Genomic analysis unveils reduced genetic variability but increased proportion of heterozygotic genotypes of the intensively managed mezcal agave,Agave angustifolia

Premise

The central Oaxaca Basin has a century-long history of agave cultivation and is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as “espadín” is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades-long clonal propagation has affected its genetics.

Methods

Using restriction-site-associated DNA sequencing and over 8000 single-nucleotide polymorphisms, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations.

Results

Genetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation.

Conclusions

The considerable heterozygosity found in espadín is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved.

     

Using seminatural and simulated habitats for seed germination ecology of banana wild relatives

1. Ecologically meaningful seed germination experiments are constrained by access to seeds and relevant environments for testing at the same time. This is particularly the case when research is carried out far from the native area of the studied species.
2. Here, we demonstrate an alternative—the use of glasshouses in botanic gardens as simulated‐natural habitats to extend the ecological interpretation of germination studies. Our focal taxa were banana crop wild relatives (Musa acuminata subsp. burmannica, Musa acuminata subsp. siamea, and Musa balbisiana), native to tropical and subtropical South‐East Asia. Tests were carried out in Belgium, where we performed germination tests in relation to foliage‐shading/exposure to solar radiation and seed burial depth, as well as seed survival and dormancy release in the soil. We calibrated the interpretation of these studies by also conducting an experiment in a seminatural habitat in a species native range (M. balbisiana—Los Baños, the Philippines), where we tested germination responses to exposure to sun/shade. Using temperature data loggers, we determined temperature dynamics suitable for germination in both these settings.
3. In these seminatural and simulated‐natural habitats, seeds germinated in response to exposure to direct solar radiation. Seed burial depth had a significant but marginal effect by comparison, even when seeds were buried to 7 cm in the soil. Temperatures at sun‐exposed compared with shaded environments differed by only a few degrees Celsius. Maximum temperature of the period prior to germination was the most significant contributor to germination responses and germination increased linearly above a threshold of 23℃ to the maximum temperature in the soil (in simulated‐natural habitats) of 35℃.
4. Glasshouses can provide useful environments to aid interpretation of seed germination responses to environmental niches.

     

Genetic structure of three populations of rhesus macaques (Macaca mulatta): Implications for genetic management

One of the prime concerns at zoos and at primate breeding facilities is to maintain genetic variability. This can be accomplished by avoiding inbreeding. It is relatively easy to assess genetic variability and the level of inbreeding by using pedigree information and genetic markers. In this study we used genetic markers controlled by 6 independent polymorphic loci (GPI, PGD, CA2, MPI, DIA1, Tf) to ascertain genetic variation in two captive and one wild population of rhesus monkeys. Two other loci ADA and NP were also examined and found to be monomorphic in the three populations. F-statistics and contingency chi-square analyses indicated that there was significant genetic differentiation among the populations. We also found that the mean heterozygosities were very similar in the three populations, in spite of the diverse breeding strategies. These data are important because rhesus monkeys are frequently used for biomedical research; and the genetic markers provide useful information for genetic management of captive colonies of nonhuman primates. © 1992 Wiley-Liss, Inc.     

Genetic structure of wild and cultivated olives in the central Mediterranean basin

BACKGROUND AND AIMS: Olive cultivars and their wild relatives (oleasters) represent two botanical varieties of Olea europaea subsp. europaea (respectively europaea and sylvestris). Olive cultivars have undergone human selection and their area of diffusion overlaps that of oleasters. Populations of genuine wild olives seem restricted to isolated areas of Mediterranean forests, while most other wild-looking forms of olive may include feral forms that escaped cultivation. METHODS: The genetic structure of wild and cultivated olive tree populations was evaluated by amplified fragment length polymorphism (AFLP) markers at a microscale level in one continental and two insular Italian regions. KEY RESULTS: The observed patterns of genetic variation were able to distinguish wild from cultivated populations and continental from insular regions. Island oleasters were highly similar to each other and were clearly distinguishable from those of continental regions. Ancient cultivated material from one island clustered with the wild plants, while the old plants from the continental region clustered with the cultivated group. CONCLUSIONS: On the basis of these results, we can assume that olive trees have undergone a different selection/domestication process in the insular and mainland regions. The degree of differentiation between oleasters and cultivated trees on the islands suggests that all cultivars have been introduced into these regions from the outside, while the Umbrian cultivars have originated either by selection from local oleasters or by direct introduction from other regions.     

Patterns of genetic variability within and among populations of wild radish,Raphanus raphanistrum (Brassicaceae)

The genetic structure of populations is an important determinant of the evolutionary potential of a species. Colonizing plants tend to be characterized by low within- and high among-population variability. Genetic differentiation of both floral traits and isozymes was studied in six populations of wild radish (Raphanus raphanistrum). Evidence for differentiation in both sets of traits was found, but patterns of differentiation of floral traits did not coincide with isozyme differentiation. Contrary to most colonizing species, wild radish showed high within- and only moderate among-population variability at isozyme loci. In addition, levels of differentiation did not correspond to geographic distance between the populations. These results are likely due at least in part to the self-incompatibility system of this species, long-distance movement of large numbers of wild radish seeds by humans, and introgression from cultivated radish (R. sativus).     

Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis)

Analysis of fine scale genetic structure in continuous populations of outcrossing plant species has traditionally been limited by the availability of sufficient markers. We used a set of 468 SNPs to characterize fine‐scale genetic structure within and between two dense stands of the wild ancestor of maize, teosinte (Zea mays ssp. parviglumis). Our analyses confirmed that teosinte is highly outcrossing and showed little population structure over short distances. We found that the two populations were clearly genetically differentiated, although the actual level of differentiation was low. Spatial autocorrelation of relatedness was observed within both sites but was somewhat stronger in one of the populations. Using principal component analysis, we found evidence for significant local differentiation in the population with stronger spatial autocorrelation. This differentiation was associated with pronounced shifts in the first two principal components along the field. These shifts corresponded to changes in allele frequencies, potentially due to local topographical features. There was little evidence for selection at individual loci as a contributing factor to differentiation. Our results demonstrate that significant local differentiation may, but need not, co‐occur with spatial autocorrelation of relatedness. The present study represents one of the most detailed analyses of local genetic structure to date and provides a benchmark for future studies dealing with fine scale patterns of genetic diversity in natural plant populations.     

Study on genetic coadaptability of wild quail populations in China

Genetic coadaptability of wild Japanese quail, wild Common quail and Domestic quail populations in China was studied using 7 microsatellite DNA markers and Monte Carlo method to test genetic disequilibrium. The molecular effects of genetic coadaptability were analyzed through a new statistical model of neutral site. The results showed that genetic coadaptability dominated the genetic disequilibrium of the three quail populations, and totally 16.67%, 9.66% and 10.05% of non-allelic combinations were in the genetic disequilibrium in wild Japanese quail, wild Common quail and Domestic quail populations, respectively. Genetic coadaptability existed at almost all the tested sites. In the molecular point of view, genetic coadaptability plays an important role of keeping lots of polymorphisms in natural populations. Therefore, it is another key factor to the genetic disequilibrium in the population except for linkage. The results enrich the conceptions and connotations of genetic disequilibrium, and help us know more about genetic coadaptability and its effects, and lay a foundation of evaluation and protection of wild quail genetic resources in China.     

栽培植物野生近缘种的保护与利用

栽培植物是人类赖以生存和发展的重要物质基础。全球人口与人均需求量的持续增长导致对植物资源的需求与日俱增。栽培植物较低的遗传多样性是限制其产量增长和质量提高的主要因素。栽培植物野生近缘种在自然环境中积累了丰富的遗传变异, 并在应对环境变化的过程中产生了很多新的适应性状, 是栽培植物种质创新和品种改良的重要遗传资源。然而, 栽培植物野生近缘种的存续和自然进化因生境破坏以及全球气候变化等正面临严重威胁, 需要采取有效的措施进行保护。本文总结了国内外对栽培植物野生近缘种进行原生境保护与迁地保护所取得的进展, 并基于我国实际情况提出了栽培植物野生近缘种的保护建议。此外, 本文还对栽培植物野生近缘种利用技术进行了梳理, 探讨了栽培植物野生近缘种遗传资源可持续利用的新思路。最后, 我们以长江流域几种代表性栽培植物为例, 对主要作物类型的保护与利用情况进行了讨论。     

Study on genetic coadaptability of wild quail populations in China

Genetic coadaptability, developed from the process of evolution, is one of the properties of gene pool as well as gene frequency of each locus. It was explained in detail by Nei[1] in 1973. He proposed that during evolutionary process, non-allelic genes o…     

ISSR primer screening and preliminary evaluation of genetic diversity in wild populations of Gycyrrhiza uralensis

Fourteen efficient inter-simple sequence repeat (ISSR) primers were screened and optimized for detecting the genetic diversity in wild populations of Glycyrrhiza uralensis Fisch. By using these primers, 249 polymorphic bands out of a total of 270 (92.2 %) were generated from 70 individuals of 4 wild G. uralensis populations sampled from Inner Mongolia Province of China. Nei’s gene diversity (h) and Shannon index (I) calculated from the data matrix of the ISSR phenotypes revealed a high level of genetic diversity with h = 0.268 and I = 0.415 within this plant. Analysis of molecular variation (AMOVA) showed that most of the genetic variation (81 %) occurred within the populations, whereas the variance among populations was only 19 %. The UPGMA tree based on Nei’s unbiased genetic diversity illustrated that populations from Bulage and Bayanwusu were genetically close related, while the population from Shanghaimiao was found to be the most diverse from the other three. The high genetic diversity implies that the wild resources of this species could be restored soon if an appropriate and efficient protection strategy was employed. Our results also provided an optimized method for evaluating genetic diversity of G. uralensis using ISSR markers which was useful for further investigation.     

