Perceptual selection and the unconscious selection of ‘volunteer’ seedlings in clonally propagated crops: an example with African cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis> Crantz) using ethnobotany and population genetics

The role of sexual reproduction in magnifying genetic diversity in clonally propagated crops is now well documented. But whereas many studies have emphasized the importance of perceptual distinctiveness and its role in arousing farmers’ curiosity towards plants with unusual morphological traits, few have considered its corollary, perceptual indistinctiveness. In this study, we investigated which factors influence farmers’ behaviours towards self-sown ‘volunteer’ seedlings of cassava (Manihot esculenta Crantz) in a cross-cultural survey in Gabon, Central Africa. Interviews revealed that farmers were seven times more likely to spare seedlings that resembled a named landrace compared to those that did not. Similarly, farmers were more likely to relax weeding pressures on cassava volunteers if they believed that volunteers were resurgences from old cuttings. The model fit significantly improved when cultural factors were accounted for, suggesting strong culture-dependent differences among communities in their perception of and attitudes towards cassava volunteers. An analysis of the structure of genetic diversity of cassava landrace populations at the community level showed that most landraces included singleton genotypes, even in villages where farmers imposed the strongest weeding pressures, suggesting that there is always some background incorporation of cassava seedlings. We show that by channelling the selective incorporation of cassava seedlings that are morphologically indistinguishable from familiar landraces, perceptual selection favors the recruitment, sometimes deliberate but more often unconscious, of new genotypes from plants germinating from seeds and contributes to balancing the disadvantages of strictly clonal propagation, while maintaining landraces within consensual combinations of perceptually distinct traits.     

Genetic diversity and relationship of Guinea yam (<Emphasis Type="Italic">Dioscorea cayenensis</Emphasis> Lam.–<Emphasis Type="Italic">D. rotundata</Emphasis> Poir. complex) germplasm in Benin (West Africa) using microsatellite markers

Guinea yam (Dioscorea cayenensis–D. rotundata complex) is an important tuber crop that highly contributes to food security and poverty alleviation in Benin. The knowledge and understanding of the extent of genetic variation of Guinea yam germplasm is important for planning of the genetic conservation, and the utilisation of this resource. The objective of this study was to assess the genetic diversity and relationships of 64 yam landraces whose dried chips are considered as resistant to insect attacks using 41 simple sequence repeat. Among these primers, 13 were found to be polymorphic, giving 113 polymorphic alleles. The number of alleles per locus ranged from 4 (Ym50) to 13 (Ym29), with an average of 8.69. Unique allele was observed with some landraces (Singou and Tchakatchaka) and can be considered as unique gene and use in yam breeding program. The mean polymorphic information content values for all markers used was 0.76 and ranged between 0.58 and 0.91 in loci YM3 and YM32 respectively. The genetic distance of yam landraces ranged from 0.45 (Yasoubagarou) to 0.04 (Assinapeira and Alahina), indicating that the yam germplasm has a high degree of genetic diversity supported by an averagely observed heterozygosity of 0.78. Cluster analysis using unweighted pair group method with arithmetic average grouped the 64 yam landraces into two distinct clusters. This tendency was also observed in the principal coordinate analysis. The analysis of molecular variance revealed that 96 % of the variation was found within the population and only 4 % between the populations. Genetic diversity and relationship assessments among the 64 yam landraces of Benin could provide useful information for efficient use of these materials, especially for genetic improvement.     

