Populations Of Wild Relatives Research Articles

Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplants.

Crop wild relatives (CWR) provide a valuable resource for improving crops. They possess desirable traits that confer resilience to various environmental stresses. To fully utilize crop wild relatives in breeding and conservation programs, it is important to understand the genetic basis of their adaptation. Landscape genomics associates environments with genomic variation and allows for examining the genetic basis of adaptation. Our study examined the differences in allele frequency of 15,416 single nucleotide polymorphisms (SNPs) generated through genotyping by sequencing approach among 153 accessions of 15 wild eggplant relatives and two cultivated species from Africa, the principal hotspot of these wild relatives. We also explored the correlation between these variations and the bioclimatic and soil conditions at their collection sites, providing a comprehensive understanding of the genetic signals of environmental adaptation in African wild eggplant. Redundancy analysis (RDA) results showed that the environmental variation explained 6% while the geographical distances among the collection sites explained 15% of the genomic variation in the eggplant wild relative populations when controlling for population structure. Our findings indicate that even though environmental factors are not the main driver of selection in eggplant wild relatives, it is influential in shaping the genomic variation over time. The selected environmental variables and candidate SNPs effectively revealed grouping patterns according to the environmental characteristics of sampling sites. Using four genotype-environment association methods, we detected 396 candidate SNPs (2.5% of the initial SNPs) associated with eight environmental factors. Some of these SNPs signal genes involved in pathways that help adapt to environmental stresses such as drought, heat, cold, salinity, pests, and diseases. These candidate SNPs will be useful for marker-assisted improvement and characterizing the germplasm of this crop for developing climate-resilient eggplant varieties. The study provides a model for applying landscape genomics to other crops' wild relatives.

Intensified Selection, Elevated Mutations, and Reduced Adaptation Potential in Wild Barley in Response to 28 Years of Global Warming

Many studies have investigated the threat of climate change on wild plants, but few have investigated the genetic responses of crop wild relative populations under threat. We characterized the genetic responses of 10 wild barley (Hordeum spontaneum K. Koch) populations in Israel, sampling them in 1980 and again in 2008, through exome capture and RNA-Seq analyses. Sequencing 48 wild barley samples of these populations representing two collection years generated six million SNPs, and SNP annotations identified 12,926 and 13,361 deleterious SNPs for 1980 and 2008 samples, respectively. The assayed wild barley samples displayed intensified selective sweeps and elevated deleterious mutations across seven chromosomes in response to 28 years of global warming. On average, the 2008 samples had lower individual and population mutational burdens, but the population adaptation potential was estimated to be lower in samples from 2008 than in 1980. These findings highlight the genetic risks of losing wild barley under global warming and support the need to conserve crop wild relatives.

VALIDACIÓN EMPÍRICA DE LA TEORÍA MULTICÉNTRICA DEL ORIGEN Y DIVERSIDAD DEL MAÍZ EN MÉXICO

Mesoamerica is considered as the center of origin and diversity of maize (Zea mays L.). The multicentric theory on the origin and diversity of maize defines five centers of origin-domestication, from which four macro regions or primary centers of diversification of this cereal were conformed, from which the different races and the concentration of diversity emerged. A center of genetic diversity is defined as the geographical area where there is morphological, genetic diversity, or both, for a certain species, characterized by harboring populations of wild relatives and constituting a genetic reserve. The objective of this study was to empirically validate the geographic regions of Mexico that conform to the definition of a center of genetic diversity for maize. Spatial analysis was used to examine the diversity and distribution of 24,126 accessions of native maize and 1,106 records of wild relatives (Teosinte: 692 and Tripsacum: 414) collected during the period 1926 2014, available at germplasm banks and herbaria of national and international agricultural research and education institutions located in Mexico and, through the use of geographic information systems and modeling. In accordance with the criteria and definitions considered in the multicentric theory on maize origin and diversity, 19 geographic regions were empirically defined and validated to be considered as centers of genetic diversity of maize native to Mexico.

