Genetic diversity and gene flow among pearl millet crop/weed complex: a case study

Weedy plants with intermediate (domesticated × wild) phenotypes occur in most pearl millet fields in West Africa, even in the absence of wild populations. They are usually found, in high numbers, both inside and outside of drills. Questions pertaining to the evolutionary dynamics of diversity within the pearl millet complex (domesticated–weedy–wild forms) were addressed in this study. The diversity of the different components of this complex sampled in two pearl millet fields in two villages of southwestern Niger was assessed at both molecular (AFLP) and morphological levels. Results show that, in both fields, weedy plants found outside of drills are morphologically distinct from weedy plants found inside drills, despite their close similarity at AFLP markers. The data suggest some introgression from the wild to the weedy population but nevertheless that the gene flow between the parapatric wild and domesticated populations is very low. This challenges the traditional view that regular hybridization between domesticated and wild pearl millets explains the abundance of these weedy plants despite farmers’ seed selection. The level of genetic differentiation between fields from the two villages was low when considering domesticated and weedy plants. This could be explained by high gene flow resulting from substantial seed exchanges between farmers. The fact that it is very difficult for farmers to keep their own selected seeds, and the consequent substantial seed exchanges between them, is probably the main factor accounting for the maintenance and dispersal of weedy pearl millets in the region, even in areas where no wild forms have been observed.C. Mariac and T. Robert contributed equally to the work.     

Allozyme variation in domesticated annual sunflower and its wild relatives

 The annual sunflower (Helianthus annuus L.) is a morphologically and genetically variable species composed of wild, weedy, and domesticated forms that are used for ornament, oilseed, and edible seeds. In this study, we evaluated genetic variation in 146 germplasm accessions of wild and domesticated sunflowers using allozyme analysis. Results from this survey showed that wild sunflower exhibits geographically structured genetic variation, as samples from the Great Plains region of the central United States were genetically divergent from accessions from California and the southwestern United States. Sunflower populations from the Great Plains harbored greater allelic diversity than did wild sunflower from the western United States. Comparison of genetic variability in wild and domesticated sunflower by principal coordinate analysis showed these groups to be genetically divergent, in large part due to differences in the frequency of common alleles. Neighbor-Joining analyses of domesticated H. annuus, wild H. annuus and two closely related wild species (H. argophyllus T. & G. and H. petiolaris Nutt.) showed that domesticated sunflowers form a genetically coherent group and that wild sunflowers from the Great Plains may include the most likely progenitor of domesticated sunflowers. Received: 2 December 1996/Accepted: 4 April 1997     

REDUCED DROUGHT TOLERANCE DURING DOMESTICATION AND THE EVOLUTION OF WEEDINESS RESULTS FROM TOLERANCE–GROWTH TRADE‐OFFS

The increased reproductive potential, size, shoot allocation, and growth rate of weedy plants may result from reduced resource allocation to other aspects of plant growth and defense. To investigate whether changes in resource allocation occurred during domestication or the evolution of weediness, we compared the mycorrhizal responsiveness, growth, and drought tolerance of nine native ruderal, nine agriculturally weedy (four U.S. weedy and five Australian weedy), and 14 domesticated populations (eight ancient landraces and six improved cultivars) of the common sunflower (Helianthus annuus). Domesticated sunflower cultivars were less drought tolerant, but had higher plant growth and fecundity and coarser roots than wild populations. There were no changes in level of drought tolerance between improved cultivars and ancient landrace plants, but there was an increase in allocation to flowers with recent selection. Weedy populations were intermediate between domesticated cultivars and native ruderal populations for plant growth rate, root architecture, and drought tolerance. Weedy populations benefited most from mycorrhizal inoculation by having fewer wilted leaves and wetter soil. Overall, we found that trade‐offs between drought tolerance and several aspects of plant growth, including growth rate, allocation to flowering, and root architecture, govern evolution during sunflower domestication and the invasion of disturbed habitat.     

Agriculture and use of wild and weedy greens by thePiik AP Oom okiek of Kenya

This study documents patterns of use of wild and weedy greens in a previously little studied context among the Piik ap Oom Okiek of Kenya. The Piik ap Oom have a hunter-gatherer history and at the time of the study lived at low population densities in a high altitude forest habitat. Leafy greens, both wild and domesticated, were the most commonly eaten fresh plant food documented. Wild greens,Solanum nigrum L. andAmaranthus graecizans ssp.sylvestris L. were the most preferred. Patterns of harvesting wild greens, a few leaves from many plants and a variety of taxa together, resulted in greater dietary diversity associated with consumption of wild than domesticated greens. Greens provided contemporary Okiek households with nutritious and low maintenance plant food. Increased use of wild and weedy greens was an important benefit of the adoption of the agricultural complex by the Okiek.     