Are <Emphasis Type="Italic">Lotus creticus</Emphasis> and <Emphasis Type="Italic">Lotus cytisoides</Emphasis> (Leguminosae) closely related species? Evidence from nuclear ribosomal ITS sequence data

Lotus creticus is a potentially important perennial legume for soil management in the Mediterranean climate. This plant is in focus of experimental research in different countries. The so-called Lotus creticus group is taxonomically problematic. Although some authors consider all members of the group as a single variable species, others segregate several species distinct from L. creticus, especially L. cytisoides. Recent morphological studies suggested that L. creticus and L. cytisoides are taxonomically distinct at specific level and not even closely related to each other. Two molecular phylogenetic studies published so far and based on one accession of L. creticus each gave conflicting results on relationships of this species. In this paper, sequences of nuclear ribosomal ITS (nrITS) are produced from multiple accessions of both L. creticus and L. cytisoides. Taxonomic identity of each accession has been tested using morphology. The new nrITS sequences are inserted in a data matrix containing a representative set of Lotus species covering all the geographical range and all major taxonomic groups of Lotus. Phylogenetic analysis of nrITS sequence data showed that L. creticus is related to L. assakensis and other species of the section Pedrosia while L. cytisoides is related to L. longisiliquosus and other species of the section Lotea. These results are important for establishing future germplasm collection, breeding and selection programs of perennial Lotus species.     

Genetic relationships among improved varieties of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) in Indonesia over the last 60 years as revealed by morphological traits and DNA markers

Morphological traits and two kinds of molecular markers were employed to study the genetic relationships among improved rice (Oryza sativa ) varieties of Indonesia since 1943. Dendrograms based on morphological traits and both molecular markers (simple sequence repeats, SSR and single nucleotide polymorphism, SNP) agreed in separating the varieties into two primary groups. Based on the morphological traits, a larger group (>60 %) contains varieties with smaller sizes compared with those in the smaller group (<40 %). SSR and SNP markers revealed that most of the varieties belonged to indica (88; 89 %) and japonica (9; 8 %) subspecies, and 3 % of varieties were not involved in two subspecies. The molecular markers revealed that the genetic diversity (H) stagnated between stage II (1967–1985) and stage III (1986–2003). However, during stage I (1943–1966), H was higher than in the other stages as revealed by SNP markers, while H in stage I was lower than in the other stages as revealed by SSR markers. In this study, the two molecular data sets were positively correlated and positive correlations between the phenotypic and molecular data depended on the kind of molecular marker: SNP had higher Mantel r values than SSRs. Besides, SSR markers seem to be appropriate for pedigree studies, while SNP markers could be used to reveal genomic relationships. These findings were attributable to the different properties of these two different markers. These results suggested that the diversity and differentiation of both the phenotypic and molecular marker variations were probably resulted from the crossing and selection in rice breeding in Indonesia. We suggest that Indonesia needs another strategy to improve new varieties to avoid a reduction in genetic diversity and similarity.     

Genetics of Wild and Managed Populations of <Emphasis Type="Italic">Leucaena esculenta</Emphasis> Subsp. <Emphasis Type="Italic">esculenta</Emphasis> (Fabaceae; Mimosoideae) in La Montaña of Guerrero,Mexico

Genetic consequences of silvicultural management of Leucaena esculenta subsp. esculenta were analyzed from eight allozyme loci in half-sib families of one wild and one managed in situ (selectively cleared) population from La Montaña de Guerrero region, Central Mexico. A reference sample (including wild, feral and cultivated individual plants) from the states of Morelos, Puebla and Guerrero, Mexico was also analyzed. Genetic variation, population structure and mating system were analyzed. All loci showed high variation (75–87.5% polymorphic loci at 95% level; 2.4–2.8 mean number of alleles per locus). All progenies showed heterozygous deficiency, but both wild and managed parental inbreeding coefficients were negative, suggesting heterosis. Progenies of managed populations differed from those of the wild and reference samples (Nei’s unbiased identities 0.874–0.934). Biparental inbreeding is suggested by Wright’s-statistics ( f = 0.313), and by outcrossing rate estimates: t_m = 0.644 (SE 0.094), and 0.645 (SE 0.193); t_s = 0.576 (SE 0.189), and 0.523 (SE 0.182), for managed and wild samples respectively. Population differentiation is significant (Θ = 0.210). The species is self-incompatible and deviations from the mixed mating model were found. Indirect estimates of products of effective population size (N_e) by the proportion of migrants (N_m) were moderate, as were the N _evalues. Variation due to ecotypic differentiation (related to altitude), prolonged artificial selection, and introduction from other areas is supported. A model of domestication of seed-propagated trees is suggested, based on extensive and in situ selection of locally adapted populations, and their diffusion to other areas.     

