Domesticated materials with well-known wild relatives provide an experimental system to reveal how human selection during cultivation affects genetic composition and adaptation to novel environments. In this paper, our goal was to elucidate how two geographically distinct domestication events modified the structure and level of genetic diversity in common bean. Specifically, we analyzed the genome-wide genetic composition at 26, mostly unlinked microsatellite loci in 349 accessions of wild and domesticated common bean from the Andean and Mesoamerican gene pools. Using a model-based approach, implemented in the software STRUCTURE, we identified nine wild or domesticated populations in common bean, including four of Andean and four of Mesoamerican origins. The ninth population was the putative wild ancestor of the species, which was classified as a Mesoamerican population. A neighbor-joining analysis and a principal coordinate analysis confirmed genetic relationships among accessions and populations observed with the STRUC-TURE analysis. Geographic and genetic distances in wild populations were congruent with the exception of a few putative hybrids identified in this study, suggesting a predominant effect of isolation by distance. Domesticated common bean populations possessed lower genetic diversity, higher F ST , and generally higher linkage disequilibrium (LD) than wild populations in both gene pools; their geographic distributions were less correlated with genetic distance, probably reflecting seed-based gene flow after domestication. The LD was reduced when analyzed in separate Andean and Mesoamerican germplasm samples. The Andean domesticated race Nueva Granada had the highest F ST value and widest geographic distribution compared to other domesticated races, suggesting a very recent origin or a selection event, presumably associated with a determinate growth habit, which predominates in this race.

In order to understand the evolution of the orchid plastome, we annotated and compared 124 complete plastomes of Orchidaceae representing all the major lineages in their structures, gene contents, gene rearrangements, and IR contractions/expansions. Fortytwo of these plastomes were generated from the corresponding author's laboratory, and 24 plastomes-including nine genera (Amitostigma, Bulbophyllum, Dactylorhiza, Dipodium, Galearis, Gymnadenia, Hetaeria, Oreorchis, and Sedirea)-are new in this study. All orchid plastomes, except Aphyllorchis montana, Epipogium aphyllum, and Gastrodia elata, have a quadripartite structure consisting of a large single copy (LSC), two inverted repeats (IRs), and a small single copy (SSC) region. The IR region was completely lost in the A. montana and G. elata plastomes. The SSC is lost in the E. aphyllum plastome. The smallest plastome size was 19,047 bp, in E. roseum, and the largest plastome size was 178,131 bp, in Cypripedium formosanum. The small plastome sizes are primarily the result of gene losses associated with mycoheterotrophic habitats, while the large plastome sizes are due to the expansion of noncoding regions. The minimal number of common genes among orchid plastomes to maintain minimal plastome activity was 15, including the three subunits of rpl (14, 16, and 36), seven subunits of rps (2, 3, 4, 7, 8, 11, and 14), three subunits of rrn (5, 16, and 23), trnC-GCA, and clpP genes. Three stages of gene loss were observed among the orchid plastomes. The first was ndh gene loss, which is widespread in Apostasioideae, Vanilloideae, Cypripedioideae, and Epidendroideae, but rare in the Orchidoideae. The second stage was the loss of photosynthetic genes (atp, pet, psa, and psb) and rpo gene subunits, which are restricted to Aphyllorchis, Hetaeria, Hexalectris, and some species of Corallorhiza and Neottia. The third stage was gene loss related to prokaryotic gene expression (rpl, rps, trn, and others), which was observed in Epipogium, Gastrodia, Lecanorchis, and Rhizanthella. In addition, an intermediate stage between the second and third stage was observed in Cyrtosia (Vanilloideae). The majority of intron losses are associated with the loss of their corresponding genes. In some orchid taxa, however, introns have been lost in rpl16, rps16, and clpP(2) without their corresponding gene being lost. A total of 104 gene rearrangements were counted when comparing 116 orchid plastomes. Among them, many were concentrated near the IRa/b-SSC junction area. The plastome phylogeny of