Genetic diversity and differentiation in Patellifolia (Amaranthaceae) in the Macaronesian archipelagos and the Iberian Peninsula and implications for genetic conservation programmes

This is the first comprehensive investigation of the patterns of genetic diversity of Patellifolia species. The main objective of our research work is to determine Most Appropriate crop Wild relative Populations (MAWP) suited to conserve in situ wild relatives of the sugar beet. Individual plant samples of P. patellaris were collected at 26 and of P. procumbens/P. webbiana at seven sites and analysed with 24 and 22 microsatellite markers, respectively. On average 15 alleles per locus were found within the set of 581 P. patellaris and an average of 12 alleles per locus in the set of 172 P. procumbens/P. webbiana individuals. The factorial analysis showed diversity patterns which agree well with the geographic origin of the samples. The genetic data suggest that P. patellaris reproduces mainly by self-fertilisation while P. procumbens/P. webbiana have the signature of out-breeders. The measure Δ was used to calculate the genetic distance of each occurrence to the pooled remaining occurrences, the complement. Occurrences with either the lowest or the highest genetic distance to the complement are particularly suited to conserve the genetic diversity of the species. Eight occurrences of P. patellaris, two of P. procumbens and one for P. webbiana were determined according to this scheme, proposed as MAWP and recommended for the establishment of genetic reserves.

Assessment of spatial–temporal variation in natural populations of Brassica incana in south Italy: implications for conservation

Brassica incana is a secondary-gene pool wild relative of Brassica oleracea. Twenty-two B. incana populations are recorded in Italy, where the species has recently been pointed out as in priority need of conservation. While data on the spatial and temporal variation of B. incana Italian populations are completely lacking, this information is useful in conservation planning for this species. Three populations from the Sorrento peninsula and from the islands of Ischia and Capri, collected in 1984 and 2012, were characterised for 12 morpho-phenological and 21 genetic traits to assess their spatial–temporal variation. The populations were quite different for morpho-phenological and genetic traits. Spatial differentiation was high and easily explained by the isolation. Temporal differentiation between the Sorrento and Ischia populations was high and explained by a reduction in the population census across time, while it was not significant between the two Capri accessions as such pointing to a major effect of genetic drift. Numerical dimension is extremely relevant in evaluating conservation priorities since it has a major impact on population dynamics over time. The Sorrento and Ischia populations are under threat and urgently need conservation actions, suggesting an alarming scenario for the survival of other crop wild relative populations which are similar in census. Our data also show that, in an allogamous and self-incompatible species like B. incana, populations of 100–200 individuals maintain high allelic diversity. According to obtained results, natural populations of species with similar reproductive system and census can be considered at low risk of genetic erosion.

Genetically engineered rice endogenous 5-enolpyruvoylshikimate-3-phosphate synthase (epsps) transgene alters phenology and fitness of crop-wild hybrid offspring

Genetically engineered (GE) rice endogenous epsps (5-enolpyruvoylshikimate-3-phosphate synthase) gene overexpressing EPSPS can increase glyphosate herbicide-resistance of cultivated rice. This type of epsps transgene can enhance the fecundity of rice crop-weed hybrid offspring in the absence of glyphosate, stimulating great concerns over undesired environmental impacts of transgene flow to populations of wild relatives. Here, we report the substantial alteration of phenology and fitness traits in F1-F3 crop-wild hybrid descendants derived from crosses between an epsps GE rice line and two endangered wild rice (Oryza rufipogon) populations, based on the common-garden field experiments. Under the glyphosate-free condition, transgenic hybrid lineages showed significantly earlier tillering and flowering, as well as increased fecundity and overwintering survival/regeneration abilities. In addition, a negative correlation was observed between the contents of endogenous EPSPS of wild, weedy, and cultivated rice parents and fitness differences caused by the incorporation of the epsps transgene. Namely, a lower level of endogenous EPSPS in the transgene-recipient populations displayed a more pronounced enhancement in fitness. The altered phenology and enhanced fitness of crop-wild hybrid offspring by the epsps transgene may cause unwanted environmental consequences when this type of glyphosate-resistance transgene introgressed into wild rice populations through gene flow.

Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes

Rapid identification of agronomically important genes is of pivotal interest for crop breeding. One source of such genes are crop wild relative (CWR) populations. Here we used a CWR population of <200 wild beets (B. vulgaris ssp. maritima), sampled in their natural habitat, to identify the sugar beet (Beta vulgaris ssp. vulgaris) resistance gene Rz2 with a modified version of mapping-by-sequencing (MBS). For that, we generated a draft genome sequence of the wild beet. Our results show the importance of preserving CWR in situ and demonstrate the great potential of CWR for rapid discovery of causal genes relevant for crop improvement. The candidate gene for Rz2 was identified by MBS and subsequently corroborated via RNA interference (RNAi). Rz2 encodes a CC-NB-LRR protein. Access to the DNA sequence of Rz2 opens the path to improvement of resistance towards rhizomania not only by marker-assisted breeding but also by genome editing.

Distorted segregation in plant hybrids and its implication for evolution.

During natural hybridization and introgression, offspring may obtain alleles from both parents unevenly, resulting in allelic segregation that significantly deviated from the Mendelian ratio, referred to as segregation distortion (SD). Segregation distortion is a common phenomenon and a number of factors can influence the ratio and pattern of segregation distortion in hybrid descendants. However, knowledge on the evolutionary implication of SD is still very limited. In this review, we summarize the current knowledge regarding mechanisms of SD such as genetic interaction, genetic divergence, cytoplasmic background, and environmental effect, and analyze its implication for evolution. In short, SD affects evolutionary potential, sex ratio, genetic diversity and maintenance of stable genetic divergence. Therefore, the effect of transgene on the evolutionary potential of wild relative populations through SD and the changes of the pattern of SD in continuous generations should be paid attention to in future studies.

Maize diversity in southern Brazil: indication of a microcenter of Zea mays L.

‘Microcenters of diversity’ are restricted geographical areas within which a significant diversity of genetic resources is accumulated. Maize genetic variability, one of the largest among cultivated species, particularly in far western Santa Catarina, southern Brazil, has shown a rich store of landraces, conserved on farm by small-scale farmers. Thus, this study aimed to characterize the diversity of Zea mays L. landraces in two municipalities of this micro-region in Santa Catarina, as well as its geographic distribution, developing the census of diversity as a methodological proposal. Diagnosis was made according to the farmers’ knowledge. The field survey was conducted in 70 rural communities involving 2049 farms. The methodology allowed identifying 136 populations of wild relatives, of which some belong to the species Zea luxurians (Durieu and Ascherson) Bird, and 1513 populations of maize landraces, comprising 1078 of popcorn, 337 of common maize, 61 of sweet maize and 37 of flour maize. The identification of 59 morphological groups, the high use, adaptive and agronomic values, and the Shannon index (H′), estimated according to the grain shape (0.79), endosperm type (0.73), size (0.87), color (1.40), and morphological group (3.16), showed at set a considerable diversity distribution conserved on farm in this micro-region. Landrace richness and the presence of wild relative species, associated with the local human activity and sociocultural aspects, allowed to characterize the far western Santa Catarina as a ‘microcenter of diversity’ of Zea mays L.

Presence of Zea luxurians (Durieu and Ascherson) Bird in Southern Brazil: Implications for the Conservation of Wild Relatives of Maize.

Records of the occurrence of wild relatives of maize in South American lowlands are unprecedented, especially in sympatric coexistence with landraces. This fact is relevant, because regions of occurrence of wild relatives of cultivated plants should be a priority for conservation, even if they do not correspond to the center of origin of the species. The aim of this study was to identify and characterize the wild relatives of maize in the Far West of Santa Catarina, southern Brazil. Therefore, phenotypic characterization was performed for five populations, based on 22 morphological traits deemed as fundamental for classifying the species of the genus Zea, and validated through the characterization of chromosomal knobs of two populations. The occurrence and distribution of teosinte populations were described through semi-structured interviews applied to a sample of 305 farmers. A total of 136 teosinte populations were identified; 75% of them occur spontaneously, 17% are cultivated populations, and 8% occur both ways, for the same farm. Populations that were characterized morphologically had trapezoidal fruits mostly, upright tassel branch (4–18), non-prominent main branch and glabrous glumes, with two protruding outer ribs and 8 inner ribs, on average. Cytogenetic analysis identified 10 pairs of homologous chromosomes (2n = 20) with 26 knobs, located in the terminal region of all chromosomes. The similarity of these results with the information reported in the literature indicates that the five populations of wild relatives of maize in this region of Santa Catarina belong to the botanical species Zea luxurians.