Development and use of microsatellite markers for genetic diversity analysis of cañahua (<Emphasis Type="Italic">Chenopodium pallidicaule</Emphasis> Aellen)

Cañahua (Chenopodium pallidicaule Aellen) is a poorly studied, annual subsistence crop of the high Andes of South America. Its nutritional value (high in protein and mineral content) and ability to thrive in harsh climates make it an important regional food crop throughout the Andean region. The objectives of this study were to develop genetic markers and to quantify genetic diversity within cañahua. A set of 43 wild and cultivated cañahua genotypes and two related species (Chenopodium quinoa Willd. and Chenopodium petiolare Kunth) were evaluated for polymorphism using 192 microsatellite markers derived from random genomic cañahua sequences produced by 454 pyrosequencing of cañahua genomic DNA. Another 424 microsatellite markers from C. quinoa were also evaluated for cross-species amplification and polymorphism in cañahua. A total of 34 polymorphic microsatellite marker loci were identified which detected a total of 154 alleles with an average of 4.5 alleles per marker locus and an average heterozygosity value of 0.49. A cluster analysis, based on Nei genetic distance, clearly separated from wild cañahua genotypes from the cultivated genotypes. Within the cultivated genotypes, subclades were partitioned by AMOVA analysis into six model-based clusters, including a subclade consisting sole of erect morphotypes. The isolation by distance test displayed no significant correlation between geographic collection origin and genotypic data, suggesting that cañahua populations have moved extensively, presumably via ancient food exchange strategies among native peoples of the Andean region. The molecular markers reported here are a significant resource for ongoing efforts to characterize the extensive Bolivian and Peruvian cañahua germplasm banks, including the development of core germplasm collections needed to support emerging breeding programs.     

“Mugnoli”: a Neglected Race of <Emphasis Type="Italic">Brassica oleracea</Emphasis> L. from Salento (Italy)

“Mugnoli”, a neglected race of Brassica oleracea L., is described from Southern Italy (Salento, Apulia). In this race, the young inflorescences together with a few leaves are harvested for use as a cooking vegetable. “Mugnoli” might be considered as an early step in the evolution of broccoli (B. oleracea L. var. italica Plenck).     

Genetic Structure of <Emphasis Type="Italic">Lycopersicon pimpinellifolium</Emphasis> (Solanaceae) Populations Collected after the ENSO Event of 1997–1998

The greatest extent of genetic variation and outcrossing for Lycopersicon pimpinellifolium occurs in northern Peru. This is also the area most affected by EI Niño Southern Oscillation (ENSO). Using morphological and the molecular markers SSRs and AFLPs, we studied the genetic structure of L. pimpinellifolium populations collected after the ENSO event of 1997–1998. This was the most intense in the last century and caused a vast increase in the size of L. pimpinellifolium populations. Populations in the area surveyed were not regionally differentiated. We did not find any cline or eco-geographic association for genetic diversity, and positive correlations between genetic and geographic distances were found only at very short distances. Flooding and water streams caused by ENSO might have facilitated a periodical seed migration from distant areas. Gene flow between populations could then occur, facilitated by the increase in the population sizes of plants and pollinators and by the high levels of stigmatic exsertion. Results revealed a significant lack of heterozygotes in comparison with those expected in a panmictic population without consanguinity. A high degree of endogamy was found in all populations. In this context, endogamy can be explained by the occurrence of crosses between relatives rather than by autogamy. In an area intensely disturbed by ENSO, we found a population that had not been reported by earlier collectors in this region. This yellow-fruited population remained morphologically and molecularly differentiated from all L. pimpinellifolium and L. esculentum populations analyzed.     

