Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system,influence of marine currents,and footprints of postglacial recolonization routes

Understanding the factors that contribute to population genetic divergence across a species' range is a long‐standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present‐day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic‐Mediterranean refugia after the last glacial period, with leading‐edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long‐distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life‐history and major geographic features interact to shape the distribution of genetic diversity.     

Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size

Homology was searched with genes annotated in the Aegilops tauschii pseudomolecules against genes annotated in the pseudomolecules of tetraploid wild emmer wheat, Brachypodium distachyon, sorghum and rice. Similar searches were performed with genes annotated in the rice pseudomolecules. Matrices of collinear genes and rearrangements in their order were constructed. Optical BioNano genome maps were constructed and used to validate rearrangements unique to the wild emmer and Ae. tauschii genomes. Most common rearrangements were short paracentric inversions and short intrachromosomal translocations. Intrachromosomal translocations outnumbered segmental intrachromosomal duplications. The densities of paracentric inversion lengths were approximated by exponential distributions in all six genomes. Densities of collinear genes along the Ae. tauschii chromosomes were highly correlated with meiotic recombination rates but those of rearrangements were not, suggesting different causes of the erosion of gene collinearity and evolution of major chromosome rearrangements. Frequent rearrangements sharing breakpoints suggested that chromosomes have been rearranged recurrently at some sites. The distal 4 Mb of the short arms of rice chromosomes Os11 and Os12 and corresponding regions in the sorghum, B. distachyon and Triticeae genomes contain clusters of interstitial translocations including from 1 to 7 collinear genes. The rates of acquisition of major rearrangements were greater in the large wild emmer wheat and Ae. tauschii genomes than in the lineage preceding their divergence or in the B. distachyon, rice and sorghum lineages. It is suggested that synergy between large quantities of dynamic transposable elements and annual growth habit have been the primary causes of the fast evolution of the Triticeae genomes.     

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin

Key message

This study revealed that the western Mediterranean provided the founder population for domesticated narrow-leafed lupin and that genetic diversity decreased significantly during narrow-leafed lupin domestication.

Abstract

The evolutionary history of plants during domestication profoundly shaped the genome structure and genetic diversity of today’s crops. Advances in next-generation sequencing technologies allow unprecedented opportunities to understand genome evolution in minor crops, which constitute the majority of plant domestications. A diverse set of 231 wild and domesticated narrow-leafed lupin (Lupinus angustifolius L.) accessions were subjected to genotyping-by-sequencing using diversity arrays technology. Phylogenetic, genome-wide divergence and linkage disequilibrium analyses were applied to identify the founder population of domesticated narrow-leafed lupin and the genome-wide effect of domestication on its genome. We found wild western Mediterranean population as the founder of domesticated narrow-leafed lupin. Domestication was associated with an almost threefold reduction in genome diversity in domesticated accessions compared to their wild relatives. Selective sweep analysis identified no significant footprints of selection around domestication loci. A genome-wide association study identified single nucleotide polymorphism markers associated with pod dehiscence. This new understanding of the genomic consequences of narrow-leafed lupin domestication along with molecular marker tools developed here will assist plant breeders more effectively access wild genetic diversity for crop improvement.

     

Genetic Diversity in Lens Species Revealed by EST and Genomic Simple Sequence Repeat Analysis

Low productivity of pilosae type lentils grown in South Asia is attributed to narrow genetic base of the released cultivars which results in susceptibility to biotic and abiotic stresses. For enhancement of productivity and production, broadening of genetic base is essentially required. The genetic base of released cultivars can be broadened by using diverse types including bold seeded and early maturing lentils from Mediterranean region and related wild species. Genetic diversity in eighty six accessions of three species of genus Lens was assessed based on twelve genomic and thirty one EST-SSR markers. The evaluated set of genotypes included diverse lentil varieties and advanced breeding lines from Indian programme, two early maturing ICARDA lines and five related wild subspecies/species endemic to the Mediterranean region. Genomic SSRs exhibited higher polymorphism in comparison to EST SSRs. GLLC 598 produced 5 alleles with highest gene diversity value of 0.80. Among the studied subspecies/species 43 SSRs detected maximum number of alleles in L. orientalis. Based on Nei’s genetic distance cultivated lentil L. culinaris subsp. culinaris was found to be close to its wild progenitor L. culinaris subsp. orientalis. The Prichard’s structure of 86 genotypes distinguished different subspecies/species. Higher variability was recorded among individuals within population than among populations.     

