Browsing by Person "Stetter, Markus"

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Speciation and domestication genomics of Amaranthus spp.
(2017) Stetter, Markus; Schmid, Karl J.
The genus Amaranthus consists of 50 to 70 species, including several cultivated and weedy species. The seeds of the three grain amaranth species, A. caudatus, A. cruentus and A. hypochondriacus have a high nutritional value and are gluten free. In this work, three main aspects of amaranth genetics are studied, because previous work was limited to few species and few genetic markers: First, the evolutionary relationship between species in the genus; second, the domestication syndrome of South American grain amaranth; and third, crossing methods and controlled growth conditions for amaranth breeding. The genus has been taxonomically split into three subgenera, A. Amaranthus, A. Albersia and A. Acnida. Together with their two relatives A. hybridus and A. quitensis, the three grain amaranths form the Hybridus complex within the A. Amaranthus subgenus. We used genotyping by sequencing (GBS) of 94 genebank accessions, representing 35 species to infer the phylogeny of Amaranthus. SNPs were called using de novo and reference genome based methods and genome sizes of the species were measured using flow cytometry. The analysis of genome size evolution within the genus revealed that with the exception of two lineages polyploidization played a minor role in the history of the genus. A distancebased neighbor joining tree of individual accessions and a species tree based on the multispecies coalescent were constructed. Both phylogenies supported the previous taxonomic classification into three subgenera, but split the A. Acnida subgenus into two distant groups. Analyzing the Hybridus complex gave insights into the domestication history of grain amaranth. The complex was well separated from the other species in the A. Amaranthus subgenus and included the three grain amaranth species and their wild relatives. Individuals within the Hybridus complex did not cluster by species, but rather by their geographic origin from South and Central America. Geographically separated lineages of A. hybridus appeared to be the common ancestor of the three cultivated grain amaranths, while A. quitensis was involved in the domestication of A. caudatus. The domestication of grain amaranth remains unclear and seems to be complex, because the domestication syndrome that differentiates crops from their wild ancestors is only weakly pronounced. Therefore, the domestication syndrome in South American grain amaranth (A. caudatus) was studied by characterizing genetic and phenotypic diversity of A. caudatus and the two potential wild relatives, A. hybridus and A. quitensis. To investigate the evolutionary relationship of A. caudatus and its potential wild ancestors, 119 amaranth accession from the Andean region were characterized using 9,485 GBS derived SNPs. Additionally, two domestication related phenotypes, seed color and seed size, were analyzed. None of the accessions of wild amaranths had white seeds, while this was the predominant seed color in A. caudatus. The seed size did not significantly differ between species, but a genetically distinct group of A. caudatus from Bolivia had significantly larger seeds than the other groups. The genetic analysis revealed a strong differentiation of A. caudatus from its wild relatives. The two relatives did not cluster according to their species assignment, but rather by their geographic origins from Peru and Ecuador. Surprisingly, A. caudatus had a higher genetic diversity than its two close relatives and shared a high proportion of polymorphisms with them, consistent with the absence of strong bottlenecks or high levels of gene flow between them. Efficient crosses are an essential tool for plant research and breeding. Three different crossing methods (open pollination, hot water emasculation and hand emasculation) were evaluated for their efficiency and validated with low cost genetic markers. We identified controlled growth conditions for amaranth that allow short generation times of only six weeks instead of six months. All three crossing methods successfully produced offspring, but with different success rates. Open pollination had the lowest (10%) and hand emasculation the highest success rate (74%). Hot water emasculation showed an intermediate success rate (26%), but high maximum of 94%. Additionally, this method is easy to perform and suitable for large-scale hybrid production. Eleven PCR-based SNP markers were found to be sufficient for intra- and interspecific hybrid identification. Despite the very small flowers, amaranth crosses can be carried out efficiently and verified with inexpensive SNP markers with short generation times under suitable conditions. The phylogeny and population genetic analysis suggest that amaranth domestication was incomplete. Gene flow from A. quitensis into A. caudatus might have prevented the fixation of domestication related alleles. The genus phylogeny and the over 200 genotyped accessions in this work provide the largest genomic resource for amaranth so far.