In a common bean plant exhibiting determinate growth, the terminal shoot meristem switches from a vegetative to reproductive state, resulting in a terminal inflorescence. Contrary to this, indeterminate growth habit results in a terminal meristem that remains vegetative where it further regulates the production of lateral vegetative and reproductive growth. In the last century, breeders have selected determinate growth habit, in combination with photoperiod insensitivity, to obtain varieties with a shorter flowering period, earlier maturation and ease of mechanized harvest. Previous work has identified TFL1 as a gene controlling determinate growth habit in Arabidopsis thaliana. In this work, we have validated that the Phaseolus vulgaris candidate gene, PvTFL1y, is the functional homolog of TFL1 using three independent lines of evidence. First, in a population of ~1,500 plants, PvTFL1y was found to co-segregate with the phenotypic locus for determinate growth habit (fin) on chromosome 01. Second, using quantitative PCR, we found that two unique haplotypes associated with determinacy at the PvTFL1y locus, a 4.1-kb retrotransposon and a splice-site mutation, cause mRNA abundance to decrease 20-133 fold, consistent with the recessive nature of fin. Finally, using a functional complementation approach, through Agrobacterium-mediated transformation of determinate Arabidopsis, we rescued tfl1-1 mutants with the wild-type PvTFL1y gene. Together, these three lines of evidence lead to the conclusion that PvTFL1y is the functional homolog of the Arabidopsis gene, TFL1, and is the gene responsible for naturally occurring variation for determinacy in common bean. Further work exploring the different haplotypes at the PvTFL1y locus may lead to improved plant architecture and phenology of common bean cultivars.

Determinacy and photoperiod insensitivity are agronomically important traits, selected during or after domestication in common bean. Determinacy reduces aboveground plant biomass and accelerates and synchronizes flowering. Photoperiod insensitivity allows common bean to be grown at higher latitudes under long days. In this study, we attempted to identify Phaseolus vulgaris homologues of 12 Arabidopsis genes that are involved in meristem identity determination and the photoperiod-dependent and autonomous flowering pathways. Amplification products with homology to the original Arabidopsis gene were obtained for 8 genes, 7 of which could be mapped onto the common bean-linkage map using the BAT93 x Jalo EEP 558 and Midas x G12873 recombinant inbred populations. Three Terminal Flower 1 homologues (PvTFL1x, PvTFL1y, and PvTFL1z) were mapped to B4, B1, and B7, respectively. PvTFL1y cosegregated with the determinacy locus, fin. In addition, PvTFL1z mapped near or at a second determinacy locus on B7. A Zeitlupe homologue mapped near a quantitative trait locus (QTL) for flowering time on linkage group B9. Constans, FCA, Flowering locus D, Gigantea, and Leafy homologues did not cosegregate with currently mapped flowering time QTLs and photoperiod insensitivity loci in common bean. Further studies are needed to confirm the role of these homologues as potential candidate genes.

Mesoamerican food agriculture is defined by the milpa cropping system, consisting of maize (Zea mays L.), common bean (Phaseolus vulgaris L.), and squash (Cucurbita spp.). In recent years, a domestication center for maize has been proposed in the Balsas River basin in west‐central Mexico, raising the question whether the Balsas basin was also the center of origin for Mesoamerican food agriculture in general. We conducted a survey of genetic diversity for 26 microsatellite markers in a representative sample of 155 wild and domesticated common bean from its Mesoamerican gene pool. Microsatellite diversity was analyzed with STRUCTURE, neighbor‐joining tree construction, and principal coordinate analysis. Most Mesoamerican domesticated accessions clustered in a single group, suggesting a single domestication. Furthermore, the most closely related wild beans to the domesticated clade originated from a restricted region in the Rio Lerma–Rio Grande de Santiago basin in west‐central Mexico, distinct from the Balsas basin. Although wild maize and Phaseolus beans grow together in the wild, they appear to have been domesticated in different regions to be reunited later on in a single cropping system. Crop domestications in Mesoamerica may therefore have a diffuse rather than a single geographic origin. Archaeological and ecological investigations into the origins of agriculture should be refocused from the arid eastern half of Mexico to the west‐central part of the country.

Although each of the determinacy haplotypes probably does not represent distinct domestication events, they are consistent with the multiple (seven) domestication pattern in the genus Phaseolus. The predominance of determinacy in the Andean gene pool may reflect domestication of common bean prior to maize introduction in the Andes.

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single‐copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian‐western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

Pod dehiscence (PD) prior to harvest results in serious yield loss in soybean. Two linkage maps with simple sequence repeat (SSR) markers were independently constructed using recombinant inbred lines (RILs) developed from Keunolkong (pod-dehiscent) £ Sinpaldalkong (pod-indehiscent) and Keunolkong £ Iksan 10 (pod-indehiscent). These soybean RIL populations were used to identify quantitative trait loci (QTLs) conditioning resistance to PD. While a single major QTL on linkage group (LG) J explained 46% of phenotypic variation in PD in the Keunolkong £ Sinpaldalkong population with four minor QTLs, three minor QTLs were identiWed in the Keunolkong £ Iksan 10 population. Although these two populations share the pod dehiscent parent, no common QTL has been identiWed. In addition, epistatic interactions among three marker loci partially explained phenotypic variation in PD in both populations. The result of this study indicates that diVerent breeding strategies will be required for PD depending on genetic background.