A Stakeholder Analysis to Assess Preferences and Willingness-to-Pay for Management of Rice Wild Relatives in Sri Lanka

Proper management of rice wild relative populations scattered in Sri Lanka in smallquantities are highly warranted as they constitute an increasingly important genetic resourcethat can be used with further research to increase yield of existing hybrid rice varieties. Inlight of this, this paper presents the outcome of a multi-phased research study carried out toassess the preferences of key stakeholders for conservation and utilisation of thosepopulations. The information contained in databases from a series of empirical analysescarried out with key stakeholders, including the: (a) Breeders (n=30); (b) Environmentmanagers (n=65); (c) Government officials (n=40); (d) Rural communities (n=50), and (e)Urban communities (n=300) were used to select the most relevant attributes pertaining tomanagement of rice wild relatives, including: (1) responsibility for conservation; (2)utilisation of WRR sites; (3) the best conservation method, and (4) Marginal Willingness-to-Pay (MWTP). The outcome of analysis, which employed both Choice Experiment andContingent Ranking methods highlights that the willingness-to-pay of rural adjacentcommunity was significantly higher (Rs. 82.73) than that of urban households (Rs. 1.34),breeders (Rs. 10.00), policy planners (Rs. 20.46) and environmental managers (Rs. 7.34). Theoverall MWTP for all stakeholders was estimated to be Rs. 4.83. It also shows that themajority of stakeholders prefer government takes the sole responsibility of conservation ofWRR and the adjacent communities should be allowed to utilise WRR sites under thesupervision of government. All the stakeholders preferred in-situ conservation. The resultsdraw attention on progressive policy measures which encompass participation of all groups ofstakeholders at equal levels; mainstreaming of conservation activities into livelihooddevelopment strategies to address the local needs, and setting up of alternative institutionalarrangements towards proper execution of policies and research programs aimingconservation of rice wild relatives for the future.

Genomics strategies for germplasm characterization and the development of climate resilient crops

Food security requires the development and deployment of crop varieties resilient to climate variation and change. The study of variations in the genome of wild plant populations can be used to guide crop improvement. Genome variation found in wild crop relatives may be directly relevant to the breeding of environmentally adapted and climate resilient crops. Analysis of the genomes of populations growing in contrasting environments will reveal the genes subject to natural selection in adaptation to climate variations. Whole genome sequencing of these populations should define the numbers and types of genes associated with climate adaptation. This strategy is facilitated by recent advances in sequencing technologies. Wild relatives of rice and barley have been used to assess these approaches. This strategy is most easily applied to species for which a high quality reference genome sequence is available and where populations of wild relatives can be found growing in diverse environments or across environmental gradients.

Spatial distribution and basic ecology of Heterodera schachtii and H. betae wild populations developing on sea beet, Beta vulgaris ssp. maritima

Most populations of crop pathogens have wild relative populations from which they can originate but for which basic knowledge of their ecological requirementsin naturais scarce. However, the study of spatial distribution and ecology of wild pathogen populations may help control them in crops through a better understanding of the environmental factors driving population dynamics. Here, we focused onHeterodera schachtiiandH. betae, two cyst nematodes that cause severe damage to sugar beet (Beta vulgarisssp.vulgaris) crops and can develop on a wild beet relative, the sea beet (B. vulgarisssp.maritima). We investigated the occurrence of both nematode species in the wild and explored some environmental factors that may influence their geographical distribution. To do so, we sampled the wild hostB. v.ssp.maritimaalong the European Atlantic and North Sea coastlines. Results showed thatH. schachtiimainly occurred in the colder environments of northern Europe, whereasH. betaewas preferentially distributed in the warm environments of southern Europe. It was previously established thatH. betaeonly recently appeared in The Netherlands, which are in the north of Europe. Thus, our results do not support this hypothesis. Overall, this study accurately documents the geographical occurrence of two nematode crop pest species in the wild and helps identify the main environmental factors affecting their distribution range.

