Phaseolin-protein Variability in Wild Forms and Landraces of the Common Bean(Phaseolus vulgaris): Evidence for Multiple Centers of Domestication

A sample of 106 wild forms and 99 landraces of common bean (Thaseolus vulgaris) from Middle America and the Andean region of South America were screened for variability in phaseolin seed protein using one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS/PAGE) and two-dimensional isoelectric focusing SDS/PAGE. The Middle American wild forms exhibited phaseolin patterns similar to the ‘S’ pattern described previously in cultivated forms, as well as a wide variety of additional banding patterns—‘M’ (Middle America) types—not encountered among common bean cultivars. The Andean wild forms showed only the ‘T’ phaseolin pattern, also described previously among cultivated forms. Landraces from Middle America showed ‘S’ or ‘S’-like patterns with the exception of 2 lines with ‘T’ phaseolin. In Andean South America, a majority of landraces had the ‘T’ phaseolin. Additional types represented in that region were (in decreasing order of frequency) the ‘S’ and ‘C’ types (already described among cultivated forms) as well as the ‘H’ (Huevo de huanchaco) and ‘A’ (Ayacucho), (new patterns previously undescribed among wild and cultivated beans). In each region—Middle America and Andean South America—the seeds of landraces with ‘T’ phaseolin were significantly larger than those of landraces with ‘S’ phaseolin. No significant differences in seed size were observed among landraces with ‘T,’ ‘C,’ ‘H,’ and ‘A’ phaseolin types of the Andean region. Our data favor 2 primary areas of domestication, one in Middle America leading to small-seeded cultivars with ‘S’ phaseolin patterns and the other in the Andes giving rise to large-seeded cultivars with ‘T’ (and possibly ‘C,’ ‘H,’ and ‘A’) phaseolin patterns.     

Mitochondrial restriction fragment length polymorphisms in wild Phaseolus vulgaris L.: insights on the domestication of the common bean

Summary Previous examination of intraspecific mitochondrial DNA (mtDNA) diversity in common bean, Phaseolus vulgaris, showed that five restriction fragment length polymorphisms (RFLPs) distinguish the mitochondrial genomes of the two major gene pools of cultivated beans, the Mesoamerican and the Andean. In the study presented here, mtDNA was used to compare the amount of diversity in cultivated beans to that in collections of wild beans to gain an understanding of how and when the mitochondrial genomes of the gene pools became distinct. The mtDNA of six wild bean accessions from Central and South America were digested with nine restriction endonucleases and analyzed by Southern hybridization. A total of twenty RFLPs were detected demonstrating a significantly higher amount of mtDNA variability in wild beans than in cultivated ones. All of the wild beans had the same mtDNA pattern for four out of the five inter-gene pool RFLPs, indicating that the polymorphism arose soon after domestication: two in the gene pool of the cultivated Mesoamerican beans and two in the gene pool of the cultivated Andean beans. The fifth RFLP must have occurred before domestication since the locus was also polymorphic in the wild beans. Wild beans from the south Andes were distinct and less variable than wild accessions of the north Andes and Mesoamerica. The distribution of mtDNA RFLPs among the wild beans supports the concept of two distinct domestication events for P. vulgaris.     

Observations on the origin of phaseolus polyanthus Greenman

Total seed protein variability in a sample of 163 entries of year-bean (Phaseolus polyanthus), including wild, feral and cultivated forms of the whole range of distribution in Latin America was studied using I-dimensional SDS/PAGE and 2-dimensional IEF-SDS/PAGE. Ten different patterns were observed in this crop. Eight of these are found in the Mesoamerican materials, the other two of those in the northern Andes. The highest diversity is found in the wild ancestral forms present in central Guatemala with six patterns. The ‘b’pattern predominant in all Mesoamerican cultivated materials is also present at low frequency in Colombia. The ‘k’ pattern, predominant in the northern Andes, is present in Costa Rica. These results together with information on indigenous names for the crop suggest that there is a single gene pool domesticated from a wild ancestor still present in Guatemala, and distributed afterwards to the northern Andes, but with a clinal genetic drift from Mesoamerica to the Andean region.     

Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines

The wild grapevine, Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain, natural populations of V. vinifera ssp. sylvestris can still be found along river banks. In this work, we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analysed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated germplasm and wild germplasm are genetically divergent with low level of introgression. Using a model‐based approach implemented in the software structure , we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships between wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current Western cultivars.     