Fine-scale spatial genetic structure in predominantly selfing plants with limited seed dispersal: a rule or exception?

Gene flow at a fine scale is still poorly understood despite its recognized importance for plant population demographic and genetic processes. We tested the hypothesis that intensity of gene flow will be lower and strength of spatial genetic structure (SGS) will be higher in more peripheral populations because of lower population density. The study was performed on the predominantly selfing Avena sterilis and included: (1) direct measurement of dispersal in a controlled environment; and (2) analyses of SGS in three natural populations, sampled in linear transects at fixed increasing inter plant distances. We found that in A.sterilis major seed dispersal is by gravity in close (less than 2m) vicinity of the mother plant, with a minor additional effect of wind. Analysis of SGS with six nuclear SSRs revealed a significant autocorrelation for the distance class of 1m only in the most peripheral desert population, while in the two core populations with Mediterranean conditions, no genetic structure was found. Our results support the hypothesis that intensity of SGS increases from the species core to periphery as a result of decreased within population gene flow related to low plant density. Our findings also show that predominant self pollination and highly localized seed dispersal lead to SGS at a very fine scale, but only if plant density is not too high.     

Genetic diversity assessment in greek Medicago truncatula genotypes using microsatellite markers

In this study we examined the genetic diversity and geographic scale of genotype distribution within the model legume species Medicago truncatula widely distributed in pasture and marginal agricultural lands in Greece and other Mediterranean countries. Thirty one Medicago truncatula and Medicago littorialis accessions were chosen on the basis of their geographical distributions and studied using 9 polymorphic simple sequence repeats (SSR) markers. The number of alleles per locus varied between 3 and 7. A total of 42 alleles were detected with a mean value of 4.66 alleles per locus. Geographic origin was not related with genotypic similarity among accessions. However, there were instances of close genetic relatedness between accessions from neighboring locations in a geographic compartment. In conclusion, the presented data revealed extensive M. truncatula genotype dispersal in Greece pointing to the significance of preserving local genetic resources in their natural environment.     

Population structure of wild wheat D‐genome progenitor Aegilops tauschii Coss.: implications for intraspecific lineage diversification and evolution of common wheat

Aegilops tauschii Coss. is the D‐genome progenitor of hexaploid wheat. Aegilops tauschii, a wild diploid species, has a wide natural species range in central Eurasia, spreading from Turkey to western China. Amplified fragment length polymorphism (AFLP) analysis using a total of 122 accessions of Ae. tauschii was conducted to clarify the population structure of this widespread wild wheat species. Phylogenetic and principal component analyses revealed two major lineages in Ae. tauschii. Bayesian population structure analyses based on the AFLP data showed that lineages one (L1) and two (L2) were respectively significantly divided into six and three sublineages. Only four out of the six L1 sublineages were diverged from those of western habitats in the Transcaucasia and northern Iran region to eastern habitats such as Pakistan and Afghanistan. Other sublineages including L2 were distributed to a limited extent in the western region. Subspecies strangulata seemed to be differentiated in one sublineage of L2. Among three major haplogroups (HG7, HG9 and HG16) previously identified in the Ae. tauschii population based on chloroplast variation, HG7 accessions were widely distributed to both L1 and L2, HG9 accessions were restricted to L2, and HG16 accessions belonged to L1, suggesting that HG9 and HG16 were formed from HG7 after divergence of the first two lineages of the nuclear genome. These results on the population structure of Ae. tauschii and the genealogical relationship among Ae. tauschii accessions should provide important agricultural and evolutionary knowledge on genetic resources and conservation of natural genetic diversity.     

