Brassica rapa Domestication: Untangling Wild and Feral Forms and Convergence of Crop Morphotypes.

The study of domestication contributes to our knowledge of evolution and crop genetic resources. Human selection has shaped wild Brassica rapa into diverse turnip, leafy, and oilseed crops. Despite its worldwide economic importance and potential as a model for understanding diversification under domestication, insights into the number of domestication events and initial crop(s) domesticated in B. rapa have been limited due to a lack of clarity about the wild or feral status of conspecific noncrop relatives. To address this gap and reconstruct the domestication history of B. rapa, we analyzed 68,468 genotyping-by-sequencing-derived single nucleotide polymorphisms for 416 samples in the largest diversity panel of domesticated and weedy B. rapa to date. To further understand the center of origin, we modeled the potential range of wild B. rapa during the mid-Holocene. Our analyses of genetic diversity across B. rapa morphotypes suggest that noncrop samples from the Caucasus, Siberia, and Italy may be truly wild, whereas those occurring in the Americas and much of Europe are feral. Clustering, tree-based analyses, and parameterized demographic inference further indicate that turnips were likely the first crop type domesticated, from which leafy types in East Asia and Europe were selected from distinct lineages. These findings clarify the domestication history and nature of wild crop genetic resources for B. rapa, which provides the first step toward investigating cases of possible parallel selection, the domestication and feralization syndrome, and novel germplasm for Brassica crop improvement.

Chenopodium polyploidy inferences from Salt Overly Sensitive 1 (SOS1) data.

PREMISE OF THE STUDY: Single-copy nuclear loci can provide powerful insights into polyploid evolution. Chenopodium (Amaranthaceae) is a globally distributed genus composed of approximately 50-75 species. The genus includes several polyploid species, some of which are considered noxious agricultural weeds, and a few are domesticated crops. Very little research has addressed their evolutionary origin to date. We construct a phylogeny for Chenopodium based on two introns of the single-copy nuclear locus Salt Overly Sensitive 1 (SOS1) to clarify the relationships among the genomes of the allotetraploid and allohexaploid species, and to help identify their genome donors. METHODS: Diploid species were sequenced directly, whereas homeologous sequences of polyploid genomes were first separated by plasmid-mediated cloning. Data were evaluated in maximum likelihood and Bayesian phylogenetic analyses. KEY RESULTS: Homeologous sequences of polyploid species were found in four clades, which we designate as A-D. Two distinct polyploid lineages were identified: one composed of American tetraploid species with A and B class homeologs and a second composed of Eastern Hemisphere hexaploid species with B, C, and D class homeologs. CONCLUSIONS: We infer that the two polyploid lineages arose independently and that each lineage may have originated only once. The American diploid, C. standleyanum, was identified as the closest living diploid relative of the A genome donor for American tetraploids, including domesticated C. quinoa, and is of potential importance for quinoa breeding. The east Asian diploid species, C. bryoniifolium, groups with American diploid species, which suggests a transoceanic dispersal.

Geographic differences in patterns of genetic differentiation among bitter and sweet manioc (Manihot esculenta subsp. esculenta; Euphorbiaceae).

PREMISE OF THE STUDY: Manioc (Manihot esculenta subsp. esculenta), one of the most important tropical food crops, is commonly divided according to cyanide content into two use-categories, "sweet" and "bitter." While bitter and sweet varieties are genetically differentiated at the local scale, whether this differentiation is consistent across continents is yet unknown. • METHODS: Using eight microsatellite loci, we genotyped 522 manioc samples (135 bitter and 387 sweet) from Ecuador, French Guiana, Cameroon, Gabon, Ghana, and Vanuatu. Genetic differentiation between use-categories was assessed using double principal coordinate analyses (DPCoA) with multivariate analysis of variance (MANOVA) and Jost's measure of estimated differentiation (D(est)). Genetic structure was analyzed using Bayesian clustering analysis. • KEY RESULTS: Manioc neutral genetic diversity was high in all sampled regions. Sweet and bitter manioc landraces are differentiated in South America but not in Africa. Correspondingly, bitter and sweet manioc samples share a higher proportion of neutral alleles in Africa than in South America. We also found seven clones classified by some farmers as sweet and by others as bitter. • CONCLUSIONS: Lack of differentiation in Africa is most likely due to postintroduction hybridization between bitter and sweet manioc. Inconsistent transfer from South America to Africa of ethnobotanical knowledge surrounding use-category management may contribute to increased hybridization in Africa. Investigating this issue requires more data on the variation in cyanogenesis in roots within and among manioc populations and how manioc diversity is managed on the farm.

Diversification of the American bulb-bearing Oxalis (Oxalidaceae): dispersal to North America and modification of the tristylous breeding system.

