Allozyme variation and evolutionary relationships of grain amaranths (Amaranthus spp.)

Summary Allozyme studies in amaranth provided useful assays of genetic variation in order to verify the patterns inferred from morphological traits, for elucidating the genetic structure of landraces, and for the studies of evolutionary relationships among wild, weedy and crop species. Thirty-four populations of cultivated New World amaranths were surveyed along with 21 weedy New World populations for allozyme variation at nine electrophoretic enzyme loci. Eleven populations of cultivated amaranths from the Indian State of Uttar Pradesh and six from Nepal were also surveyed for a comparison. In the New World populations, heterozygosity was low, and different populations ranged from 0 to 44% polymorphic loci. Adjacent populations were often fixed for different alleles or had very different allele frequencies at certain loci, with no apparent geographical patterns. Diversity index H was partitioned into the intra- and interpopulation as well as the interspecific components of variability. The crop versus weed genetic distances were the largest, whereas the intra- and interpopulation components of H were about equal. Genetic structure of all three species of the New World amaranths together can be described as a collection of distinct populations, each more or less a heterogeneous collection of highly homozygous individuals. The North Indian populations showed relatively less allozyme variability with the most common alleles same as those of Mexican landraces. Alleles at several loci proved to be diagnostic of the crop and weed groups, and of the three individual crop species. Genetic distances based on pooled gene frequencies showed the three crop species to be generally more closely related inter se than they were to their putative weedy progenitor species, respectively (with the exception of the weed-crop pair A. quitensis and A. caudatus). This implies a single domestication event involving A. hybridus as the common ancestor rather than three separate domestication events. Close similarity between A. caudatus and A. quitensis might have resulted from transdomestication based on a weedy or semi-domesticated species having migrated from Meso-America to South America. This preliminary report must now be expanded by further ecogeographical, cytogenetic and population studies on new extensive collections from the areas of early domestication. Some evidence of recent introgression and/or segregation of crop-weed hybrids between A. caudatus and A. retroflexus is available in the form of rare individuals in crop populations with crop allozyme genotypes except for a single homozygous weedy allele.     

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     

Comparative Analysis of Phylogenetic Relationships of Grain Amaranths and Their Wild Relatives (Amaranthus; Amaranthaceae) Using Internal Transcribed Spacer, Amplified Fragment Length Polymorphism, and Double-Primer Fluorescent Intersimple Sequence Repeat Markers

The most economically important group of species in the genus Amaranthus is the A. hybridus species complex, including three cultivated grain amaranths, A. cruentus, A. caudatus, and A. hypochondriacus, and their putative wild progenitors, A. hybridus, A. quitensis, and A. powellii. Taxonomic confusion exists among these closely related taxa. Internal transcribed spacer (ITS) of nuclear ribosomal DNA, amplified fragment length polymorphism (AFLP), and double-primer fluorescent intersimple sequence repeat (ISSR) were employed to reexamine the taxonomic status and phylogenetic relationships of grain amaranths and their wild relatives. Low ITS divergence in these taxa resulted in poorly resolved phylogeny. However, extensive polymorphisms exist at AFLP and ISSR loci both within and among species. In phylogenetic trees based on either AFLP or ISSR or the combined data sets, nearly all intraspecific accessions can be placed in their corresponding species clades, indicating that these taxa are well-separated species. The AFLP trees share many features in common with the ISSR trees, both showing a close relationship between A. caudatus and A. quitensis, placing A. hybridus in the same clade as all grain amaranths, and indicating that A. powellii is the most divergent taxon in the A. hybridus species complex. This study has demonstrated that both AFLP and double-primer fluorescent ISSR have a great potential for generating a large number of informative characters for phylogenetic analysis of closely related species, especially when ITS diversity is insufficient.     

Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus)

The domestication syndrome comprises phenotypic changes that differentiate crops from their wild ancestors. We compared the genomic variation and phenotypic differentiation of the two putative domestication traits seed size and seed colour of the grain amaranth Amaranthus caudatus, which is an ancient crop of South America, and its two close wild relatives and putative ancestors A. hybridus and A. quitensis. Genotyping 119 accessions of the three species from the Andean region using genotyping by sequencing (GBS) resulted in 9485 SNPs that revealed a strong genetic differentiation of cultivated A. caudatus from its two relatives. A. quitensis and A. hybridus accessions did not cluster by their species assignment but formed mixed groups according to their geographic origin in Ecuador and Peru, respectively. A. caudatus had a higher genetic diversity than its close relatives and shared a high proportion of polymorphisms with their wild relatives consistent with the absence of a strong bottleneck or a high level of recent gene flow. Genome sizes and seed sizes were not significantly different between A. caudatus and its relatives, although a genetically distinct group of A. caudatus from Bolivia had significantly larger seeds. We conclude that despite a long history of human cultivation and selection for white grain colour, A. caudatus shows a weak genomic and phenotypic domestication syndrome and proposes that it is an incompletely domesticated crop species either because of weak selection or high levels of gene flow from its sympatric close undomesticated relatives that counteracted the fixation of key domestication traits.     

Low-Cot DNA sequences for fingerprinting analysis of germplasm diversity and relationships in Amaranthus

We examined genetic diversity and relationships among 24 cultivated and wild Amaranthus accessions using the total low-Cot DNA and five individual repetitive sequences as probes. These low-Cot DNA probes were obtained by the isolation of various classes of repetitive-DNA sequences, including satellites, minisatellites, microsatellites, rDNA, retrotransposon-like sequences, and other unidentified novel repetitive sequences. DNA fingerprints generated by different types of repetitive-DNA probes revealed different levels of polymorphism in the Amaranthus genomes. A repetitive sequence containing microsatellites was found to be a suitable probe for characterizing intraspecific accessions, whereas more conservative sequences (e.g. rDNA) were informative for resolving phylogenetic relationships among distantly related species.Genetic diversity, measured as restriction fragment length polymorphism (RFLP) and the similarity index at the low-Cot DNA level, was equally high among intraspecific accessions between the two species groups: grain amaranths (A. caudatus, A. cruentus, and A. hypochondriacus) and their putative wild progenitors (A. hybridus, A. powellii, and A. quitensis). At the interspecific level, however, the grain amaranth species are less divergent from each other than their wild progenitors. With the rare exceptions of certain A. caudatus accessions, grain amaranths were found to be closely related to A. hybridus. The results based on low-Cot DNA were comparable with previous RAPD and isozyme studies of the same set of species/accessions of Amaranthus, indicating that low-Cot DNA sequences are suitable probes for a fingerprinting analysis of plant germplasm diversity and for determining phylogenetic relationships. Received: 19 October 1998 / Accepted: 8 January 1999     

