Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

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Genome evolution in polyploids

It is often anticipated that many of today’s diploid plant species are in fact paleopolyploids. Given that an ancient large-scale duplication will result in an excess of relatively old duplicated genes with similar ages, we analyzed the timing of duplication of pairs of paralogous genes in 14 model plant species. Using EST contigs (unigenes), we identified pairs of paralogous genes in each species and used the level of synonymous nucleotide substitution to estimate the relative ages of gene duplication. For nine of the investigated species (wheat [Triticum aestivum], maize [Zea mays], tetraploid cotton [Gossypium hirsutum], diploid cotton [G. arboretum], tomato [Lycopersicon esculentum], potato [Solanum tuberosum], soybean [Glycine max], barrel medic [Medicago truncatula], and Arabidopsis thaliana), the age distributions of duplicated genes contain peaks corresponding to short evolutionary periods during which large numbers of duplicated genes were accumulated. Large-scale duplications (polyploidy or aneuploidy) are strongly suspected to be the cause of these temporal peaks of gene duplication. However, the unusual age profile of tandem gene duplications in Arabidopsis indicates that other scenarios, such as variation in the rate at which duplicated genes are deleted, must also be considered.

/pdf/widespread-paleopolyploidy-in-model-plant-species-inferred-525akap2m8.pdf

Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes

The cotton genus ( Gossypium ) includes approximately 50 species distributed in arid to semi-arid regions of the tropic and subtropics. Included are four species that have independently been domesticated for their fiber, two each in Africa–Asia and the Americas. Gossypium species exhibit extraordinary morphological variation, ranging from herbaceous perennials to small trees with a diverse array of reproductive and vegetative characteristics. A parallel level of cytogenetic and genomic diversity has arisen during the global radiation of the genus, leading to the evolution of eight groups of diploid ( n =13) species (genome groups A–G, and K). The evolutionary history of the genus included multiple episodes of trans-oceanic dispersal, invasion of new ecological niches, and a surprisingly high frequency of natural interspecific hybridization among lineages that are presently both geographically isolated and intersterile. Recent investigations have clarified many aspects of this history, including relationships within and among the eight genome groups, the domestication history of each of the four cultivated species, and the origin of the allopolyploid cottons. Data implicate an origin for Gossypium 5–15 million years ago (mya) and a rapid early diversification of the major genome groups. Allopolyploid cottons appear to have arisen within the last million years, as a consequence of trans-oceanic dispersal of an A-genome taxon to the New World followed by hybridization with an indigenous D-genome diploid. Subsequent to formation, allopolyploids radiated into three modern lineages, including those containing the commercially important species G. hirsutum and G. barbadense . Genome doubling has led to an array of molecular genetic interactions, including inter-locus concerted evolution, differential rates of genomic evolution, inter-genomic genetic transfer, and probable alterations in gene expression. The myriad underlying mechanisms are also suggested to have contributed to both ecological success and agronomic potential.

https://www.fs.fed.us/pnw/pubs/journals/pnw_2002_wendel001.pdf

Polyploidy and the Evolutionary History of Cotton

The domestication of the Eurasian grape (Vitis vinifera ssp. sativa) from its wild ancestor (Vitis vinifera ssp. sylvestris) has long been claimed to have occurred in Transcaucasia where its greatest genetic diversity is found and where very early archaeological evidence, including grape pips and artefacts of a 'wine culture', have been excavated. Whether from Transcaucasia or the nearby Taurus or Zagros Mountains, it is hypothesized that this wine culture spread southwards and eventually westwards around the Mediterranean basin, together with the transplantation of cultivated grape cuttings. However, the existence of morphological differentiation between cultivars from eastern and western ends of the modern distribution of the Eurasian grape suggests the existence of different genetic contribution from local sylvestris populations or multilocal selection and domestication of sylvestris genotypes. To tackle this issue, we analysed chlorotype variation and distribution in 1201 samples of sylvestris and sativa genotypes from the whole area of the species' distribution and studied their genetic relationships. The results suggest the existence of at least two important origins for the cultivated germplasm, one in the Near East and another in the western Mediterranean region, the latter of which gave rise to many of the current Western European cultivars. Indeed, over 70% of the Iberian Peninsula cultivars display chlorotypes that are only compatible with their having derived from western sylvestris populations.