Genomic analysis of the emergent aquatic plant Sparganium stoloniferum provides insights into its clonality,local adaptation and demographic history

Clonal propagation and extensive dispersal of seeds and asexual propagules are two important features of aquatic plants that help them adapt to aquatic environments. Accurate measurements of clonality and effective clonal dispersal are essential for understanding the evolution of aquatic plants. Here, we first assembled a high-quality chromosome-level genome of a widespread emergent aquatic plant Sparganium stoloniferum to provide a reference for its population genomic study. We then performed high-depth resequencing of 173 individuals from 20 populations covering different basins across its range in China. Population genomic analyses revealed three genetic lineages reflecting the northeast (NE), southwest (SW) and northwest (NW) of its geographical distribution. The NE lineage diverged in the middle Pleistocene while the SW and NW lineages diverged until about 2400 years ago. Clonal relationship analyses identified nine populations as monoclonal population. Dispersal of vegetative propagules was identified between five populations covering three basins in the NE lineage, and dispersal distance was up to 1041 km, indicating high dispersibility in emergent aquatic plant species. We also identified lineage-specific positively selected genes that are likely to be involved in adaptations to saline wetlands and high-altitude environments. Our findings accurately measure the clonality, determine the dispersal range and frequency of vegetative propagules, and detect genetic signatures of local adaptation in a widespread emergent aquatic plant species, providing new perspectives on the evolution of aquatic plants.     

走出中国：酿酒酵母的起源、驯养与演化

酿酒酵母(Saccharomyces cerevisiae)被广泛应用于酒类酿造和食品发酵等行业,其被人类利用的历史已有近万年。酿酒酵母也是遗传学、分子生物学、基因组学和合成生物学等研究中常用的模式生物。近年来研究者对其自然和驯养种群进行了全球范围的生态学、群体遗传学和群体基因组学等方面的研究,更新了对其生态分布、遗传多样性、自然进化和驯养史以及进化动力等方面的认知。发现酿酒酵母在原始森林等自然环境中普遍存在,并可能偏好阔叶树树干、腐木和周围土壤等生境。中国酿酒酵母的遗传多样性显著高于世界其他地区,该物种最古老的谱系也仅发现于中国,说明中国可能是该物种的起源地。生态适应是塑造该物种群体结构的主要力量,导致其野生和驯养群体之间的明显分化。驯养群体又分化为固态发酵和液态发酵两大类群,每个类群内又形成不同的驯养谱系。该物种野生群体的遗传多样性远高于其驯养群体,而野生群体遗传多样性的形成主要由中性突变引起。中国野生和驯养群体在麦芽糖利用能力、基因组杂合性、子囊孢子形成率和孢子活力等方面表现出显著差异,表明这2个群体采取不同的生活策略来适应其不同的生活环境。驯养群体通过群体或谱系特异性基因拷贝数...     

Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum

The halophyte model plant Eutrema salsugineum (Brassicaceae) disjunctly occurs in temperate to subarctic Asia and North America. This vast, yet extremely discontinuous distribution constitutes an ideal system to examine long‐distance dispersal and the ensuing accumulation of deleterious mutations as expected in expanding populations of selfing plants. In this study, we resequenced individuals from 23 populations across the range of E. salsugineum. Our population genomic data indicate that E. salsugineum migrated “out of the Altai region” at least three times to colonize northern China, northeast Russia and western China. It then expanded its distribution into North America independently from northeast Russia and northern China, respectively. The species colonized northern China around 33.7 thousand years ago (kya) and underwent a considerable expansion in range size approximately 7–8 kya. The western China lineage is likely a hybrid derivative of the northern China and Altai lineages, originating approximately 25–30 kya. Deleterious alleles accumulated in a stepwise manner from (a) Altai to northern China and North America and (b) Altai to northeast Russia and North America. In summary, E. salsugineum dispersed from Asia to North America and deleterious mutations accumulated in a stepwise manner during the expansion of the species’ distribution.     

