Cultivated Pool Research Articles

Evaluation of Introgressed Lines of Sunflower (Helianthus annuus L.) under Contrasting Water Treatments

Drought stress is a major production constraint in crops globally. Crop wild relatives are important sources of resistance and tolerance for both biotic and abiotic stresses, respectively. A breeding program was initiated to introgress drought tolerance in sunflowers through hybridization between the wild species Helianthus argophyllus and the cultivated pool of H. annuus. Selection was carried out from the F2 to F5 segregating populations for the silver canopy, high cuticular wax, small leaf area, single heading and high oil content. Cuticular wax ranged between 8.72 µg g−1 and 17.19 µg g−1 in the F5 offspring. The selected F5 breeding lines were self-pollinated to obtain the F6 generation. Thereafter, this F6 was compared with the non-adapted elite sunflower germplasm in a factorial complete randomized design with different water treatments; i.e., comparing fully irrigated (100%, T0) versus 75% (T1), 50% (T2) and 25% (T3) of total irrigation. The comparison between the two types of the germplasm showed that drought-tolerant breeding lines had a comparatively lesser decrease in leaf area (0, 11, 22%) and shoot length (4, 21, 28%) than the elite germplasm, which experienced a decrease in leaf area (21%, 33% and 40%) and shoot length (17, 27 and 34%) under the various drought treatments. Moreover, drought-tolerant breeding lines had 100% more root shoot ratios than the elite germplasm (20%) in T3 when compared with control. Several drought-tolerant promising lines (D-2, D-5 and D-27) were selected due to their high leaf area, great root length and increased root to shoot ratio under T3. Some of the lines could be directly used for the development of drought-tolerant hybrids. Combining ability testing indicated that D-27 (F7) was a good general combiner for seed yield plant−1 and oil content after mating with male-line RSIN.82. Resulting hybrids could help to minimize seed yield loss due to water stress and to achieve profitable cultivation of sunflowers in arid regions of Pakistan.

Population Structure of a Worldwide Collection of Tropical Japonica Rice Indicates Limited Geographic Differentiation and Shows Promising Genetic Variability Associated with New Plant Type

Abating the approaching yield plateau in rice requires taking advantage of potential technologies that requires knowledge on genetic diversity. Hybrid breeding, particularly in indica rice, requires the recruitment of large genetic variability from outside because the available genetic diversity of the cultivated pool has already been utilized to a great extent. In this study, we examined an assembly of 200 tropical japonica lines collected worldwide for population genetic structure and variability in yield-associated traits. Tested along with 30 indica and six wild rice lines belonging to India, the tropical japonica lines indicated great phenotypic variability, particularly related to new plant type (NPT) phenology, and formed six clusters. Furthermore, a marker-based characterization using a universal diversity marker panel classified the genotype assembly into four clusters, of which three encompassed tropical japonica lines, while the last cluster included mostly indica lines. The population structure of the panel also revealed a similar pattern, with tropical japonica lines forming three subpopulations. Remarkable variation in the allelic distribution was observed between the subpopulations. Superimposing the geographical sources of the genotypes over the population structure did not reveal any pattern. The genotypes sourced closer to the center of origin of rice showed relatively little diversity compared with the ones obtained from other parts of the world, suggesting migration from a common region of origin. The tropical japonica lines can be a great source of parental diversification for hybrid development after confirming the presence of widely compatible genes.

Contribution of non‐native plants to the phylogenetic homogenization of U.S. yard floras

AbstractCultivation and spread of non‐native plant species may result in either phylogenetic homogenization (increasing similarity) or differentiation (decreasing similarity) of urban floras. However, it is unknown how non‐native species influence homogenization of cultivated versus spontaneously occurring species in cities, and which traits are associated with species that promote homogenization versus differentiation. In this study, we compared homogenization effects of cultivated and spontaneous non‐native species in yard floras across and within seven widely distributed U.S. cities. Additionally, we explored which traits explained their particular contribution to homogenization. We recorded plant presence/absence in 178 private yards distributed among seven metropolitan statistical areas in the United States. We compared phylogenetic homogenization effects of non‐native species within both the cultivated and spontaneous species pools using phylogenetic dissimilarities and the homogenization index. Then, we expressed contributions of non‐native species to the homogenization of each pool as a function of two different sets of plant functional traits using phylogenetic generalized least square (PGLS) models across and within cities. Across cities, spontaneous non‐native species homogenized, and cultivated non‐native species differentiated, yard floras. Within the spontaneous pool, short, small‐seeded non‐native plants and non‐native grasses significantly homogenized yard floras. Within the cultivated pool, species contribution to homogenization was best predicted by plant height, presence of showy flowers, and growth form, with non‐native grasses significantly homogenizing cultivated yard floras. Within cities, non‐native species—whether they were cultivated or spontaneous—consistently homogenized yard floras of the three northern cities and differentiated yard floras of three of the four southern cities, suggesting that homogenization processes are context‐ and scale‐dependent. Likewise, traits explaining homogenization differed substantially among cities. The inconsistent patterns among cities in the plant traits that promoted homogenization of both cultivated and spontaneous species suggest that local environmental and anthropogenic conditions of individual cities imposed strong constraints on trait selection. Linking plant functional traits that promote homogenization with residents’ preferences for vegetation may further enhance understanding of how yard plant communities assemble at regional and local scales.