PREMISE OF THE STUDY: The American bulb-bearing Oxalis (Oxalidaceae) have diverse heterostylous breeding systems and are distributed in mountainous areas from Patagonia to the northeastern United States. To study the evolutionary processes leading to this diversity, we constructed the first molecular phylogeny for the American bulb-bearing Oxalis and used it to infer biogeographic history and breeding system evolution. METHODS: We used DNA sequence data (nuclear ribosomal internal transcribed spacer, trnL-trnL-trnF, trnT-trnL, and psbJ-petA) to infer phylogenetic history via parsimony, likelihood, and Bayesian analyses. We used Bayes Multistate to infer ancestral geographic distributions at well-supported nodes of the phylogeny. The Shimodaira-Hasegawa (SH) test distinguished among hypotheses of single or multiple transitions from South America to North America, and tristyly to distyly. KEY RESULTS: The American bulb-bearing Oxalis include sampled members of sections Ionoxalis and Pseudobulbosae and are derived from a larger clade that includes members of sections Palmatifoliae, Articulatae, and the African species. The American bulb-bearing Oxalis comprise two clades: one distributed in SE South America and the other in the Andes and North America. An SH test supports multiple dispersals to North America. Most sampled distylous species form a single clade, but at least two other independent distylous lineages are supported by the topologies and SH tests. CONCLUSIONS: Phylogenetic results suggest the American bulb-bearing Oxalis originated in southern South America, dispersed repeatedly to North America, and had multiple transitions from tristyly to distyly. This study adds to our understanding of biogeographic history and breeding system evolution and provides a foundation for more precise inferences about the study group.

Documenting domestication: the intersection of genetics and archaeology.

Domestication, a process of increasing mutual dependence between human societies and the plant and animal populations they target, has long been an area of interest in genetics and archaeology. Geneticists seek out markers of domestication in the genomes of domesticated species, both past and present day. Archaeologists examine the archaeological record for complementary markers--evidence of the human behavior patterns that cause the genetic changes associated with domestication, and the morphological changes in target species that result from them. In this article, we summarize the recent advances in genetics and archaeology in documenting plant and animal domestication, and highlight several promising areas where the complementary perspectives of both disciplines provide reciprocal illumination.

Origins of domestication and polyploidy in oca (Oxalis tuberosa; Oxalidaceae). 3. AFLP data of oca and four wild, tuber-bearing taxa.

Many crops are polyploids, and it can be challenging to untangle the often complicated history of their origins of domestication and origins of polyploidy. To complement other studies of the origins of polyploidy of the octoploid tuber crop oca (Oxalis tuberosa) that used DNA sequence data and phylogenetic methods, we here compared AFLP data for oca with four wild, tuber-bearing Oxalis taxa found in different regions of the central Andes. Results confirmed the divergence of two use-categories of cultivated oca that indigenous farmers use for different purposes, suggesting the possibility that they might have had separate origins of domestication. Despite previous results with nuclear-encoded, chloroplast-expressed glutamine synthetase suggesting that O. picchensis might be a progenitor of oca, AFLP data of this species, as well as different populations of wild, tuber-bearing Oxalis found in Lima Department, Peru, were relatively divergent from O. tuberosa. Results from all analytical methods suggested that the unnamed wild, tuber-bearing Oxalis found in Bolivia and O. chicligastensis in NW Argentina are the best candidates as the genome donors for polyploid O. tuberosa, but the results were somewhat equivocal about which of these two taxa is the more strongly supported as oca's progenitor.

Ploidy levels among species in the 'Oxalis tuberosa alliance' as inferred by flow cytometry.

The 'Oxalis tuberosa alliance' is a group of Andean Oxalis species allied to the Andean tuber crop O. tuberosa Molina (Oxalidaceae), commonly known as 'oca'. As part of a larger project studying the origins of polyploidy and domestication of cultivated oca, flow cytometry was used to survey DNA ploidy levels among Bolivian and Peruvian accessions of alliance members. In addition, this study provided a first assessment of C-values in the alliance by estimating nuclear DNA contents of these accessions using chicken erythrocytes as internal standard. Ten Bolivian accessions of cultivated O. tuberosa were confirmed to be octoploid, with a mean nuclear DNA content of approx. 3.6 pg/2C. Two Peruvian wild Oxalis species, O. phaeotricha and O. picchensis, were inferred to be tetraploid (both with approx. 1.67 pg/2C), the latter being one of the putative progenitors of O. tuberosa identified by chloroplast-expressed glutamine synthetase data in prior work. The remaining accessions (from 78 populations provisionally identified as 35 species) were DNA diploid, with nuclear DNA contents varying from 0.79 to 1.34 pg/2C.

Origins of domestication and polyploidy in oca (Oxalis Tuberosa: Oxalidaceae). 2. Chloroplast-expressed glutamine synthetase data.

In continuing study of the origins of the octoploid tuber crop oca, Oxalis tuberosa Molina, we used phylogenetic analysis of DNA sequences of the chloroplast-active (nuclear encoded) isozyme of glutamine synthetase (ncpGS) from cultivated oca, its allies in the "Oxalis tuberosa alliance," and other Andean Oxalis. Multiple ncpGS sequences found within individuals of both the cultigen and a yet unnamed wild tuber-bearing taxon of Bolivia were separated by molecular cloning, but some cloned sequences appeared to be artifacts of polymerase chain reaction (PCR) recombination and/or Taq error. Nonetheless, three classes of nonrecombinant sequences each joined a different part of the O. tuberosa alliance clade on the ncpGS gene tree. Octoploid oca shares two sequence classes with the Bolivian tuber-bearing taxon (of unknown ploidy level). Fixed heterozygosity of these two sequence classes in all ocas sampled suggests that they represent homeologous loci and that oca is allopolyploid. A third sequence class, found in eight of nine oca plants sampled, might represent a third homeologous locus, suggesting that oca may be autoallopolyploid, and is shared with another wild tuber-bearing species, tetraploid O. picchensis of southern Peru. Thus, ncpGS data identify these two taxa as the best candidates as progenitors of cultivated oca.