Exploring genetic variation,oil and α-tocopherol content in avocado (<Emphasis Type="Italic">Persea americana</Emphasis>) from northwestern Mexico

The Hass cultivar of avocado is the most widely grown commercial cultivar in Mexico. Unfortunately, this cultivar is poorly adapted to the Mexican low-lands with hot dry climates characteristic of northwestern Mexico. Other well-adapted avocado accessions are available for these regions, but their nutritional traits and genetic diversity have yet to be explored. In this study, we analyze oil content, (α-tocopherol) and genetic variation among five local varieties from northwest Mexico that grow in high temperatures regimes in unfertilized soils and without any agronomic management. We report significant phenotypic variability in oil and α-tocopherol components in different accessions of avocado as determined by HPLC. Interestingly, we find higher α-tocopherol content (45.02–50.66 μg/g of fresh pulp) in some local avocados compared to Hass (32.28 μg/g of fresh pulp). The analyzed accessions represent a moderately polymorphic set of genotypes as measured by microsatellite (10 alleles by locus) and SNP (1 SNP every 164.4 bp) analysis of the VTE3 and VTE4 genes, implied in the biosynthesis of tocopherols. SNP data allowed also identifying differences between the local varieties and controls (Hass and the Mexican race accession). The variation observed at the genetic, morphologic and nutritional levels provide significant new information that may be valuable in selecting and developing avocado genotypes adapted to high-temperature environments.     

‘Ladakhi tea’ <Emphasis Type="Italic">Bidens pilosa</Emphasis> L. (Asteraceae): a cultivated species in the cold desert of Ladakh Himalaya,India

Bidens pilosa L., a less-known cultivated tea species was collected from cold desert of Ladakh Himalaya, Jammu and Kashmir, India during 2004. The freshly harvested leaves are used in preparation of ‘Ladakhi tea’ locally known as ‘Saja’ or ‘Soljaa’ in cold desert of Ladakh Himalaya, Western Himalaya, Jammu and Kashmir. The local inhabitants were growing this species in their kitchen garden for this use. In the present communication, the method of preparation of this beverage is also discussed.     

Maiden hair ferns (<Emphasis Type="Italic">Adiantum</Emphasis> L., Pteridaceae–Vittarioideae) of North East India: diversity,phytochemistry and utilization

The genus Adiantum L. (Pteridaceae–Vittarioideae) are medicinal ferns with around 200 species and distributed in temperate and tropical regions. Several species of the genus are used in traditional medicine in different parts of the world including the Chinese Herbal Medicine, United States Pharmacopoeia and Ayurveda System of Medicine and Homeopathy. In the present paper, an updated and comprehensive data on species diversity of Adiantum found in the seven (7) states of North East India will be discussed. Altogether, nine (9) species are recorded and this includes A. capillus–veneris L. with two (2) races, A. caudatum L., A. edgeworthii Hook., A. flabellulatum L., A. hispidulum Sw., A. incisum Forssk., A. peruvianum Klotzsch, A. philippense L. with three (3) subspecies and A. raddianum C. Presl. Brief morphological parameters, utilization including medicinal, economical and traditional aspects, along with their bioactive components are described. The paper also aims to provide for the first time an updated compilation of species information including correct nomenclature, synonyms, distribution and propagation.     