Sequence diversity of five Medicago sativa genes involved in agronomic traits to set up allele mining in breeding

Lucerne (Medicago sativa) is an autotetraploid forage legume, whose breeding mainly relies on phenotypic recurrent selection to create synthetic populations. Allele mining could be a strategy to take advantage of the large genetic diversity of the species. This paper reports the polymorphism of five genes impacting the phenotype for selected traits: CAD1 and CCoaOMT (digestibility), CONSTANS-like (forage yield), NHX1 (salt tolerance), and WXP1 (drought tolerance). Complete genes were sequenced for 387 genotypes of 43 cultivated accessions and 20 genotypes of wild accessions. Wild versus cultivated polymorphism were compared, adaptive evolution was evaluated by comparing M. sativa and Medicago truncatula sequences and variants of the cultivated pool were characterized. We showed that the wild pool was more variable than the cultivated pool, with 36.6% and 8.4% of the variants that were specific to the wild pool and the cultivated pool, respectively. This result confirmed a bottleneck effect during domestication and selection. We also found that CAD1, CCoaOMT, and NHX1 were under a strong purifying selection and contained few non-synonymous variants (8, 5, and 8, respectively), while CONSTANS-like and WXP1 were under a less pronounced purifying selection and were more polymorphic (45 and 91 non-synonymous variants, respectively). This result suggests that adaptive evolution could be an indicator of expected polymorphism. The application of allele mining strategy for plant breeding in autotetraploid species is discussed.

Assessment of genetic relationships between cultivated arracacha (Arracacia xanthorrhiza Bancr.) and its wild close relatives in the area of domestication using microsatellite markers

Arracacha (Arracacia xanthorrhiza Bancr.) is an asexual propagated root crop domesticated in the Andean highlands, which exists naturally with polycarpic and monocarpic forms. Wild A. xanthorrhiza are present in the area of domestication and can occasionally be mistaken in the same field for a crop or a weed. To study genetic relationships between cultivated arracacha and the wild forms, we surveyed the diversity of 178 plant samples at 11 microsatellite (SSR) loci. As expected, wild A. xanthorrhiza forms showed a significantly higher allelic diversity for all the examined SSR markers. The cultivated pool showed an excess of heterozygosity as opposed to a deficit found in the wild compartment. High Fst values and AMOVA analysis suggest that the cultivated variety has genetically differentiated from the wild forms and is more related to the wild polycarpic than to the monocarpic. Both the wild forms were well distinguished from the cultivars. Nevertheless, among a set of F1 experimental hybrids (cultivated × wild polycarpic), some other genotypes were revealed, also being admixed. Our results highlight a large genetic base available in the wild populations of A. xanthorrhiza with potential implications for the utilization and breeding of this promising crop.

Effect of high temperature on the production of 2n pollen grains in diploid roses and obtaining tetraploids via unilateral polyploidization

AbstractTo integrate the gene pool of a wild species (primarily diploid) into a cultivated pool (primarily tetraploid), a crossing between a dihaploid cultivated rose and a hybrid of Rosa wichurana allowed to obtain interspecific diploid hybrids that produced 2n pollen grains. A return to a tetraploid level sought by breeders can then be considered using sexual polyploidization, obtained by crossing a tetraploid cultivated rose with these hybrids. Application of a high‐temperature regime led to a small but significant increase in the percentage of 2n pollen grains in these hybrids of up to 4.6%. This result was obtained by applying high temperatures close to 32°C during the day to plants cultivated in a glasshouse during recurrent cycles of bloom. Crosses were made between an unreleased tetraploid hybrid tea rose, as a female, and the diploid hybrid that produces the most 2n pollen grains. Tetraploid (42.1%) and triploid (57.9%) offspring were obtained. The use of these 2n pollen grains of the first division restitution type should facilitate the introgression of complex traits of interest.

Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild–weedy–crop complex in a western African region

Gene flow between domesticated plants and their wild relatives is one of the major evolutionary processes acting to shape their structure of genetic diversity. Earlier literature, in the 1970s, reported on the interfertility and the sympatry of wild, weedy and cultivated sorghum belonging to the species Sorghum bicolor in most regions of sub-Saharan Africa. However, only a few recent surveys have addressed the geographical and ecological distribution of sorghum wild relatives and their genetic structure. These features are poorly documented, especially in western Africa, a centre of diversity for this crop. We report here on an exhaustive in situ collection of wild, weedy and cultivated sorghum assembled in Mali and in Guinea. The extent and pattern of genetic diversity were assessed with 15 SSRs within the cultivated pool (455 accessions), the wild pool (91 wild and weedy forms) and between them. F (ST) and R (ST) statistics, distance-based trees, Bayesian clustering methods, as well as isolation by distance models, were used to infer evolutionary relationships within the wild-weedy-crop complex. Firstly, our analyses highlighted a strong racial structure of genetic diversity within cultivated sorghum (F (ST) = 0.40). Secondly, clustering analyses highlighted the introgressed nature of most of the wild and weedy sorghum and grouped them into two eco-geographical groups. Such closeness between wild and crop sorghum could be the result of both sorghum's domestication history and preferential post-domestication crop-to-wild gene flow enhanced by farmers' practices. Finally, isolation by distance analyses showed strong spatial genetic structure within each pool, due to spatially limited dispersal, and suggested consequent gene flow between the wild and the crop pools, also supported by R (ST) analyses. Our findings thus revealed important features for the collection, conservation and biosafety of domesticated and wild sorghum in their centre of diversity.

Impact of past climatic and recent anthropogenic factors on wild yam genetic diversity

Forests of the Dahomey Gap are considered as refugia for many species. They play a crucial role in providing ecosystem services in an area devoid of forests. However, the impact of the way they are managed on the biodiversity they host has barely been investigated. Wild yams existing in these forests play a crucial role in maintaining the genetic diversity of cultivated yams. Indeed, studies of farmer practices have shown that, by way of ennoblement, wild yams collected and selected in the forests and old fallow areas are integrated into the cultivated pool. However, the genetic structure of wild yams is poorly understood. Using nine microsatellite loci, we investigated the population genetics of Dioscorea praehensilis in five forests in Benin, involving different management strategies and bioclimatic areas. Populations of D. praehensilis were strongly differentiated, consistent with an ancient separation of the forests. While the D. praehensilis population in a holly forest was undergoing mutation and drift equilibrium, the population collected from the most conserved forest was in a bottleneck. Moreover, in two forests with different management strategies, accessions from other forests were found, resulting from the displacement of yams following farmer migrations. No isolation by distance was detected, but a differentiation was found between populations of the Sudano-Guinean climate and the Guineo-Congolian climate. Our findings suggest differentiation due to forest isolations under past climatic conditions and more recent tuber flow through anthropogenic impacts.

The origin and evolution of a recent agricultural weed: population genetic diversity of weedy populations of sunflower (Helianthus annuus L.) in Spain and France.

The recurrent evolution of crop-related weeds during agricultural history raises serious economic problems and challenging scientific questions. Weedy forms of sunflower, a species native from America, have been reported in European sunflower fields for a few decades. In order to understand their origin, we analysed the genetic diversity of a sample of weedy populations from France and Spain, and of conventional and ornamental varieties. A crop-specific maternally inherited marker was present in all weeds. At 16 microsatellite loci, the weedy populations shared most of their diversity with the conventional varieties. But they showed a large number of additional alleles absent from the cultivated pool. European weedy populations thus most probably originated from the unintentional pollination of maternal lines in seed production fields by wild plants growing nearby, resulting in the introduction of crop-wild hybrids into the farmers’ fields. The wide diversity and the low population structure detected were indicative of a multiplicity of introductions events rather than of field-to-field propagation. Further studies are required to understand the local evolutionary dynamics of a weedy population, and especially the respective roles of crop-to-weed gene flow and selection in the fate of an initial source of crop-wild hybrids.

