Periodic Reporting for period 3 - BOSADMIX (Genetic admixture and its impact on domestication in the Bos genus: a model for genetic improvement of livestock)
Periodo di rendicontazione: 2023-02-01 al 2024-07-31
BOSADMIX aims to address the complex evolution of the Bos genus in Asia, focusing on two topics that are central in evolutionary biology: domestication and genetic admixture (or hybridization between species). What makes the Bos genus special in this regard is that genetic admixture has likely taken place between most of the nine species co-existing in southern and eastern Asia, and that domestication has happened no fewer than five times independently. This makes the Bos genus something of an evolutionary treasure trove for investigating these two important phenomena separately, but even more interestingly we can study how they may interact. For example, it is speculated that genetic variants that came into the domestic Bos populations from mixing with wild Bos species may in some cases have been beneficial, either naturally or through being co-opted by human artificial selection to change the form and function of their livestock. In BOSADMIX we study these two processes and their interaction by sequencing and analyzing whole genome data from all of the Asian Bos species. We are interested in answering:
- When, where and between which populations admixture took place.
- Whether some of the incoming genetic variants were beneficial.
- What made them beneficial, i.e. which aspect of the livestock populations did they improve.
- How we should conserve the maximum amount of potentially useful genetic variation that is segregating in wild Bos.
By addressing these questions, the project will provide fundamental new insights into how wild species have historically contributed to the genetic makeup of domesticated Bos and bring together two important areas of evolutionary biology research, namely domestication and genetic admixture. It will also shed light on the potential value of genetic variants segregating in wild species that may be beneficial for genetic enrichment of domestic species.
- When, where and between which populations admixture took place.
- Whether some of the incoming genetic variants were beneficial.
- What made them beneficial, i.e. which aspect of the livestock populations did they improve.
- How we should conserve the maximum amount of potentially useful genetic variation that is segregating in wild Bos.
By addressing these questions, the project will provide fundamental new insights into how wild species have historically contributed to the genetic makeup of domesticated Bos and bring together two important areas of evolutionary biology research, namely domestication and genetic admixture. It will also shed light on the potential value of genetic variants segregating in wild species that may be beneficial for genetic enrichment of domestic species.
Covid19 has delayed some aspects of the project and forced us to adapt to the new situation. Specifically, we have not been able to sequence as many samples as we planned. We therefore progressed by first optimizing some of the bioinformatics and population genetics methods and pipelines we would need for the Bos data, using a different whole-genome data set available to us as training data. In addition, we have managed to secure and analyze whole-genome data from a large set of cattle from around the World and domesticated banteng (also known as Bali cattle), as well as from a small number of wild Bos individuals. We have analyzed these data using the pipelines mentioned above and found surprisingly large amounts of introgression from banteng into the domestic cattle breeds. Following this finding we have worked on identifying regions of the genome that have exceptionally high proportions of banteng ancestry in the breeds that have experienced introgression, as these are candidates of adaptive introgression, or introgressed regions that have been co-opted by selection in the receiving cattle populations. This is a very important part of what BOSADMIX aims to achieve. We are currently working to understand the types of selection acting on regions introgressed from banteng into cattle, and the historical details such as time and place of admixture.
Moreover, we have managed to get access to a set of museum samples, which we have DNA extracted and sequenced. These represent a wide geographical range of both banteng and gaur, the two wild Bos species that are most severely lacking in existing genome data. These samples will be most valuable in a broader analysis of where and when admixture has occurred between different Bos species, which introgressed elements have been retained in recipient populations and what their functions are.
Moreover, we have managed to get access to a set of museum samples, which we have DNA extracted and sequenced. These represent a wide geographical range of both banteng and gaur, the two wild Bos species that are most severely lacking in existing genome data. These samples will be most valuable in a broader analysis of where and when admixture has occurred between different Bos species, which introgressed elements have been retained in recipient populations and what their functions are.
Our results so far already challenge the perception of hybridization between wild and domestic Bos populations, both by the amount of inferred introgression in some populations and also in the (preliminary) results regarding the types of selection acting on introgressed genomic elements. We are therefore very confident that BOSADMIX will provide novel insights about this important group of bovines, as well as for the fundamental principles of admixture, selection and domestication. The next phase of the project will focus on 1) inferring the functionality of introgressed genomic elements, 2) broadening out the results to more branches of the Bos tree and 3) shifting the emphasis to the conservation implications of the findings.