Morphological Variation in the Wild-Weedy Complex of Sorghum bicolor In Situ in Western Kenya: Preliminary Evidence of Crop-to-Wild Gene Flow?

Crop wild relatives are important components of agroecosystems and have over the years been exploited in breeding programs as sources of genes for novel traits. Information on the extent and patterns of variability is important in formulating effective conservation and utilization strategies for existing crop wild relative populations. We conducted surveys and collections of wild and weedy accessions of Sorghum bicolor (L.) Moench in Lambwe Valley in western Kenya in order to investigate occurrence, distribution, and morphological variability in the wild-weedy complex of S. bicolor under local agroecological conditions. We also attempted to understand the role, if any, of crop-to-wild gene flow in structuring variability within and among populations. The morphological data presented here showed wide variability within wild-weedy sorghum populations with respect to habitats and morphotypes. True wild sorghum populations in national parks and the sugarcane belt were clearly distinguishable from the putative hybrids or intermediate forms found in sorghum fields, in sorghum field margins, and, to some extent, by the roadside near sorghum fields. The existence of these intermediate forms is empirical evidence of introgression between cultivated sorghum and its wild-weedy relatives. Extensive introgression, especially within in situ conservation areas and/or in areas of high diversity, would lead to genetic erosion and possible depletion of these important wild sorghum genetic resources.

Transgene introgression in crop relatives: molecular evidence and mitigation strategies

Incorporation of crop genes into wild and weedy relative populations (i.e. introgression) has long been of interest to ecologists and weed scientists. Potential negative outcomes that result from crop transgene introgression (e.g. extinction of native wild relative populations; invasive spread by wild or weedy hosts) have not been documented, and few examples of transgene introgression exist. However, molecular evidence of introgression from non-transgenic crops to their relatives continues to emerge, even for crops deemed low-risk candidates for transgene introgression. We posit that transgene introgression monitoring and mitigation strategies are warranted in cases in which transgenes are predicted to confer selective advantages and disadvantages to recipient hosts. The utility and consequences of such strategies are examined, and future directions provided.

Existence of vigorous lineages of crop-wild hybrids in Lettuce under field conditions.

Plant to plant gene flow is a route of environmental exposure for GM plants specifically since crosses with wild relatives could lead to the formation of more vigorous hybrids, which could increase the rate of introgression and the environmental impact. Here, we test the first step in the process of potential transgene introgression: whether hybrid vigor can be inherited to the next generation, which could lead to fixation of altered, i.e., elevated, quantitative traits. The potential for a permanent elevated fitness was tested using individual autogamous progeny lineages of hybrids between the crop Lactuca sativa (Lettuce) and the wild species Lactuca serriola (Prickly Lettuce). We compared progeny from motherplants grown under either greenhouse or field conditions. The survival of young plants depended strongly on maternal environment. Furthermore, we observed that offspring reproductive fitness components were correlated with maternal fitness. Our study demonstrates that post-zygotic genotypic sorting at the young plants stage reduces the number of genotypes non-randomly, leading to inheritance of high levels of reproductive traits in the surviving hybrid lineages, compared to the pure wild relatives. Consequently, directional selection could lead to displacement of the pure wild relative and fixation of more vigorous genome segments originating from crops, stabilizing plant traits at elevated levels. Such information can be used to indentify segments which are less likely to introgress into wild relative populations as a target for transgene insertion.

GENE FLOW FROM DOMESTICATED SPECIES TO WILD RELATIVES: MIGRATION LOAD IN A MODEL OF MULTIVARIATE SELECTION

Domesticated species frequently spread their genes into populations of wild relatives through interbreeding. The domestication process often involves artificial selection for economically desirable traits. This can lead to an indirect response in unknown correlated traits and a reduction in fitness of domesticated individuals in the wild. Previous models for the effect of gene flow from domesticated species to wild relatives have assumed that evolution occurs in one dimension. Here, I develop a quantitative genetic model for the balance between migration and multivariate stabilizing selection. Different forms of correlational selection consistent with a given observed ratio between average fitness of domesticated and wild individuals offsets the phenotypic means at migration-selection balance away from predictions based on simpler one-dimensional models. For almost all parameter values, correlational selection leads to a reduction in the migration load. For ridge selection, this reduction arises because the distance the immigrants deviates from the local optimum in effect is reduced. For realistic parameter values, however, the effect of correlational selection on the load is small, suggesting that simpler one-dimensional models may still be adequate in terms of predicting mean population fitness and viability.