A weed-crop complex in sorghum: The dynamics of genetic diversity in a traditional farming system

Despite the major ecological and economic impacts of gene flow between domesticated plants and their wild relatives, many aspects of the process, particularly the relative roles of natural and human selection in facilitating or constraining gene flow, are still poorly understood. We developed a multidisciplinary approach, involving both biologists and social scientists, to investigate the dynamics of genetic diversity of a sorghum weed-crop complex in a village of Duupa farmers in northern Cameroon. Farmers distinguish a gradient from weedy morphotypes (naa baa see, haariya, and genkiya) to domesticated morphotypes; haariya and genkiya have intermediate morphological traits. We investigated the pattern of diversity in this complex using both morphological and genetic data. Our biological results are interpreted in the light of data on farmers' taxonomy and practices such as spatial pattern of planting and plant selection. Both morphological and genetic data are congruent with farmers' taxonomy and confirm the introgressed status of intermediate weedy morphotypes. Farmers actively select against weedy morphotypes, but several practices unconsciously favor gene flow. Furthermore, haariya and genkiya may facilitate introgression between naa baa see and domesticated morphotypes by virtue of their intermediate flowering period and their mode of management by farmers.     

Molecular Evidence and the Origin and Development of the Domesticated Sunflower (Helianthus annum, Asteraceae)

The domesticated sunflower,Helianthus annuus, is an important economic crop, yet molecular data regarding its evolution are limited. Here we review morphological, geographical, archaeological, and molecular evidence pertaining to its origin and development. New isozyme and chloroplast DNA (cpDNA) evidence is also presented. Morphological, geographical, and archaeological evidence has led to the hypothesis that the domesticated sunflower was derived from a wild/weedy form ofH. annuus possibly in the Midwest. Molecular evidence was concordant with this hypothesis. A high degree of enzymatic and cpDNA sequence similarity was observed between wild and domesticatedH. annuus, and domesticatedH. annuus contained a subset of the alleles and cpDNAs found in wildH. annuus. The extensive polymorphism in the wild plants and the virtual monomorphism in cultivated lines for both isozyme and cpDNA phenotypes further suggest a single origin of the domesticated sunflower from a very limited gene pool. In addition, Native American varieties of the domesticated sunflower were genetically more variable than other cultivated lines, possibly indicating that they gave rise to the other cultivated stocks. Molecular evidence did not, however, allow conclusions as to the exact geographic origin of the domesticated sunflower.     

Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice

Rice is often found as various weedy forms in temperate or newly cultivated rice growing regions throughout the world. The emergence of these forms in the absence of true wild rice remains unclear. A genetic analysis of domestication-related traits (weed syndrome) has been conducted to better understand the appearance of these plants in rice fields. A doubled haploid (DH) population was derived from a cross between a japonica variety and a weedy plant collected in Camargue (France) to set up a genetic linkage map consisting of 68 SSR and 31 AFLP loci. Five qualitative traits related to pigmentation of different organs and 15 developmental and morphological quantitative traits were scored for genes and QTLs mapping. Despite a good reactivity in anther culture and a high fertility of the DH lines, segregation distortions were observed on chromosomal segments bearing gametophytic and sterility genes and corresponded to various QTLs evidenced in indica×japonica distant crosses. Mapping of the coloration genes was found to be in agreement with the presence of several genes previously identified and according to the genetic model governing the synthesis and distribution of anthocyan pigment in the plant. In addition, the main specific traits of weedy forms revealed the same genes/QTLs as progeny derived from a cross between Oryza sativa and its wild progenitor O. rufipogon. A large variation for most characters was found in the DH population, including transgressive variation. Significant correlations were observed between morphology and traits related to weeds and corresponded to a distinct colocalization of most of the QTLs on a limited number of chromosomal regions. The significance of these results on the origin of weedy forms and the de-domestication process is discussed. Received: 25 February 2000 / Accepted: 14 April 2000     

Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

Background  

Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution.     