Arbitrarily primed-PCR based diversity assessment reflects hierarchical groupings of Indian tetraploid wheat genotypes

Genetic diversity analysis using PCR with arbitrary decamer primers (RAPD — random amplified polymorphic DNA) was carried out in a set of 63 tetraploid wheat genotypes which comprised 24 durum landraces, 18 durum cultivars, nine dicoccum cultivars, ten less commonly cultivated species and two wild tetraploid species. The durum and dicoccum wheat genotypes are a part of the germplasm used in Indian tetraploid wheat breeding programs. A total of 206 amplification products were obtained with 21 informative primers, of which 162 were polymorphic. The highest degree of polymorphism was seen in the wild and less commonly cultivated species (68.9%). Durum released cultivars showed greater polymorphism (50.6%) than landraces (44.8%), while dicoccum cultivars showed a considerably low level of polymorphism (23.6%). Cluster analysis led to the separation of wild and cultivated genotypes, and among cultivated emmer wheat distinct groups were formed by the durum cultivars, durum landraces and dicoccum cultivars. The subgroupings of landraces had no relation to their geographical distribution. The durum cultivars formed subgroups based on common parentage in their pedigree. Among species, wild timopheevi wheat (T. araraticum) and its cultivated form (T. timopheevi) formed a distinct group distant from all other genotypes. The present study is a first attempt at determining the genetic variation in Indian tetraploid wheats at the molecular level. Received: 10 January 1999 / Accepted: 30 January 1999     

Wild grapevine: silvestris,hybrids or cultivars that escaped from vineyards? Molecular evidence in Sardinia

Vitis vinifera ssp. silvestris, the spontaneous subspecies of V. vinifera L., is believed to be the ancestor of present grapevine cultivars. In this work, polymorphism at 13 SSR loci was investigated to answer the following key question: are wild plants (i) true silvestris, (ii) hybrids between wild and cultivated plants or (iii) or ‘escapes’ from vineyards? In particular, the objective of the present study was to identify truly wild individuals and to search for possible hybridization events. The study was performed in Sardinia, the second largest island in the Mediterranean Sea, which is characterized by a large and well‐described number of both grape cultivars and wild populations. This region was ideal for the study because of its spatial isolation and, consequently, limited contamination from outside material. The results of this study show that domesticated and wild grapevine germplasms are genetically divergent and thus are real silvestris. Pure lineages (both domesticated and wild) show very high average posterior probabilities of assignment to their own clusters, with a low level of introgression.     

RFLP diversity of common bean (Phaseolus vulgaris) in its centres of origin.

Eighty-five wild and cultivated accessions of common bean (Phaseolus vulgaris L.), representing a wide geographic area in the centres of domestication were tested for restriction fragment length polymorphisms (RFLPs). Genomic DNA was digested with one of three restriction enzymes (EcoRI, EcoRV, and HindIII) and hybridized to 12 probes distributed throughout the common bean genome. Accessions could be classified into two major groups with a distinct geographical distribution in Middle America and the Andes. Within each gene pool, cultivated accessions clustered together with wild forms from the same geographical area supporting the multiple domestications hypothesis for this crop. Estimates of Nei's genetic distances among the cultivated races from the two different gene pools varied from 0.12 to 0.56 and among races from the same gene pool from 0.04 to 0.12, suggesting that the divergence in Phaseolus vulgaris has reached the subspecies level. The level of genetic diversity (Ht = 0.38) was twice the value obtained with isozyme analysis. Genetic diversity within races (Hs = 0.27) was four to five times higher compared with isozymes, but genetic diversity between races (Dst = 0.11) was similar for both categories of markers. These results corroborate previous studies on the characterization of genetic diversity in common bean that clearly showed two distinct gene pools, Middle American and Andean. Moreover, RFLP markers are superior to isozymes because they provide better coverage of the genome and reveal higher level of polymorphisms.     