Evolution and improvement of cultivated amaranths

Summary This group of amaranths was studied using four domesticated species (A. hypochondriacus, A. cruentus, A. caudatus, A. caudatus var. atropurpureus and A. edulis), two ancestral weedy species (A. hybridus, A. powellii) and eight hybrids, namely A. edulis A. hypochondriacus, A. edulis X A. caudatus, A. edulis X A. caudatus var. atropurpureus, A. caudatus X A. hybridus, A. edulis X A. hybridus, A. caudatus X A. hypochondriacus, A. hybridus X A. hypochondriacus and A. powellii X A. hypochondriacus.The parents have perfectly normal meiosis and pollen and seed fertility. Except for A. powellii and A. cruentus (n = 17), the species have n = 16. However, the hybrids may be divided into three groups. The first group contains A. edulis X A. cruentus, involving parents with n = 16 and 17, which failed totally, although, under the same conditions, crosses between A. powellii (x = 17) and A hypochondriacus (n = 16) and those between species with n = 16 succeeded with ease. The second group is made up of A. edulis X A. hypochondriacus, A. caudatus X A. hypochondriacus, A. caudatus X A. hybridus, A. edulis X A. hybridus and probably also A. powellii X A. hypochondriacus. Of these, the two combinations, A. caudatus X A. hybridus and A. edulis X A. hybridus, did not proceed beyond the two-leaf stage. At pachytene, the other hybrids showed unmistakable evidence of structural hybridity, with deletions, long or short differentiated segments and inversions. Although bivalents were formed, they possessed a chiasma frequency lower than that of either parent. There was total pollen and seed sterility.The third group comprises A. edulis X A. caudatus, A. edulis X A. caudatus var. atropurpureus and A. hybridus X A. hypochondriacus, which did not show serious developmental defects, the F₁ being vigorous, with good meiotic pairing associated with a reasonable amount of differentiation in the chromosomes leading to 25– 55% fertile pollen and 49 to 66% threshable seed. In the F₂ there were 11–18% unthrifty plants, which disturb the ratios of gene combinations controlling the different characters in the two parents. Plants very near one or both parental phenotypes were recovered, and also those showing different degrees of recombination of characters. Amphidiploids from the F₁ hybrids showed the typical autoploid or segmental alloploid type of meiosis indicating that the parental chromosomes are quite homologous.In view of the present experimental evidence and possible parallel mutations in different grains and weed amaranths, it is not certain whether the cases of natural hybridization and, in particular, of introgression can be taken as evidence for or against the two hypotheses proposed by Sauer (1967) on the basis of his brilliant ecogeographical, morphological, ethnobotanical and archaeological studies of this group of amaranths.The only point that can be stated categorically is that A. caudatus has given rise to A. edulis. The dominance of the characters of A. caudatus over those of A. edulis strengthens such a view, but the latter is sufficiently differentiated morphologically and genetically to deserve independent status. A. caudatus var. atropurpureus is a fertile but unstabilized hybrid segregate between A. caudatus and A. edulis. This is borne out by its morphological, cytogenetic and breeding behaviour, and its hybrids with A. edulis, and, above all, by the recovery of plants identical with this variety from the F₂ progeny of A. edulis X A. caudatus.Whatever the origin of grain types, at present they exist only in cultivation and appear to have a long history, having been selected for large plant body, huge compound inflorescences, large number of female flowers per glomerule, small and soft bracts and pale coloured seed in a dehiscent utricle. At the same time, there has also been inadvertent selection for higher and correctly balanced amounts of protein, carbohydrate and fat.     

Taxonomical observation on the grain amaranths and new varieties of Amaranthus cruentus (Amaranthaceae)

The grain amaranths (Amaranthus hypochondriacus, A. caudatus and A. cruentus) have a long history and a unique process of domestication. They are supposedly derived from a weed progenitor. The hypothesis proposing a monophyletic origin of the grain amaranths from the close relative A. hybridus is widely favoured. The present study applied morphological and biochemical tools, and revealed a close affinity between A. hypochondriacus and A. caudatus, and a distinct divergence of A. cruentus from the others, in accordance with previous observations. Accessions of A. cruentus showed a prominent variability, especially in seed surface features, which strongly proposed a segregation of the population into two groups; one having rusty brown seeds with reticulate spermoderm and another group having greyish white seeds with rugulate spermoderm: Amaranthus cruentus var. albus var. nov. and Amaranthus cruentus var. cruentus var. nov. This introduction was well supported by cluster analysis, showing a clear delimitation of brown and greyish white seeded accession of A. cruentus.     

Absorption,translocation, and metabolism of14C-clomazone in soybean (Glycine max) and threeAmaranthus weed species