MORPHOLOGICAL DIFFERENTIATION OF PROBOSCIDEA PARVIFLORA SSP. PARVIFLORA (MARTYNIACEAE) UNDER DOMESTICATION

Aboriginal groups in the southwestern United States have grown Proboscidea parviflora ssp. parviflora for basketry fiber. It has been hypothesized that cultivated plants of this subspecies with white seeds and long-clawed fruit (which provide the fiber) have been domesticated. Cluster, multiple discriminant, and unvariate statistical analyses presented here show that the putative domesticate is indeed morphologically distinct from “wild” plants. It has clearly been domesticated, and has diverged from wild populations to the extent that a new variety, var. Hohokamiana, is proposed for the domesticate. Wild and domesticated varieties differ especially in seed color, rostrum, crest, style, and anther lengths. Most characteristics of the wild variety seem to be genetically dominant to those of the domesticate, which may account for absence of a weedy form intermediate between the wild and domesticated varieties. The wild variety is morphologically more variable than the domesticate, probably because of its broader geographical range and its intergradation with another subspecies. Ethnological data and the variational patterns reported here suggest that the domesticate originated in southern Arizonanorthern Sonora, but probably not north of that region.     

Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild‐to‐weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed‐shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.     

Gene Flow and its Consequences in Sorghum spp.

Gene flow between crops and their weedy or wild relatives can be problematic in modern agricultural systems, especially if it endows novel adaptive genes that confer tolerance to abiotic and biotic stresses. Alternatively, gene flow from weedy relatives to domesticated crops may facilitate ferality through introgression of weedy characteristics in the progeny. Cultivated sorghum (Sorghum bicolor), is particularly vulnerable to the risks associated with gene flow to several weedy relatives, johnsongrass (S. halepense), shattercane (S. bicolor ssp. drummondii) and columbusgrass (S. almum). Johnsongrass and shattercane are common weeds in many sorghum production areas around the world. Sorghum varieties with adaptive traits developed through conventional breeding or novel transgenesis pose agronomic and ecological risks if transferred into weedy/wild relatives. Knowledge of the nature and characteristics of gene flow among different sorghum species is scarce, and existing knowledge is scattered. Here, we review current knowledge of gene flow between cultivated sorghum and its weedy and wild relatives. We further discuss potential avenues for addressing gene flow through genetic, molecular, and field level containment, mitigation and management strategies to facilitate successful deployment of novel traits in this economically important crop species.     

Plant resources of the Tehuacán-Cuicatlán valley, Mexico

Information on richness of plant resources, and their forms of use and management in the biosphere reserve Tehuacan-Cuicatlan, Mexico is analyzed. This 10 000 km² region hosts nearly 2700 vascular plant species, and it is acknowledged as one of the arid areas with the highest floristic diversity in North America. The seven indigenous ethnic groups that live in this region have cultural roots that date back almost 10 000 years. Based upon ethnobotanical and floristic studies, as well as bibliographical sources, a total of 808 useful plant species were identified, most of them (90%) being native, and 44 species being endemic to the region. A total of 681 species are wild plants, 109 are weeds and ruderal plants, and 86 are domesticated crops. However, it was noted that considerable overlap exists between the species of these 3 categories. For example, while wild and ruderal plants (706 species) are foraged by both humans and domestic animals, 59 species of this group are also managed in situ. On the other hand, 168 wild, ruderal and domesticated species are cultivated. The Tehuacán-Cuicatlan Valley is one of the richest regions of Mexico in plant resources. Local knowledge on use and management of plants is a valuable source of information for designing conservation and social development strategies for the biosphere reserve.     

Genetic evidence for the origin of Californian wild beets (genus Beta)

The genus Beta L. is a morphologically and genetically variable group composed of wild, weedy, and domesticated forms that are used for sugar production or as vegetables. In this study, we have evaluated genetic variation in 64 germplasm accessions of wild and domesticated beets and examined the origin of wild beet accessions in California using allozyme analysis. UPGMA analysis showed overall that domesticated and wild beets form genetically coherent groups. Wild beets in California have two different origins, from European Beta vulgaris or from Beta macrocarpa. Population-level patterns of allozyme variation for wild California beets related to B. vulgaris suggest that those populations evolved from naturalized populations of the cultivated B. vulgaris ssp. vulgaris which had hybridized to varying degrees with the sea beets B. vulgaris ssp. maritima. Wild California beets related to B. macrocarpa are essentially genetically identical to European accessions. In addition, we found substantial evidence for hybridization and introgression of B. vulgaris alleles in one B. macrocarpa accession in California. The obligate outcrosser B. vulgaris exhibits more allelic diversity than the self-compatible B. macrocarpa. Beta vulgaris ssp. maritima exhibits more genetic diversity than domesticated B. vulgaris ssp. vulgaris. Received: 2 November 1998 / Accepted: 29 April 1999     

Persistence of sunflower crop traits and fitness in Helianthus petiolaris populations