Compact genomes and complex evolution in the genus <Emphasis Type="Italic">Brachypodium</Emphasis>

The temperate annual grass Brachypodium distachyon is a diploid species with a chromosome base number of 5. It is strikingly different from other Eurasian species of the genus, which are perennial and often polyploid, with the diploids typically having base numbers of 8 or 9. Previously, phylogenies indicated that B. distachyon split from the other species early in the evolution of the genus, while its genome sequence revealed that extensive synteny on a chromosomal scale had been maintained with rice, a tropical grass with a base number of 12. Here we show evidence that B. distachyon may have a homoploid origin, involving ancestral interspecific hybridisation, although it does not appear to be a component of any of the perennial Eurasian allopolyploids. Using a cytogenetic approach, we show that dysploidy in Brachypodium has not followed a simple progression.     

Islands and streams: clusters and gene flow in wild barley populations from the Levant

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter‐mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analysing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication.     

Fine-scale spatial genetic structure in predominantly selfing plants with limited seed dispersal:a rule or exception?

Gene flow at a fine scale is still poorly understood despite its recognized importance for plant population demographic and genetic processes.We tested the hypothesis that intensity of gene flow will be lower and strength of spatial genetic structure(SGS) will be higher in more peripheral populations because of lower population density.The study was performed on the predominantly selfing Avena sterilis and included:(1) direct measurement of dispersal in a controlled environment;and(2) analyses of SGS in three natural populations,sampled in linear transects at fixed increasing inter-plant distances.We found that in A.sterilis major seed dispersal is by gravity in close(less than 2 m) vicinity of the mother plant,with a minor additional effect of wind.Analysis of SGS with six nuclear SSRs revealed a significant autocorrelation for the distance class of 1 m only in the most peripheral desert population,while in the two core populations with Mediterranean conditions,no genetic structure was found.Our results support the hypothesis that intensity of SGS increases from the species core to periphery as a result of decreased within-population gene flow related to low plant density.Our findings also show that predominant self-pollination and highly localized seed dispersal lead to SGS at a very fine scale,but only if plant density is not too high.     

Single‐nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula

Extensive genomic resources are available in the model legume Medicago truncatula. Here, we present the discovery and design of the first array of single‐nucleotide polymorphism (SNP) markers in M. truncatula through large‐scale Sanger resequencing of genomic fragments spanning the genome, in a diverse panel of 16 M. truncatula accessions. Both anonymous fragments and fragments targeting candidate genes for flowering phenology and symbiosis were surveyed for nucleotide variation in almost 230 kb of unique genomic regions. A set of 384 SNP markers was designed for an Illumina's GoldenGate assay, genotyped on a collection of 192 inbred lines (CC192) representing the geographical range of the species and used to survey the diversity of two natural populations. Finally, 86% of the tested SNPs were of high quality and exhibited polymorphism in the CC192 collection. Even at the population level, we detected polymorphism for more than 50% of the selected SNPs. Analysis of the allele frequency spectrum in the CC192 showed a reduced ascertainment bias, mostly limited to very rare alleles (frequency <0.01). The substantial polymorphism detected at the species and population levels, the high marker quality and the potential to survey large samples of individuals make this set of SNP markers a valuable tool to improve our understanding of the effect of demographic and selective factors that shape the natural genetic diversity within the selfing species Medicago truncatula.     

Effects of forest management on mating patterns,pollen flow and intergenerational transfer of genetic diversity in wild Arabica coffee (Coffea arabica L.) from Afromontane rainforests

