Universität zu Köln

Goncalves-Dias, Jose Miguel ORCID: 0000-0001-9230-6004 (2024). Uncovering and Popularizing the Genomic Mosaic of Grain Amaranth Domestication. PhD thesis, Universität zu Köln.

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Abstract

Crop evolution, especially that of amaranth, has long been thought to be a linear progression from wild to domesticated. However, amaranth's incomplete domestication and extensive cultivation history make it an excellent model for studying the complex genome dynamics of crops. This thesis aims to unravel the intricate genomic mosaic of the domestication process in five amaranth sub-species, wild and domesticated. Through population genomics and computational biology, this study investigates the genetic impact on amaranth populations, including gene flow and the potential for speciation. The primary objective of this thesis is to explore the genomic effects of post-domestication contact on five amaranth populations, both wild and domesticated, found in the Americas. The study shows that not only do amaranth crop species exchange genetic material after domestication, but contact with their wild ancestor also contributes to maintaining their genetic diversity and, consequently, evolutionary rescue. Moreover, this research creates computational tools and resources to handle and analyze the vast amount of genomic data generated. The thesis introduces PopAmaranth, a novel genome browser for population genetics. PopAmaranth provides an intuitive interface integrating various features such as selection signals, gene annotation, and variant calls, enabling interdisciplinary researchers to explore population-scale genomic data and facilitate investigations in population genomics and crop breeding. In summary, this doctoral thesis provides novel insights into the evolutionary history of amaranth, unraveling the intricate interplay between domesticated and wild populations. The research highlights the importance of computational tools like Genome Browsers in facilitating population-scale genomic analyses. These findings contribute to the field of population genomics, advancing our understanding of the genetic dynamics underlying species diversification.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Goncalves-Dias, Jose Miguel josemgdias@outlook.com orcid.org/0000-0001-9230-6004 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-732631
Date:	2024
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Botanical Institute
Subjects:	Life sciences
Uncontrolled Keywords:	Keywords Language gene flow English evolutionary rescue English genome browser English amaranth English genomics English population genomics English WGS English
Date of oral exam:	12 June 2024
Referee:	Name Academic Title Stetter, Markus G Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/73263