/pdf/multiple-origins-of-cultivated-grapevine-vitis-vinifera-l-3l17lm2hjs.pdf

Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms.

Agriculture is the lever with which humans transformed the earth over the last 10,000 years and created new forms of plant and animal species that have forever altered the face of the planet In the last decade, significant technological and methodological advances in both molecular biology and archaeology have revolutionized the study of plant and animal domestication and are reshaping our understanding of the transition from foraging to farming, one of the major turning points in human history This groundbreaking volume for the first time brings together leading archaeologists and biologists working on the domestication of both plants and animals to consider a wide variety of archaeological and genetic approaches to tracing the origin and dispersal of domesticates It provides a comprehensive overview of the state of the art in this quickly changing field as well as reviews of recent findings on specific crop and livestock species in the Americas, Eurasia, and Africa Offering a unique global perspective, it explores common challenges and potential avenues for future progress in documenting domestication

Documenting Domestication: New Genetic and Archaeological Paradigms

One hundred and two olive RAPD profiles were sampled from all around the Mediterranean Basin. Twenty four clusters of RAPD profiles were shown in the dendrogram based on the Ward’s minimum variance algorithm using chi-square distances. Factorial discriminant analyses showed that RAPD profiles were correlated with the use of the fruits and the country or region of origin of the cultivars. This suggests that cultivar selection has occurred in different genetic pools and in different areas. Mitochondrial DNA RFLP analyses were also performed. These mitotypes supported the conclusion also that multilocal olive selection has occurred. This prediction for the use of cultivars will help olive growers to choose new foreign cultivars for testing them before an eventual introduction if they are well adapted to local conditions.

Genetic relationships in the olive (Olea europaea L.) reflect multilocal selection of cultivars

The olive tree is usually hermaphrodite but self-incompatible. In the Western Mediterranean some cultivars are totally male-sterile. Three different male-sterile phenotypes have been recognised. To infer the genetic basis of male sterility we studied its inheritance and cytoplasmic diversity in wild (oleaster) and cultivated Mediterranean olive. In the cross Oliviere×Arbequina, the male-sterile trait was maternally inherited and affected all progenies. We also checked that both chloroplast and mitochondrial DNAs are maternally inherited. RFLP studies on chloroplast and mitochondrial DNAs revealed several cytotypes: two chlorotypes and four mitotypes in cultivars and oleaster (wild or feral Mediterranean olive). Furthermore, a total linkage desequilibrium between the CCK chlorotype and the MCK mitotype in cultivars and oleaster from different regions supports the fact that paternal leakage of organelles was not observed. The male sterility (ms 2) displayed by Oliviere, plus six other cultivars and three oleaster was strictly associated with the CCK chlorotype and the MCK mitotype. These facts suggest that Oliviere carries cytoplasmic male sterility. Male-fertile and male-sterile oleasters carrying this cytotype showed the presence of restorer alleles. This CMS might be due to a distant cross between olive taxa. The two other male-sterile phenotypes displayed by Lucques (ms 1) and Tanche (ms 3) were associated with the ME1 mitotype but we have not demonstrated CMS.

Cytoplasmic male sterility in the olive (Olea europaea L.)

Forty taxa belonging to 36 species and four unclassified accessions of Helianthus were studied using RAPD technology. Single ten-mer primers were screened for those amplifying fragments common to several species. We found that when several species shared a common fragment, they belong to the same section of the genus. Moreover, we also found that some fragments are common to all species of the Helianthus. Most of the fragments were found to be of the same size in these species and to share the homology indicated by molecular hybridization. Out of 118 retained fragments, 33 were common to all Helianthus species, 56 were unique to perennial species of sects. Atrorubentes and Ciliares, 24 were unique to sect. Atrorubentes, 29 were unique to sect. Helianthus, whereas 0 were unique to sect. Ciliares. Each set of common or specific fragments was assumed to belong to a genome: (1) the C genome carrying the fragments common to all species of the three sections, (2) the H genome unique to sect. Helianthus, (3) the P genome common to perennial species (sects. Atrorubentes and Ciliares), and (4) the A genome unique to sect. Atrorubentes. The genomic structure was therefore HC for sect. Helianthus, CPA for sect. Atrorubentes, and CP? for sect. Ciliares. Molecular hybridizations with amplification products revealed homologies between Helianthus genomes and several other genera in the Helianthinae sub-tribe. The simple method used to characterize these fragments led to powerful tools for recognizing genomes which reconcile the section organization of the genus and the degree of difficulty in crossing perennial and annual forms.