The patterns of clomazone (2-[(2-chlorophenyl) methyl-4,4-dimethyl-3-isoxazolidinone) absorption, translocation, and metabolism and their contribution to the plant selectivity of this herbicide were studied in tolerant soybean [Glycine max (L.) Merr.] andAmaranthus hybridus and in susceptibleA. retroflexus andA. lividus. Differential root absorption appeared to play a significant role in the differential response of these four plant species to clomazone. Absorption of root-applied¹⁴C-clomazone was greater by the two sensitiveAmaranthus weeds than by the tolerant soybean andA. hybri-dus. Following application of¹⁴C-clomazone to roots, most of the absorbed radioactivity was translocated to the leaves of all four species. Approximately 50% of the absorbed¹⁴C-clomazone was metabolized by all four plant species as early as 12 h after treatment. Thin layer Chromatographic (TLC) analysis of plant tissue extracts from all four species revealed the formation of two major metabolites of clomazone. These unidentified metabolites had Rf values of 0.4 and 0.8, respectively, in a butanol∶acetic acid∶water (12∶3∶5, vol/vol/vol) developing system. The Rf value of unaltered clomazone in this system was 0.95. Differential metabolism or differential rate of metabolism of clomazone was not observed in this study and did not seem to account for the tolerance of soybean andA. hybridus or the suceptibility ofA. retroflexus andA. lividus to this herbicide.     

Cutlassfishes of the genusLepidopus (Trichiuridae), with two new eastern pacific species

Three of the five known species ofLepidopus occur in the eastern Pacific.Lepidopus manis sp. nov. is described from a single specimen from the Galápagos Islands. The holotype ofL. xantusi Goode et Bean, 1895, supposedly from Cape San Lucas, Lower California, is shown to be conspecific withL. caudatus (Euphrasen, 1788). The species heretofore reported under the nameL. xantusi is described, and namedL. fitchi sp. nov. It ranges from Oregon to the Gulf of California and occurs disjunctly in southern Ecuador and northern Peru. A key to the described species ofLepidopus is given and certain morphological features ofL. caudatus are described. Geographic variability ofL. caudatus andL. fitchi is discussed.     

Domestication,phylogeny and taxonomic delimitation in underutilized grain Amaranthus (Amaranthaceae) – a status review

Many neglected, underutilized species are extremely important for food production especially in Low Income Food Deficient Countries (LIFDCs). Grain amaranth is one of such crops originated and domesticated in different parts of American continent. Lack of knowledge on taxonomy and phylogenetic relationship with other related crops, analysis of the extent and distribution of genetic diversity together with work on local and traditional knowledge, are the main constrains for genetic improvement of neglected, underutilized and crop related wild species. The phylogenetic relationship and taxonomic delimitation in genus Amaranthus are still not resolved with extreme clarity. But classification of the genus Amaranthus into three subgenera viz., Acnida, Amaranthus and Albersia, based on morphological parameters is quite acceptable. Phylogenetic analysis revealed clear separation of vegetable and grain amaranths. The derivation of grain and vegetable amaranths represent two lines of descent from weed progenitor. Amaranthus hybridus L. along with grain amaranths supposed to have formed a complex in which taxonomic problems are far from being clarified, especially because of apparent common hybridization and misapplication of nomenclature. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Cytogenetic characterization of <Emphasis Type="Italic">Amaranthus caudatus</Emphasis> L. and <Emphasis Type="Italic">Amaranthus hybridus</Emphasis> subsp<Emphasis Type="Italic">. cruentus</Emphasis> (L.) Thell.

The present study is aimed to identify genetic variability between two species of Amaranthus viz., A. caudatus and A. hybridus subsp. cruentus, two economically important species, cultivated mainly for grain production. Karyomorphological studies in Amaranthus are scarce, probably due to higher number of small sized chromosomes. Karyomorphological studies were conducted using mitotic squash preparation of young healthy root tips. Karyological parameters and karyotypic formula were established using various software programs and tabulated the karyomorphometric and asymmetry indices viz., Disparity index, Variation coefficient, Total forma percentage, Karyotype asymmetry index, Syi index, Rec index, Interchromosomal and Intrachromosomal asymmetry index and Degree of asymmetry of karyotypes. The mitotic chromosome number observed for A. caudatus was 2n = 32 with a gametic number n = 16 and A. hybridus subsp. cruentus was 2n = 34 with a gametic number n = 17. In A. caudatus the chromosome length during somatic metaphase ranged from 0.8698 to 1.7722 μm with a total length of 39.1412 μm. In A. hybridus subsp. cruentus the length of chromosome ranged from 0.7756 to 1.9421 μm with a total length of 44.9922 μm. Various karyomorphometry and asymmetry indices analyzed revealed the extend of interspecific variation and their evolutionary status.     