Coffea arabica, the wild ancestor of all commercial Arabica coffee cultivars worldwide, is endemic to the montane rainforests of Ethiopia. These forests, which harbour the most important C. arabica gene pool, are threatened by increasing anthropogenic disturbance, potentially altering the mating patterns, pollen dispersal and maintenance of genetic diversity in C. arabica understorey populations. We genotyped 376 adult coffee shrubs and 418 progenies from three natural unmanaged, and three highly managed coffee populations, using 24 microsatellite markers. Mating system analysis of C. arabica yielded an overall multilocus outcrossing rate of 76%, which contrasts with the common knowledge that C. arabica is a predominantly selfing species. In highly managed coffee populations, paternity could be assigned to 78% of the progenies, whereas in the unmanaged natural coffee populations, only 57% of the progenies could be assigned to a father, indicating reduced long‐distance pollen dispersal in managed forests. Furthermore, the fraction of selfed progenies was significantly higher in managed (23%) than unmanaged (10%) coffee forests. Finally, the lack of spatial genetic structure in all studied populations suggests high seed dispersal in unmanaged populations, and intense berry harvesting and coffee planting in the managed populations. Our results imply that in situ conservation of the wild gene pool of C. arabica must focus on limiting intensification of coffee forest management, as decreased pollen dispersal and increased selfing in C. arabica in intensively managed populations may increase the risk of genetic erosion. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 76–88.     

A population genomics insight into the Mediterranean origins of wine yeast domestication

The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole‐genome data of oak‐associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.     

Biological performance of Myzus persicae and Macrosiphum euphorbiae (Homoptera: Aphididae) on seven wild Solanum species

Resistance level of seven accessions of wild Solanum species (Solanaceae) to Myzus persicae and Macrosiphum euphorbiae (Homoptera: Aphididae) was evaluated by measuring survival and fecundity during sleeve cage experiments and population growth on whole plants in a controlled environment. The survival was lowest on the Solanum circaeifolium spp. capsicibaccatum, Solanum pinnatisectum and Solanum trifidum accessions for M. persicae and on the S. circaeifolium spp. capsicibaccatum, Solanum okadae and S. trifidum, accessions with M. euphorbiae. Plant species significantly influenced the fecundity of both aphid species. Aphid population growth on whole plants was negatively affected by the age of the plant, but generally followed the levels of net reproductive rate on different plant species observed during the sleeve cage experiment. The population of M. persicae varied among the seven wild potato accessions with the lowest growth rates on S. circaeifolium spp. capsicibaccatum, Solanum polyadenium, Solanum tarijense and S. trifidum. The number of M. euphorbiae also varied among accessions but the smallest population was collected from S. polyadenium. The results can be used to identify sources of resistance to aphids within those accessions already known to be resistant to the Colorado potato beetle. This study highlights the difficulties involved in developing a high-throughput screening test for aphid resistance compatible with a potato breeding programme.     

Insights Gained From 50 Years of Studying the Evolution of Self-Compatibility in <Emphasis Type="Italic">Leavenworthia</Emphasis> (Brassicaceae)

The shift from outcrossing to selfing is one of the most common evolutionary trends in plants, and there is intense interest in why this is so. The genus Leavenworthia has been the focus of research on this question for half of a century, with particular attention paid to the evolution of self-compatibility from self-incompatibility. In this review, we discuss the last 50 years of research concerning this evolutionary transition in Leavenworthia. Selfing appears to have evolved independently at minimum three times within this genus of eight species. Work on the ecological basis of mating system evolution in Leavenworthia has clarified that selection among individuals is likely a major force behind the recurrent evolution of selfing. Although inadequate pollination is appreciated as a factor favoring selfing, definitive ecological mechanisms that act to favor selfing are still not known and future work on the efficacy of pollinating bees and the effects of climate change is needed. Recent research has likely identified the SRK ortholog at the S-locus controlling self-incompatibility in Leavenworthia alabamica. Analyses of S-locus variation have revealed substantial S-allele diversity in outcrossing populations, with the recurrent fixation of mutations at the S-locus permitting the parallel evolution of selfing in this species. Although we appreciate some of the factors that may explain the evolution of selfing in this group, there is less known about the mechanisms underlying the widespread maintenance of outcrossing at the population and species levels. Studies in Leavenworthia have revealed that genetic diversity is lost over the long-term within selfing populations and leads to elevated population subdivision, but work is needed to determine why these genetic consequences of selfing cause lineages to become evolutionary dead ends.