Application of High-Throughput Sequencing to Evaluate the Genetic Diversity Among Wild Apple Species Indigenous to Shandong,China, and Introduced Cultivars

The Taiyi mountainous region of Shandong province in eastern China has an abundance of wild Malus species. We evaluated the genetic diversity of 88 Malus accessions (45 Asian apple cultivars, 10 American apple cultivars, 12 European apple cultivars, 19 Chinese wild apples, and two apple cultivars with unknown origins) based on single-nucleotide polymorphism (SNP) markers. A total of 38,364 SNPs were obtained with an average of 2256 SNPs per chromosome. The average of the polymorphism information content (PIC), gene diversity, and allele frequency for SNPs was 0.268, 0.306, and 0.364, respectively. A circular phylogenetic tree constructed based on SNP data revealed that the 88 Malus accessions could be divided into three groups. However, a population structure analysis suggested the 88 Malus accessions could be divided into four groups. A principal component analysis (PCA) revealed some population stratification. The first three PCs accounted for 41.62% of the population-wide SNP variation, with PC1 accounting for 33.9%. Moreover, the kinship values of the 88 Malus accessions ranged from 0 to 2.36, with 96.42% of the kinship values between 0 and 0.2. A phylogenetic tree and a PCA indicated the Chinese wild apples widely distributed among the cultivated apples had a diverse genetic background. Characterizing the genetic relationships between cultivated apples and Chinese wild apples is essential for increasing the genetic diversity of the germplasms used by apple breeders.

     

Genetic diversity and relationships detected by isozyme and RAPD analysis of crop and wild species of Amaranthus

 Genetic diversity and relationships of 23 cultivated and wild Amaranthus species were examined using both isozyme and RAPD markers. A total of 30 loci encoding 15 enzymes were resolved, and all were polymorphic at the interspecific level. High levels of inter-accessional genetic diversity were found within species, but genetic uniformity was observed within most accessions. In the cultivated grain amaranths (A. caudatus, A. cruentus, and A. hypochondriacus), the mean value of H_T was 0.094, H_S was 0.003, and G_ST was 0.977 at the species level. The corresponding values in their putative wild progenitors (A. hybridus, A. powellii, and A. quitensis) were 0.135, 0.004, and 0.963, respectively. More than 600 RAPD fragments were generated with 27 arbitrary 10-base primers. On average, 39.9% of the RAPD fragments were polymorphic among accessions within each crop species; a similar level of polymorphism (42.8%) was present in the putative progenitors, but much higher levels of polymorphism were found in vegetable (51%) and other wild species (69.5%). The evolutionary relationships between grain amaranths and their putative ancestors were investigated, and both the RAPD and isozyme data sets supported a monophyletic origin of grain amaranths, with A. hybridus as the common ancestor. A complementary approach using information from both isozymes and RAPDs was shown to generate more accurate estimates of genetic diversity, and of relationships within and among crop species and their wild relatives, than either data set alone. Received: 13 March 1997/Accepted: 6 May 1997     

Genetic diversity and ecological distribution ofPhaseolus vulgaris (Fabaceae) in northwestern South America

Our goal was to investigate in more detail wild and cultivated common bean (Phaseolus vulgaris) accessions from northwestern South America (Colombia, Ecuador, and northern Peru) because prior research had shown this region to be the meeting place of the two major gene pools (Middle American and Andean) of common bean. Explorations were conducted in these countries to collect additional materials not represented in germplasm collections. It was possible to identify wild common bean populations in Ecuador and northern Peru, where they had never been described before. In addition, we were able to extend the distribution of wild common bean in Colombia beyond what was known prior to this study. In all areas, the wild common bean habitat had suffered severely from destruction of natural vegetation. In Colombia, wild common beans were found on the Eastern slope of the Andes (in continuation of its distribution in Venezuela), whereas in Ecuador and northern Peru they were found on the western slope of this mountain range. This geographic distribution was correlated with an ecological distribution in relatively dry environments with intermediate temperatures (known as “dry mountain forest”). Isozyme andphaseolin seed protein analyses of the northern Peruvian and Ecuadoran wild populations showed that they were intermediate between the Middle American and Andean gene pools of the species. Phaseolin analyses conducted on landraces of the Upper Magdalena Valley in Colombia showed that Andean domesticates were grown at a higher altitude than Middle American domesticates suggesting that the former are adapted to cooler temperatures. Our observations and results have the following consequences for the understanding and conservation of genetic diversity in common bean and other crops: 1) Our understanding of the distribution of the wild relative of common bean (and other crops) is imperfect and further explorations are needed to more precisely identify and rescue wild ancestral populations; 2) For crops for which the wild ancestor has not yet been identified, it may be worthwhile to conduct additional explorations in conjunction with genetic diversity studies at the molecular level to guide the explorations; 3) Our study shows the benefit for more efficient germplasm conservation which can be derived from the dynamic interplay between field explorations (and other conservation operations) and molecular analyses to determine genetic distances and diversities; 4) The intermediate materials identified in northern Peru and Ecuador may have basic importance to understand the origin of the common bean and an applied role as a bridge between the Middle American and Andean gene pools; and 5) The differential adaptation to temperature of the two major cultivated gene pools may help breeders select genotypes based at least partially on their evolutionary origin.     