Biosystematics and agronomic potential of some weedy and cultivated amaranths

Summary Three weedy amaranths (Amarantkus hybridus, A. retroflexus and A. powellii) from nine California sites, three domesticated species (A. caudatus, A. hypochondriacus and A. cruentus) from the USDA plant inventory as well as other sources and a naturally-occurring crop-weed hybrid were studied for numerical taxonomy using morphological and allozyme variation data. The crop and weedy species groups were easily separated and the hybrid populations were found to be intermediate. Surprisingly, very little intraspecific variation was present. Crop, weed and hybrid amaranths were also compared for their yielding ability, harvest index, seed efficiency of grain production and protein, popping quality and other agronomic traits. Although field plot yields were similar among the three groups of species (700 Kg/ha seed without fertilizer treatment and water, ranging to 3000 Kg/ha with fertilizer applications of 170 Kg N/ha, and abundant water), the harvest index of the weedy group was much higher (25–40%) than the domesticated species (10–15%). The allocation of biomass to seed production is positively correlated with seed yield in the domesticated but not in the weedy types, whereas the percentages of biomass as stem material and as seeds are negatively correlated. Several weedy and crop characteristics together should provide the basis of new improved cultivars through genetic recombination and selection.     

A cytological basis for the separation of Geropogon from Tragopogon (Compositae: Lactuceae)

The single species ofGeropogon, G. hybridus (L.) Schultz-Bip., is sometimes submerged in the morphologically similarTragopogon. A comparative study of the karyotypes ofGeropogon andTragopogon sensu stricto clarified their relationship. The karyotype ofG. hydridus (2n=14) was compared with that ofT. dubius Scop. (2n=12). The karyotypes are distinct, offering a compelling reason to recognizeGeropogon as a separate genus.     

Genome analysis of amaranths: Determination of inter- and intra-species variations

Amaranths are an important group of plants and include grain, vegetable and ornamental types. Despite the economic importance of the amaranths, there is very little information available about the extent and nature of genetic diversity present in the genus Amaranthus at molecular level. We now report the randomly amplified polymorphic DNA (RAPD) profiles of different species of Amaranthus as well as different accessions of the species. These RAPD analyses have been carried out using 65 arbitrary sequence decamer primers. From the RAPD data, an UPGMA dendrogram illustrating the inter-as well as intra-species relationships has been computed. The putative hybrid origin of A.dubious from A. hybridus and A. spinosus is also ruled out by the RAPD data. The trends of species relationships amongst the amaranths determined by RAPDs is consistent with their cytogenetic and evolutionary relationships that have already been determined. NBRI Communication No:464 (N.S.).     

AsianPerilla crops and their weedy forms: Their cultivation, utilization and genetic relationships

The cultivation and utilization of two Perilla crops were surveyed in Asia. Perilla frutescens var. frutescens is essentially an oil crop and is now widely cultivated in China and Korea. Its seeds are also used as a flavor for traditional foods in Japan, Korea, China and Nepal. In Korea, leaves of var. frutescens are used as a fresh vegetable and for making pickles. Whereas P. frutescens var. crispa is a Chinese medicine and afresh vegetable in the Far East, it has almost disappeared in many parts of Asia. Cultivation of var. crispa is still continued in Japan and Vietnam. In particular, it is cultivated in a large scale for coloring pickles in the areas where a large amount of plum pickles are produced in Japan. In China and Korea, it remains only as a relict form. Weedy plants ofPerilla are found in Japan, Korea and China. We can classify them into two forms; one, which is closely related to var. frutescens, and the other, which is similar to var. crispa We foundP citriodora andR hirtella in Guandong and Jiangxi provinces of China, respectively. It is clear that they are not endemic to Japan. A phylogenetic tree of samples of two Perilla crops and their weedy forms based on RAPD markers revealed that the weedy forms similar to var. crispa and var. frutescens are genetically closely related to var. crispa and var. frutescens, respectively. Var. crispa and its closely related weedy form seem to be more primitive.     