Phenotypic variation of life‐history traits in native,invasive, and landrace populations of Brassica tournefortii

Varying environments can result in different patterns of adaptive phenotypes. By performing a common greenhouse experiment, we identified phenotypic differentiation on phenology, leaf morphology, branch architecture, size, and reproduction, among native, invasive, and landrace ranges of Brassica tournefortii. We first compared trait means and fitness functions among ranges, then we analyzed how trait means and selection strength of populations respond to varying aridity. Most traits varied such that landrace > invasive > native. Excluding reproduction, which was positively selected, most trait PCs experienced nonlinear selection in the native range but frequently shifted to directional selection in invasive and/or landrace ranges. The absence of strong clines for trait means in landrace and invasive populations suggest that agricultural practices and novel environments in source locations affected adaptive potential. Selection strength on faster reproductive phenology (negative directional) and leaf margin trait (disruptive) PCs coincided with increasing moisture. In native populations, higher aridity was associated with more days to reproduction, but landrace and invasive populations show stable mean time to reproduction with increasing moisture. A stable adaptive trait can increase range expansion in the invasive range, but stability can be beneficial for future harvest of B. tournefortii seed crops in the face of climate change.     

Endemic wild potato (Solanum spp.) biodiversity status in Bolivia: Reasons for conservation concerns

Crop wild relatives possess important traits, therefore ex situ and in situ conservation efforts are essential to maintain sufficient options for crop improvement. Bolivia is a centre of wild relative diversity for several crops, among them potato, which is an important staple worldwide and the principal food crop in this country. Despite their relevance for plant breeding, limited knowledge exists about their in situ conservation status. We used Geographic Information Systems (GIS) and distribution modelling with the software Maxent to better understand geographic patterns of endemic wild potato diversity in Bolivia. In combination with threat layers, we assessed the conservation status of all endemic species, 21 in total. We prioritised areas for in situ conservation by using complementary reserve selection and excluded 25% of the most-threatened collection sites because costs to implement conservation measures at those locations may be too high compared to other areas. Some 70% (15 of 21 species) has a preliminary vulnerable status or worse according to IUCN red list distribution criteria. Our results show that four of these species would require special conservation attention because they were only observed in <15 locations and are highly threatened by human accessibility, fires and livestock pressure. Although highest species richness occurs in south-central Bolivia, in the departments Santa Cruz and Chuquisaca, the first priority area for in situ conservation according to our reserve selection exercise is central Bolivia, Cochabamba; this area is less threatened than the potato wild relatives’ hotspot in south-central Bolivia. Only seven of the 21 species were observed in protected areas. To improve coverage of potato wild relatives’ distribution by protected areas, we recommend starting inventories in parks and reserves with high modelled diversity. Finally, to improve ex situ conservation, we targeted areas for germplasm collection of species with <5 accessions conserved in genebanks.     

Use of molecular markers in participatory plant breeding: assessing the genetic variability in cotton populations bred by farmers

In participatory plant breeding, farmers are involved in simple selection schemes that are not suitable for assessing genetic variability in the segregating populations. We propose to use information derived from molecular marker analyses to help monitoring such populations. In this study, we used three indicators to compare genetic variability in eight genetic structures, that is three plant populations selected by farmers over five generations, three nonselected populations and two commercial varieties. The three indicators were the polymorphic locus rate, heterozygosity rate and dissimilarity index. The results highlighted that the genetic variability decreased more with farmers’ selection than with environmental factors. The breeding process was not complete because genetic variability in the selected populations was midway between that of the nonselected populations and that of the commercial varieties monitored. The three proposed indicators were relevant for describing the studied populations. They could be interpreted according to a grid drawn up on the basis of the results of the present study.     

中国野生稻遗传资源的保护及其在育种中的利用

我国有三种野生稻,即普通野生稻(Oryza rufipogon)、药用野生稻(O.officinalis)和瘤粒野生稻(O.meyeriana)。这三种野生稻均被列为国家二级保护植物(渐危种)。调查结果表明,野生稻由于其自然群落大量丧失而濒危,濒危程度为普通野生稻>药用野生稻>瘤粒野生稻。造成濒危的主要原因是人为的破坏活动。人类的经济活动导致了野生稻生境丧失、生境质量不断恶化、栖息地越来越少;人类的活动也导致了外来种的入侵。目前,对野生稻的保护措施主要有就地保护(原地保护或原位保护)和迁地保护(易地保护或异位保护)。易地保护包括以种子保存的种质厍、以种茎保存的种质圃和以器官培养物作为材料的超低温保存。野生稻具有许多优良特性,如特强的耐寒性、高的抗病虫性、优质蛋白质含量高、功能叶片耐衰老的特异性、特强的再生性、良好的繁茂性及生长优势等等,这些优良特性已被广泛用于水稻常规育种和杂交育种中,并取得了巨大的社会效益和经济效益。有关野生稻生物技术方面的研究,如花药培养、原生质培养、体细胞杂交和基因工程等方面已取得了较大的进展。野生稻将在水稻育种中发挥越来越重要的作用。