Structured diversity in octoploid strawberry cultivars: importance of the old European germplasm

Understanding genetic structure and diversity information is critical for genetic association studies. In the octoploid cultivated strawberry (Fragaria×ananassa), genetic analyses were focussed on diversity, whereas genetic structure has been poorly explored. This study investigated the genetic structure in a genetic resources collection representing a wide range of the octoploid strawberry cultivars released mainly by North America and western and southern Europe, at different breeding periods and with various pedigrees. The relationship between varieties was examined using 23 microsatellite (simple sequence repeat, SSR) markers. Eight SSR markers were diploid, useful for cultivar discrimination with polymorphic information content (PIC) values between 0.29 and 0.74. Bayesian analyses of genetic structure identified four subpopulations. Three of them, American and modern northern European cultivars (AMNECs), American and modern southern European cultivars (AMSECs) and old European cultivars (OECs), reflected the European breeding history of the cultivated octoploid strawberry. The fourth subpopulation, ‘Intermediate’ group cultivars (IGCs), comprised various origins including OECs that were introgressed with wild species such as Fragaria chiloensis or Fragaria moschata. The OEC group gathered cultivars dating before 1960s, forming the most homogenous and stable subpopulation. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on modified Nei and Li distance confirmed the separation of the AMSEC, AMNEC and OEC groups. In addition, significant differences were observed among the four subpopulations (AMNEC, AMSEC, OEC, IGC), with high variability within groups and between AMSEC and IGC. Our work underlined that the structure within the studied collection was mainly explained by the pedigree and the year of release than the geographical origin of cultivars. In addition, the important loss of diversity observed in the modern European cultivars and a trend towards using mainly American cultivars for breeding programmes led to the progressive abandonment of old European germplasm, which was revealed as a relative distinct and rich group. This European material should be protected and maintained, because it represents a potential source of original traits for broadening the genetic base of cultivated strawberry. In addition, diploid markers we identified can be used without ambiguity in phylogenetic and diversity studies, because they are genome‐specific. This study is the first step for further association studies in strawberry.     

Dissemination pathways of common bean (Phaseolus vulgaris,Fabaceae) deduced from phaseolin electrophoretic variability. I. The Americas

Dissemination pathways of common bean (Phaseolus vulgaris) cultivars from their areas of domestication to other parts of the Americas were determined using phaseolin type, as determined by 1-dimensional SDS/PAGE. Common bean cultivars of lowland South America exhibited approximately equal numbers of ‘S’ and ‘T’ phaseolin types. ‘S2019 cultivars of that region may have been introduced along a route starting in Middle America and leading into Colombia, Venezuela, and eventually Brazil. ‘T’ phaseolin cultivars in lowland South America may have been introduced directly from the Andes or indirectly by European immigrants. In the southwestern U.S.A., most of the cultivars showed an ‘S’ phaseolin, confirming the Middle American origin of these cultivars, as suggested previously by the archaeological record. In northeastern U.S.A. and Canada, the ‘T’and ‘C’ phaseolin types were more frequent than the ‘S’ phaseolin cultivars. While most of the former were possibly introduced into that region by European immigrants, most of the latter may have been introduced by the pre-Columbian Indian populations. Seed size analysis revealed that ‘T’ or ‘C’ phaseolin cultivars had significantly larger seeds than ‘S’ phaseolin cultivars, as had been observed previously in Middle America and the Andes. The phaseolin types of commercial seed types and of early northeastern U.S. cultivars are discussed.     

