Cahn J, Roche B, de Santis Alves C, Lynn J, Scheben A, Grimanelli D, Siepel A, Ross-Ibarra J, Kermicle J, Martienssen RA. Teosinte Pollen Drive guides maize diversification and domestication by RNAi. Nature. 2024 Sep;633(8029):380-388. doi: 10.1038/s41586-024-07788-0.
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