Impact of farmer selection on yam genetic diversity

In the traditional yam agricultural system, by way of an ennoblement practice, farmers select tubers from the wild for cultivation. In order to assess the impact of that practice on the genetic diversity of yam, we studied the genetic structure of yams obtained after at least 3 years of ennoblement, to which farmers gave the name of traditional varieties. Cultivated yams do not always have the same genotype as homonymous traditional varieties. For the first time, we demonstrated selection by farmers through the ennoblement of genotypes found in neighbouring villages. Their adoption has a double impact: it allows an increase in the polyclonality of varieties and an indirect exchange of yam tubers between farmers. We also demonstrated that wild yams and hybrids between wild and cultivated yams are also selected. However, their adoption seems less frequent, suggesting selection and valuation of ennobled yams before integration into the cultivated pool. Finally, the adaptive advantage of wild and hybrid yams and their role in yam agrosystems are discussed.

Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions

BackgroundUnlike in tomato, little is known about the genetic and molecular control of fleshy fruit development of perennial fruit trees like grapevine (Vitis vinifera L.). Here we present the study of the sequence polymorphism in a 1 Mb grapevine genome region at the top of chromosome 18 carrying the fleshless berry mutation (flb) in order, first to identify SNP markers closely linked to the gene and second to search for possible signatures of domestication.ResultsIn total, 62 regions (17 SSR, 3 SNP, 1 CAPS and 41 re-sequenced gene fragments) were scanned for polymorphism along a 3.4 Mb interval (85,127-3,506,060 bp) at the top of the chromosome 18, in both V. vinifera cv. Chardonnay and a genotype carrying the flb mutation, V. vinifera cv. Ugni Blanc mutant. A nearly complete homozygosity in Ugni Blanc (wild and mutant forms) and an expected high level of heterozygosity in Chardonnay were revealed. Experiments using qPCR and BAC FISH confirmed the observed homozygosity. Under the assumption that flb could be one of the genes involved into the domestication syndrome of grapevine, we sequenced 69 gene fragments, spread over the flb region, representing 48,874 bp in a highly diverse set of cultivated and wild V. vinifera genotypes, to identify possible signatures of domestication in the cultivated V. vinifera compartment. We identified eight gene fragments presenting a significant deviation from neutrality of the Tajima's D parameter in the cultivated pool. One of these also showed higher nucleotide diversity in the wild compartments than in the cultivated compartments. In addition, SNPs significantly associated to berry weight variation were identified in the flb region.ConclusionsWe observed the occurrence of a large homozygous region in a non-repetitive region of the grapevine otherwise highly-heterozygous genome and propose a hypothesis for its formation. We demonstrated the feasibility to apply BAC FISH on the very small grapevine chromosomes and provided a specific probe for the identification of chromosome 18 on a cytogenetic map. We evidenced genes showing putative signatures of selection and SNPs significantly associated with berry weight variation in the flb region. In addition, we provided to the community 554 SNPs at the top of chromosome 18 for the development of a genotyping chip for future fine mapping of the flb gene in a F2 population when available.

Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs

A series of 320 mapped simple sequence repeats (SSRs) have been used to screen the allelic diversity of tetraploid Gossypium species. Fourty-seven genotypes were analyzed representing (i) the wide spectrum of diversity of the cultivated pool and of the primitive landraces of species G. hirsutum (‘marie-galante’, ‘punctatum’, ‘richmondi’, ‘morrilli’, ‘palmeri’, and ‘latifolium’, and ‘yucatanense’), and (ii) species G. barbadense, G. darwinii and G. tomentosum. The polymorphism of 201 SSR loci revealed 1128 allelic variants ranging from 3 to 17 per locus. Neighbor-joining (NJ) method based on genetic dissimilarities produced groupings consistent with the assignments of accessions both at species and at race level. Our data confirmed the proximity of the Galapagos endemic species G. darwinii to species G. barbadense. Within species G. hirsutum, and as compared to the other 6 races, race yucatanense appeared as the most distant from cultivated genotypes. Race yucatanense also exhibited the highest number of unique alleles. The important informative heterogeneity of the 201 SSR loci was exploited to select the most polymorphic ones that were assembled into three series of genome-wide (i.e. each homoeologous AD chromosome pair being equally represented) and mutliplexable (× 3) SSRs. Using one of these ‘genotyping set’, consisting of 39 SSRs (one 3-plex for each of the 13 AD chromosomes pairs) or 45 loci, we were able to assess the relationships between accessions and the topology in the genetic diversity sampled. Such genotyping set of highly informative SSR markers assembled in PCR-multiplex, while increasing genotyping throughput, will be applicable for molecular genetic diversity studies of large germplasm collections.