Eco-geographical distribution of &lt;i&gt;Lactuca saligna&lt;/i&gt; natural populations in Israel

Crops can be drastically improved by effective utilization of the immense variation in genetic resources for resistance to abiotic and biotic stresses possessed by natural populations of wild relatives. To protect Israel's and the world's lettuce crop, samples of seeds from 562 plants that morphologically seemed to be the wild species Lactuca saligna L. (least lettuce, willow-leaf lettuce) were collected from 41 localities, representing different climatic and edaphic environments throughout Israel. Searching and collecting trips were conducted in September—October of 2004-2006. L. saligna was recorded throughout Israel except for desert areas (e.g., Negev and Judean deserts) and extreme environmental/soil conditions (Dead Sea area). L. saligna was recorded at various altitudes (10 to 1277 m asl) and different habitats and soil types. In all, the taxonomic status of 214 of the accessions was morphologically validated as L. saligna during multiplication of 220 accessions in the greenhouse. In rosette format...

Polymorphism for interspecific hybridisation within a population of wild radish ( Raphanus raphanistrum ) pollinated by oilseed rape ( Brassica napus )

The within-population polymorphism of wild radish (Raphanus raphanistrum) for interspecific hybridisation with two cultivars of oilseed rape (Brassica napus) was investigated by hand crossing experiments and fluorescence microscopy. Wide variability among plants was observed in the ability of oilseed rape pollen to germinate on the wild radish stigma; the frequency of pistils showing pollen tubes ranged from 0 to 1, depending on the female plant. The ratio of fertilised ovules to the total number of ovules in ovaries where pollen tubes arrived ranged from 0.02 to 0.51. Overall, the results provide evidence for the presence of different phenotypes. In 40% of the plants, pistils had no or very few pollen tubes and few fertilised ovules. In 23%, the foreign pollen tubes grew through the style towards the ovary, but had low ovule fertilisation efficiency. The remaining 37% showed a large number of pollen tubes in the style and frequent ovule fertilisation, and two plants showed no difference between foreign and conspecific pollen. With regard to post-zygotic barriers, pollen germination and ovule fertilisation represent minor barriers to interspecific hybridisation between oilseed rape and wild radish. It is suggested that the effectiveness of these barriers could be improved through plant breeding; this could reduce the risk of gene flow from transgenic oilseed rape to populations of wild relatives.

Genetic diversity in wild wheats and goat grass

The genetic structure of 35 populations of wild relatives of cultivated wheats, all collected in Syria and Lebanon, was assessed using ten isozymes. The populations consisted of diploid goat grass, Aegilops speltoides, diploid wild wheats, Triticum monococcum spp. aegilopoides and T. urartu, and tetraploid wild wheat, T. turgidum ssp. dicoccoides. The majority of the populations were polymorphic (P=0–70%) having low within-population mean genetic diversity (Hep=0.05–0.10) and relatively high within-species genetic diversity (Hes=0.14–0.31). The linkage between loci did not seem to be one of the causes for the observed polymorphism. All four species showed significant inbreeding at both the population (0.31–0.64) and species (0.77–0.96) levels, and the extent of inbreeding did not correlate with mating systems. Despite their apparent common ecological and evolutionary history, between-population or between-species level genetic identity was low (I=0.43–0.86). Among the diploid species, populations of Ae. speltoides clustered distinctly from those overlapping clusters of T. monococcum ssp. aegilopoides and T. urartu. The tetraploid species T. turgidum ssp. dicoccoides had relatively less genetic diversity (Hes=0.14) and was highly homozygous (F=0.96). The results suggest that these wild progenitors of cultivated wheats have undergone extensive local differentiation and inbreeding. We discuss the implications of our results on the management of wild wheat and goat grass populations.