Genetic structure of highland papayas (<Emphasis Type="Italic">Vasconcellea pubescens</Emphasis> (Lenné et C. Koch) Badillo) cultivated along a geographic gradient in Chile as revealed by Inter Simple Sequence Repeats (ISSR)

In Chile Vasconcellea pubescens is cropped to produce canned fruit, juice, jam and processed sweets. Additionally this species produces latex with a high level of papain, an important and valuable proteolytic enzyme with industrial applications. In this investigation seven ISSR primers were used to study the level and organization of genetic diversity in 333 samples of V. pubescens. Out of the 114 bands recorded, 63 proved to be polymorphic (P = 55.3%). At the species level, the genetic diversity was rather low (h = 0.01 ± 6,80188E-05, Shannon’s Index I = 0.16 ± 0,000148). The major portion of the genetic diversity was found within groups (65%). The genetic differentiation between the different groups was significant, as the AMOVA analysis suggested (Φ_pt = 0.35). When analysing the Northern area alone, the differentiation increased to Φ_pt = 0.40. When only the Southern area was analysed, Φ_pt decreased to 0.18, indicating greater genetic similarity among the samples. The results generated from Structure and Bayesian Analysis of Population Structure distinguished 8 genetically different groups, five of them located in the north and three in the south. The results are discussed in the light of the growers’ practices.     

Identification and relationships of accessions grown in the grapevine (<Emphasis Type="Italic">Vitis vinifera</Emphasis> L.) Germplasm Bank of Castilla y Léon (Spain) and the varieties authorized in the VQPRD areas of the region by SSR-marker analysis

A total of sixty-five accessions from the Spanish region of Castilla y León including those authorized in the VQPRD areas were characterized for six SSR loci. All the samples but one unknown were identified by comparison to other databases. Thirty synonymous samples and three cases of homonymy were found out, confirming in most cases ampelographic expectations. Five unique genotypes belonging to local varieties in risk of extinction were detected. Several parameters were calculated to assess the usefulness of the chosen loci in this work. A dendrogram representing the genetic similarities among the accessions was constructed using the neighbor-joining method to investigate possible parentage relationships in the sample, and to explain them from an historical and cultural point of view.     

Trends and drivers of on-farm conservation of the root legume ahipa (<Emphasis Type="Italic">Pachyrhizus ahipa</Emphasis>) in Bolivia over the period 1994/96–2012

The leguminous Andean root crop ahipa has become scarce and the current status of in situ conservation in Bolivia is concerning. Agro-biodiversity changes affect the use, conservation and socio-economic trends for ahipa (Pachyrhizus ahipa) and to substantiate this, a comparison of two cropping periods were made. Aspects of root production and the shift from cultivation of ahipa to cash crops such as maize were compared for two periods: (a) 1994/96 and (b) 2012. Our study showed that the price of ahipa had not increased in 70% of the urban markets; hence, there is little incentive to retain the cultivation of ahipa. We found that rural ahipa growers selected the largest seeds, but did not select seeds by colour. The mixed seed colour predominated the conservation of ahipa. Laborious yield enhancing practices required in field management and low market value endanger future conservation of the ahipa. We conclude that additional research is needed in order to safeguard the extant variation of ahipa, i.e. nutritional value, taste, stress tolerance and market potential.     

Adaptive values of wild × cultivated sorghum (<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench) hybrids in generations F<Subscript>1</Subscript>, F<Subscript>2</Subscript>, and F<Subscript>3</Subscript>

Gene flow between cultivated and their wild relatives is one of the main ecological concerns associated with the introduction genetically modified (GM) cultivars. GM sorghum cultivar has been developed and its commercial production may be possible in the near future. The rate of gene flow depends on the fitness of wild × cultivated sorghum hybrids. The study aimed at estimating adaptive values of wild × cultivated sorghum hybrids in generations F₁, F₂, and F₃ compared to their parents. Artificial crosses of four wild sorghums, five cultivated sorghums, and two male sterile lines were made to produce the F₁ generation, which were advanced to F₂ and F₃. Each hybrid generation and their respective parents were evaluated for their adaptive value at two sites in a randomised complete block design with seven replicates. The resulting progenies did not show serious fitness penalties. Some hybrids were as fit as their respective wild parents and no consistent differences exist between the three generations studied. Thus, the resultant wild × cultivated hybrids may act as avenue for introgression.