Microsatellite segregation analysis and cytogenetic evidence for tetrasomic inheritance in the American yam Dioscorea trifida and a new basic chromosome number in the Dioscoreae

Despite the economic and cultural importance of the indigenous "Amerindian" yam Dioscorea trifida, very little is known about their origin, phylogeny, diversity and genetics. Consequently, conventional breeding efforts for the selection of D. trifida genotypes resistant to potyviruses which are directly involved in the regression of this species have been seriously limited. Our objective of this paper is to contribute to the clarification of the cytogenetic status, i.e., inheritance and chromosome number. Our results provide genetic evidence supporting tetrasomic behaviour of the genome of D. trifida based on chromosomal segregation pattern analysis using eight SSRs markers in three different crosses. This is the first reliable evidence of an autopolyploid species in the genus Dioscorea. The second major result in this study is the revealing of a new base chromosome number in the botanical section Macrogynodium to which D. trifida belongs. To date, our assumptions about the ploidy level of yams are based on the observations that the basic chromosome number is 10 or 9, and D. trifida was described as octoploid. The chromosome number of D. trifida accessions was also assessed using somatic chromosomic count techniques. Flow cytometry did not show significant variation of 2C DNA content among 80 accessions indicating homogeneity of the ploidy level of the cultivated D. trifida. This suggests that autotetraploidy is well established as well as the rule for the cultivated pool of D. trifida, even if the direct diploid ancestor remains to be identified. The data presented in this paper are significant and important for the effective breeding and conservation of the species and for elucidating the phylogeny and the origins of the yam and the evolution of the genus Dioscorea.

Morphologic and Agronomic Diversity of Wild Genetic Resources of Medicago sativa L. Collected in Spain

One hundred and three natural populations of Medicago L. were collected in Spain, mainly from roadsides, non-irrigated or grazed lands. This germplasm was evaluated at Montpellier (France) with control cultivars and Spanish landraces under completely random block design, replicated four times, and observed for 64 qualitative or quantitative characters. Differences between natural populations and cultivated controls are highly significant, but gene flow occurs between wild and cultivated compartment and hybrid populations were identified. On the basis of multivariable analysis, the accessions were grouped into four clusters depending on their proximity with the cultivated pool to facilitate their management and ex situ conservation. The relationship between environment of the site of collection and phenotypic characteristics of the natural populations was also discussed. Different policies of conservation of these genetic resources are suggested to avoid their disappearance even when they disappeared from the other regions of the western Mediterranean. Spanish wild pool of alfalfa, also called ‘Mielga’, appears of great interest for the breeding of alfalfa because it contains a large diversity of characteristics (prostrate habit, rhizomes) linked to tolerance to grazing or drought environment. With the need for more sustainable systems in agriculture, the erosion of natural habitats and the necessity for rehabilitation of degraded ecosystems, the importance of this wild pool is really inestimable.

Inferences from mitochondrial DNA patterns on the domestication history of alfalfa (Medicago sativa)

The evolutionary history of a wild-cultivated complex is the outcome of different factors, among which are the domestication of the cultivated form, its geographical and demographic expansion, as well as gene flow between natural and cultivated populations. To clarify this history for alfalfa (Medicago sativa), we adopted a phylogeographical approach based on a sample of natural and cultivated populations of the M. sativa species complex. This sample was characterized for mtDNA variation through restriction fragment length polymorphisms. Twenty-two mitotypes were identified in the whole data set (155 individuals). In the wild pool from the presumed area of origin (Near East to Central Asia), the diversity was high but the absence of geographical differentiation hinders a more precise location of the centre of domestication. Within the cultivated alfalfa, the geographical structure suggests strongly the existence of at least two independent routes of dissemination of alfalfa from its centre of origin. In particular, original mitotypes detected in some regions suggest that wild populations not sampled in this study, and located outside the presumed area of domestication, may have contributed to the diversity of the cultivated pool. Finally, analysis of the mtDNA variation shows that natural populations collected in Spain constitute an endemic wild pool now introgressed partially by cultivated alfalfa.