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.     

Parasites ofSpodoptera exigua,S. eridania [Lep.: Noctuidae] andHerpetogramma bipunctalis [Lep.: Pyralidae] collected fromAmaranthus hybridus in field corn

Three species of lepidopterous larvae were collected fromAmaranthus hybridus L. growing in field corn during 1975 and 1976 at Hastings, Florida.Spodoptera exigua (Hubner) was the predominant species in May.Spodoptera eridania (Cramer) was predominant in June andHerpetogramma bipunctalis (F.) in July and August. Nine native species of parasites, representing theBraconidae, Eulophidae, Ichneumonidae andTachinidae, emerged from these larvae.Meteorus autographae Muesebeck emerged from bothS. exigua andS. eridania. TheTachinidae, Winthemia rufopicta (Bigot),Eucelatori rubentis (Coquillett) andLespensia sp., emerged from mixtures ofS. exigua andS. eridania. Apanteles marginiventris (Cresson),Temelucha sp., andChelonus texanus Cresson emerged from bothS. exigua andH. bipunctalis larvae, andEuplectrus platyhypenae Howard andOphion sp. emerged fromS. eridania. All the species of parasites from the lepidopterous larvae that feed onAmaranthus hybridus are also reported as parasites ofS. frugiperda, a serious pest of corn. Therefore these larvae onA. hybridus may be a source of the parasites found attackingS. frugiperda.     

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.     

History and traditional cultivation ofLathyrus sativus L. andLathyrus citera L. in the Iberian peninsula

Recent ethnographic research carried out in Spain has allowed the cultivation ofLathyrus sativus L. andL. cicera L. to be documented. Both species already appear in the Spanish archaeological record. Grown under traditional farming systems,L. sativus L. andL. cicera L. are still used for human consumption (onlyL. sativus L.) and both are used for fodder. Data on cultivation history, fanning practices, crop processing sequence and uses are here presented, which will enable a better understanding of their possible roles in prehistoric times.     

Cultivated and weedy rice interactions and the domestication process

Examining the targets of selection in crop species and their wild and weedy relatives sheds light on the evolutionary processes underlying differentiation of cultivars from progenitor lineages. On one hand, human‐mediated directional selection in crops favours traits associated with the streamlining of controllable and predictable monoculture practices alongside selection for desired trait values. On the other hand, natural selection in wild and especially weedy relatives presumably favours trait values that increase the probability of escaping eradication. Gene flow between crops and wild species may also counter human‐mediated selection, promoting the evolution and persistence of weedy forms. In this issue, two studies from a group of collaborators examine diversity and divergence patterns of genes underlying two traits associated with red rice (Oryza sp.), the conspecific relative of cultivated rice (Oryza sativa) that is a non‐native weed (see Fig. 1 ). In the first study by Gross et al. (2010) , genetic variation in the major gene underlying the hallmark red pigmentation characterizing most weedy rice (Rc) is found to have a pattern consistent with non‐reversion from U.S. cultivated rice (i.e. the cultivar did not ‘go feral’). This suggests that U.S. weedy rice is not an escaped lineage derived from U.S. cultivated rice populations; weedy rice likely differentiated prior to the selective sweep occurred in this gene within cultivated rice populations. Using the major seed shattering locus sh4 gene and the neighbouring genomic region, Thurber et al. (2010) track the molecular evolutionary history of the high shattering phenotype, a trait contributing dramatically to the success of crop selection in cultivated rice as well as the persistence and expansion of weedy red rice. In this study, the shared fixation of a sh4 mutation in both cultivated rice and weedy rice indicates that weedy rice arose subsequent to the strong selective sweep leading to significant reduction in seed shattering in cultivated rice.

Figure 1 Open in figure viewer PowerPoint A weedy, brown hulled red rice individual with long awns surrounded by a field of cultivated rice (photo by A. Lawton‐Rauh).