Transgenic plants have increased interest in the study of crop gene introgression in wild populations. Genes (or transgenes) conferring adaptive advantages persist in introgressed populations, enhancing competitiveness of wild or weedy plants. This represents an ecological risk that could increase problems of weed control. Introgression of cultivar alleles into wild plant populations via crop–wild hybridisations is primarily governed by their fitness effect. To evaluate this, we studied the second generation of seven wild–crop interspecific hybrids between weedy Helianthus petiolaris and cultivated sunflower, H. annuus var. macrocarpus. The second generation comprised open‐pollinated progeny and backcrosses to the wild parent, mimicking crosses that occur in natural situations. We compared a number of morphological, life history and fitness traits. Multivariate analysis showed that the parental species H. annuus and H. petiolaris differed in a number of morphological traits, while the second hybrid generation between them was intermediate. Sunflower crop introgression lowered fitness of interspecific hybrids, but fitness parameters tended to recover in the following generation. Relative frequency of wild/weedy and introgressed plants was estimated through four generations, based on male and female parent fitness. In spite of several negative selection coefficients observed in the second generation, introgressed plants could be detected in stands of <100 weedy H. petiolaris populations. The rapid recovery of fecundity parameters leads to prediction that any trait conferring an ecological advantage will diffuse into the wild or weedy population, even if F1 hybrids have low fitness.     

Bimodal phenotypic structure of two wild pearl millet samples collected in an agricultural area

On the basis of botanical and ecological characters, pearl millet species have been separated into three subspecies:Pennisetum americanum subsp. americanum, cultivated form,P. americanum subsp. monodii, wild form andP. americanum subsp. stenostachyum, weedy form. It has been shown, by enzyme electrophoresis, that these three forms could be discriminated between by their respective enzyme composition even in agricultural areas where they co-exist. Morphological and enzyme analyses of two seed samples collected from monodii plants growing in an agricultural area has shown that the monodii form is not isolated from cultivated plants in its reproduction. The proportion of seeds descending from a cultivated pollen is estimated respectively at 31% and 19%. However, Brunken's typology is corroborated: both samples comprise the two distinct groups of monodii and stenostachyum. This dichotomy is due to the pollen population structure having generated the analysed seeds. Detailedin situ observations on sympatric wild and cultivated populations are essential to explain the absence of recombinant monodii × cultivated pollens and the preservation of monodii millets in spite of their invasion by cultivated pollens.     

Molecular evolution of shattering loci in U.S. weedy rice

Cultivated rice fields worldwide are plagued with weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.). The persistence of weedy rice has been attributed, in part, to its ability to shatter (disperse) seed prior to crop harvesting. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Here, we investigate the shattering phenotype in a collection of U.S. weedy rice accessions, as well as wild and cultivated relatives. We find that all U.S. weedy rice groups shatter seeds easily, despite multiple origins, and in contrast to a decrease in shattering ability seen in cultivated groups. We assessed allelic identity and diversity at the major shattering locus, sh4, in weedy rice; we find that all cultivated and weedy rice, regardless of population, share similar haplotypes at sh4, and all contain a single derived mutation associated with decreased seed shattering. Our data constitute the strongest evidence to date of an evolution of weeds from domesticated backgrounds. The combination of a shared cultivar sh4 allele and a highly shattering phenotype, suggests that U.S. weedy rice have re‐acquired the shattering trait after divergence from their progenitors through alternative genetic mechanisms.     

Traditional management and morphological variation inLeucaena Esculenta (Fabaceae: Mimosoideae) in the mixtec region of Guerrero,Mexico

Ethnobotanical information about uses, management and traditional classification ofLeucaena esculenta by the Mixtec in Guerrero, Mexico, is presented. This plant is mainly used as human food. Buds of leaves and flowers as well as seeds and young pods are the main edible parts. Size, flavor and digestibility of seeds and pods are shown to be important in the Mixtec classification ofLeucaena species and in selection of trees to harvest during gathering. Artificial selection inL. esculenta subsp.esculenta by the Mixtec occurs not only under cultivation, but also in wild populations where people eliminate some individuals while promoting the growth of others with favorable phenotypes. Morphological characters of seeds and pods of individual trees of this subspecies were measured in order to compare phenotypic variation in populations subject to different regimes of management. Samples of trees were analyzed from a) a wild population not affected by intentional disturbances; b) a wild population selectively managed in situ; and c) a sample of cultivated individuals. Ordination methods and analysis of variance were used to examine differences between populations. A marked divergence between the three samples was found, especially between the wild populations managed and unmanaged. The frequency of the phenotypes preferred by people was found to be higher in the wild populationin situ managed. Our study confirms that through in situ forms of management, people are able to modify the phenotypic structure of plant populations. Possible routes of plant domestication within plant populationsin situ are suggested.     