Origins and Domestication of Cultivated Banana Inferred from Chloroplast and Nuclear Genes

Background

Cultivated bananas are large, vegetatively-propagated members of the genus Musa. More than 1,000 cultivars are grown worldwide and they are major economic and food resources in numerous developing countries. It has been suggested that cultivated bananas originated from the islands of Southeast Asia (ISEA) and have been developed through complex geodomestication pathways. However, the maternal and parental donors of most cultivars are unknown, and the pattern of nucleotide diversity in domesticated banana has not been fully resolved.

Methodology/Principal Findings

We studied the genetics of 16 cultivated and 18 wild Musa accessions using two single-copy nuclear (granule-bound starch synthase I, GBSS I, also known as Waxy, and alcohol dehydrogenase 1, Adh1) and two chloroplast (maturase K, matK, and the trnL-F gene cluster) genes. The results of phylogenetic analyses showed that all A-genome haplotypes of cultivated bananas were grouped together with those of ISEA subspecies of M. acuminata (A-genome). Similarly, the B- and S-genome haplotypes of cultivated bananas clustered with the wild species M. balbisiana (B-genome) and M. schizocarpa (S-genome), respectively. Notably, it has been shown that distinct haplotypes of each cultivar (A-genome group) were nested together to different ISEA subspecies M. acuminata. Analyses of nucleotide polymorphism in the Waxy and Adh1 genes revealed that, in comparison to the wild relatives, cultivated banana exhibited slightly lower nucleotide diversity both across all sites and specifically at silent sites. However, dramatically reduced nucleotide diversity was found at nonsynonymous sites for cultivated bananas.

Conclusions/Significance

Our study not only confirmed the origin of cultivated banana as arising from multiple intra- and inter-specific hybridization events, but also showed that cultivated banana may have not suffered a severe genetic bottleneck during the domestication process. Importantly, our findings suggested that multiple maternal origins and a reduction in nucleotide diversity at nonsynonymous sites are general attributes of cultivated bananas.     

AFLP based assessment of genetic relationships among shiitake (<Emphasis Type="Italic">Lentinula</Emphasis> ssp.) mushrooms

Despite the economical importance of shiitake (Lentinula ssp.) mushrooms, until the present date little information exists on cultivated and wild species in correlation with geographic origin applying molecular techniques. Use of a high resolution molecular tool like AFLP for assessing genetic similarity and geographical diversity would be an important step towards understanding of different Lentinula species. Thirteen wild and 17 cultivated accessions of 3 Lentinula species were analysed with 64 EcoRI–MseI primer combinations and finally 32 reproducible and polymorphic primer combinations were considered for the analysis. A total of 816 informative AFLP markers were generated and scored as binary data. These data were analysed using various method packages for cluster analysis, genetic diversity and genetic differentiation. Percentage polymorphism was high (62.99%) among the species studied. Different clustering analysis segregated the wild and the cultivated species into two major branches, with the wild samples being further grouped according to their geographic location. Overall polymorphisms among cultivated strains in the USA were higher than that of the cultivated strains in Japan (58.9%).     

Phylogeny and origin of pearl millet (Pennisetum glaucum [L.] R. Br) as revealed by microsatellite loci

During the last 12,000 years, different cultures around the world have domesticated cereal crops. Several studies investigated the evolutionary history and domestication of cereals such as wheat in the Middle East, rice in Asia or maize in America. The domestication process in Africa has led to the emergence of important cereal crops like pearl millet in Sahelian Africa. In this study, we used 27 microsatellite loci to analyze 84 wild accessions and 355 cultivated accessions originating from the whole pearl millet distribution area in Africa and Asia. We found significantly higher diversity in the wild pearl millet group. The cultivated pearl millet sample possessed 81% of the alleles and 83% of the genetic diversity of the wild pearl millet sample. Using Bayesian approaches, we identified intermediate genotypes between the cultivated and wild groups. We then analyzed the phylogenetic relationship among accessions not showing introgression and found that a monophyletic origin of cultivated pearl millet in West Africa is the most likely scenario supported by our data set.     

Simple sequence repeat diversity in diploid and tetraploid Coffea species.

