Convergent seed color adaptation during repeated domestication of an ancient new world grain

Abstract

Out of the almost 2,000 plants that have been selected as crops, only a few are fully domesticated, and many intermediates between wild plants and domesticates exist. Genetic constraints might be the reason why incompletely domesticated plants have few characteristic crop traits, and retained numerous wild plant features. Here, we investigate the incomplete domestication of an ancient grain from the Americas, amaranth. We sequenced 121 genomes of the crop and its wild ancestors to show that grain amaranth has been selected three times independently from a single wild ancestor, but has not been fully domesticated. While only few domestication traits have been adapted during amaranth domestication, the seed color converted from dark seeds to white seeds between the ancestor and the crops. To investigate the seed color adaptation in amaranth we produced a mapping population between wild and domesticated amaranth, a whole genome sequenced bulked segregant population and perform genome wide association mapping in our divers panel. All three methods agree on two quantitative trait loci controlling the trait. We identify a MYB-like transcription factor gene, a known regulator for seed color variation in other plant species, within one of the significant regions and shows that the trait was independently converted in Central and South America. We propose that a low effective population size at the time of domestication might have contributed to the lack of adaptation of complex domestication traits. Our results show how genetic constraints influenced domestication and might have set the fate of hundreds of crops. SignificanceEarly farmers cultivated hundreds of plant species and altered their morphological and physiological characteristics during domestication to be well suited for human consumption. Despite long cultivation histories, many crops remained of minor importance, because they were limited in their adaptation to agro-ecological systems. We investigate the domestication history of the ancient minor crop amaranth and show that it was independently domesticated three times from the same ancestor. In all three domesticates, white seed color, which is controlled by only two genes, was independently selected. In contrast, more complex domestication traits like seed size were not changed during domestication, and our analyses suggest that this may have resulted from a lack of functional genetic variation in the ancestor during domestication.

Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus

“…1 B and C ). Genetic differentiation (F ST ) between individuals with ancestry homogenous for different lineages at K = 2 was 0.212, on par with or greater than that between other congeners (30). Moreover, both longitude and latitude significantly explained both PC1 and PC2 of the SNP matrix ( SI Appendix , Table S2), with PC1 separating var.…”

Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus

“…1B,C). Genetic differentiation (F ST ) between individuals with ancestry homogenous for different lineages at K=2 was 0.212, on par with or greater than that between congeners (29). Moreover, both longitude and latitude significantly explained both PC1 and PC2 of the SNP matrix (Sup Table 2), with PC1 separating var.…”

Understanding Molecular Mechanisms of Seed Dormancy for Improved Germination in Traditional Leafy Vegetables: An Overview

“…Adebo et al [160] reported two colours for seed coat (black and brown) among Corchorus olitorius cultivars from Benin. In amaranth species, a MYB-like transcription factor gene controls the seed colour variation especially between the ancestor, which is black, and the domesticated species, which is white [161]. Most of the seed dormancy constraints observed in TLVs seeds are due to the seed coat structure.…”