AFLP analysis of the phenetic organization and genetic diversity of Vigna unguiculataL. Walp. reveals extensive gene flow between wild and domesticated types

Amplified fragment length polymorphisms (AFLPs) were used to evaluate genetic relationships within cowpea [Vigna unguiculata (L.) Walp.] and to assess the organization of its genetic diversity. Nei’s genetic distances were estimated for a total of 117 accessions including 47 domesticated cowpea (ssp. unguiculata var. unguiculata), 52 wild and weedy annuals (ssp. unguiculata var. spontanea), as well as 18 perennial accessions of the wild subspecies pubescens, tenuis and alba. AFLP variation was also used to study genetic variation among and within domesticated and wild accessions based on their geographical origin (western, eastern and southern Africa). Wild annual cowpea (var. spontanea) (H _T =0.175) was more diverse than domesticated cowpea (H _T =0.108). Wild cowpea was more diverse in eastern (H _S =0.168) than in western Africa (H _S =0.129), suggesting an eastern African origin for the wild taxon. The AFLP data were consistent with earlier findings of a unique domestication event in cowpea in the northern part of the continent and suggested that domestication in eastern or southern Africa was unlikely. It did not allow a more precise localization of domestication due to extensive gene flow between wild and domesticated forms that has led to a large crop-weed complex distributed over the entire African continent. In addition, wild materials from northeastern Africa are still lacking. Overall, the superiority of the AFLP technique over isozymes resided in its ability to uncover variation both within domesticated and wild cowpea, and should be a powerful tool once additional wild material becomes available. Received: 11 September 2000 / Accepted: 14 June 2001     

Development of PCR-based chloroplast DNA markers that characterize domesticated cowpea (Vigna unguiculata ssp. unguiculata var. unguiculata) and highlight its crop-weed complex

In 1992, Vaillancourt and Weeden discovered a very important mutation for studying cowpea evolution and domestication. A loss of a BamHI restriction site in chloroplast DNA characterized all domesticated accessions and a few wild (Vigna unguiculata ssp. unguiculata var. spontanea) accessions. In order to screen a larger number of accessions, primers were designed to check this mutation using PCR RFLP or direct PCR methods. Using these new primers, 54 domesticated cowpea accessions and 130 accessions from the wild progenitor were screened. The absence of haplotype 0 was confirmed within domesticated accessions, including primitive landraces from cultivar-groups Biflora and Textilis, suggesting that this mutation occurred prior to domestication. However, 40 var. spontanea accessions distributed from Senegal to Tanzania and South Africa showed haplotype 1. Whereas this marker could not be used to identify a precise center of origin, it did highlight the widely distributed cowpea crop-weed complex. Its very high frequency in West Africa could be interpreted as a result of either genetic swamping of the wild/weedy gene pool by the domesticated cowpea gene pool or as the result of domestication by ethnic groups focusing primarily on cowpea as fodder.     

Seeing red: the origin of grain pigmentation in US weedy rice

Weedy forms of crop species infest agricultural fields worldwide and are a leading cause of crop losses, yet little is known about how these weeds evolve. Red rice (Oryza sativa), a major weed of cultivated rice fields in the US, is recognized by the dark‐pigmented grain that gives it its common name. Studies using neutral molecular markers have indicated a close relationship between US red rice and domesticated rice, suggesting that the weed may have originated through reversion of domesticated rice to a feral form. We have tested this reversion hypothesis by examining molecular variation at Rc, the regulatory gene responsible for grain pigmentation differences between domesticated and wild rice. Loss‐of‐function mutations at Rc account for the absence of proanthocyanidin pigments in cultivated rice grains, and the major rc domestication allele has been shown to be capable of spontaneous reversion to a functional form through additional mutations at the Rc locus. Using a diverse sample of 156 weedy, domesticated and wild Oryzas, we analysed DNA sequence variation at Rc and its surrounding 4 Mb genomic region. We find that reversion of domestication alleles does not account for the pigmented grains of weed accessions; moreover, we find that haplotypes characterizing the weed are either absent or very rare in cultivated rice. Sequences from genomic regions flanking Rc are consistent with a genomic footprint of the rc selective sweep in cultivated rice, and they are compatible with a close relationship of red rice to Asian Oryzas that have never been cultivated in the US.