Thirty-four fluorescently labeled microsatellite markers were used to assess genetic diversity in a set of 30 Coffea accessions from the CENICAFE germplasm bank in Colombia. The plant material included one sample per accession of seven East African accessions representing five diploid species and 23 wild and cultivated tetraploid accessions of Coffea arabica from Africa, Indonesia, and South America. More allelic diversity was detected among the five diploid species than among the 23 tetraploid genotypes. The diploid species averaged 3.6 alleles/locus and had an average polymorphism information content (PIC) value of 0.6, whereas the wild tetraploids averaged 2.5 alleles/locus and had an average PIC value of 0.3 and the cultivated tetraploids (C. arabica cultivars) averaged 1.9 alleles/locus and had an average PIC value of 0.22. Fifty-five percent of the alleles found in the wild tetraploids were not shared with cultivated C. arabica genotypes, supporting the idea that the wild tetraploid ancestors from Ethiopia could be used productively as a source of novel genetic variation to expand the gene pool of elite C. arabica germplasm.     

Horticulture,hybrid cultivars and exotic plant invasion: a case study of Wisteria (Fabaceae)

Exotic Wisteria species are highly favoured for their horticultural qualities and have been cultivated in North America since the early 1800s. This study determines the identity, genetic diversity and hybrid status of 25 Asian Wisteria cultivars using plastid, mitochondrial and nuclear DNA data. Fifteen (60%) hybrid cultivars were identified. All of the ‘Wisteria sinensis’ cultivars sampled are hybrids with W. floribunda. Although W. sinensis and W. floribunda are recognized invasive species in the southeastern USA, the relationships of horticultural cultivars to naturalized plants was previously unknown. Haplotype analysis of nuclear data identifies four haplotypes shared between cultivated stock and naturalized populations in the southeastern USA. In addition, US invasive haplotypes are present in New Zealand‐derived cultivars although, to date, naturalized Wisteria has not been documented in New Zealand. Finally, these data are used to make recommendations to horticulturalists of select species cultivars which may be less likely to invade US landscapes. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158 , 593–601.     

Small-spored Alternaria spp. (section Alternaria) are common pathogens on wild tomato species

The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are, to some degree, all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus. On tomatoes, several species cause early blight, leaf spots and other diseases. We collected Alternaria-like infection lesions from the leaves of eight wild tomato species from Chile and Peru. Using molecular barcoding markers, we characterized the pathogens. The infection lesions were caused predominantly by small-spored species of Alternaria of the section Alternaria, like A. alternata, but also by Stemphylium spp., Alternaria spp. from the section Ulocladioides and other related species. Morphological observations and an infection assay confirmed this. Comparative genetic diversity analyses show a larger diversity in this wild system than in studies of cultivated Solanum species. As A. alternata has been reported to be an increasing problem in cultivated tomatoes, investigating the evolutionary potential of this pathogen is not only interesting to scientists studying wild plant pathosystems. It could also inform crop protection and breeding programs to be aware of potential epidemics caused by species still confined to South America.     

Evolutionary Genomics of Weedy Rice in the USA

Red rice is an interfertiie, weedy form of cultivated rice (Oryza sativa L.) that competes aggressively with the cropin the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America andthe weed has been proposed to have evolved through multiple mechanisms, including "de-domestication" of UScrop cultivars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedyOryza strains. The phenotype of US red rice ranges from "crop mimics", which share some domestication traitswith the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity haveindicated that many weed strains are closely related to Asian taxa (including indica and aus rice varieties, whichhave never been cultivated in the US, and the Asian crop progenitor O. rufipogon), whereas others show geneticsimilarity to the tropical japonica varieties cultivated in the southern US. Herein, we review what is known aboutthe evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to furthercharacterize the evolutionary genomics of this aggressive weed.     

Evolutionary Genomics of Weedy Rice in the USA

Red rice Is an Interfertlle, weedy form of cultivated rice （Oryza sativa L.） that competes aggressively with the crop In the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America and the weed has been proposed to have evolved through multiple mechanisms, Including ＂de-domestication＂ of US crop cultlvars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedy Oryza strains. The phenotype of US red rice ranges from ＂crop mimics＂, which share some domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have Indicated that many weed strains are closely related to Asian taxa （Including indica and aus rice varieties, which have never been cultivated In the US, and the Asian crop progenitor O. ruflpogon）, whereas others show genetic similarity to the tropical Japonica varieties cultivated In the southern US. Herein, we review what Is known about the evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to further characterize the evolutionary genomlcs of this aggressive weed.