Evidence for several genomes in Helianthus

Hybridisation between the annual diploid sunflower (Helianthus annuus) and the perennial diploid species Helianthus mollis and Helianthus orgyalis was obtained by means of a normal crossing procedure or embryo rescue. Hybridisation success was low. All plants examined cytologically appeared to be diploid. However, the phenotypes of these diploids were not intermediate between the parents and, despite great variation, they resembled the female parent-type predominantly. Thirty five percent of plants issued from sunflower pollinated with perennial Helianthus had a phenotype resembling the female sunflower parent. On average, only 5% of the minimum number of expected RAPD and RFLP bands from male parents were recovered in plants produced from mature seeds after pollination of sunflower by H. mollis. More hybrids were found among plants obtained from embryo rescue, with an average of 25% of the male parent bands recovered per plant. Analysis of individual plants indicated the occurrence of various levels of hybridisation. There was a significant positive correlation between the number of phenotype traits related to hybrid status and the number of bands derived from the male parent. A single hybrid plant might possibly represent the product of a ’normal’ hybridisation event. The mechanisms behind these unusual events and the consequences for the breeder are discussed.

Occurrence of partial hybrids in wide crosses between sunflower (Helianthus annuus) and perennial species H. mollis and H. orgyalis

With more than 500 trees and about one hundred accessions, the olive collection in the Conservatoire Botanique National Mediterraneen de Porquerolles (CBNMP) forms the major part of the national French germplasm. We performed a molecular characterization and genetic structure analysis of the olive germplasm collection of CBNMP using nuclear RAPDs and RFLPs of mitochondrial DNA. Using four primers, 32 markers were determined allowing the identification of 114 multilocus profiles. Each of the 78 denominations were identified by one specific multilocus profile. Among the remaining 36 multilocus profiles, we noted several homonyms, synonymies and mislabeling. A dendrogram was constructed according to the Ward algorithm and Euclidean distance based on a FCA coordinate matrix. This dendrogram showed 8 clusters of olive profiles. Oil cultivars were present in all clusters, whereas cultivars used for oil and canned olive were restricted to clusters 1, 2, 3 and 4. This suggested that the selection for genotypes with large olive has been performed in a more restricted genetic pool. RFLP analysis of mitochondrial DNA showed that 85 % out of 114 olive profiles were characterized by the mitotype ME1, which is characteristic of the Eastern Mediterranean. The remaining profiles were characterized by mitotypes MOM and MCK specific of the Western Mediterranean. AMOVA analysis, based on RAPD data, showed no genetic differentiation between groups of genotypes defined according to the four mitotypes. These results showed that French olive germplasm has been derived from different gene pools with a predominance of the Eastern group. The absence of genetic differentiation suggests that some cultivars have originated from hybrids between plants from different origins.

Molecular characterization and genetic structure of olive germplasm collection in Conservatoire Botanique National Méditerraneen de Porquerolles using nuclear RAPD markers and RFLP of mitochondrial DNA

A. Bervillé

Papers

Genetic relationships in the olive (Olea europaea L.) reflect multilocal selection of cultivars

Cytoplasmic male sterility in the olive (Olea europaea L.)

Evidence for several genomes in Helianthus

Occurrence of partial hybrids in wide crosses between sunflower (Helianthus annuus) and perennial species H. mollis and H. orgyalis

Molecular characterization and genetic structure of olive germplasm collection in Conservatoire Botanique National Méditerraneen de Porquerolles using nuclear RAPD markers and RFLP of mitochondrial DNA