Microsatellites for three distantly related genera in the Brassicaceae

Microsatellites are important genetic markers both in population genetics and for delimitation of closely related species. However, to develop microsatellites for each target organism is expensive and time consuming. In this study, we have therefore developed 65 new microsatellite primers for the species Draba nivalis and tested cross-species and cross-genus transfer success of these primers for two other genera in the Brassicaceae; Cardamine and Smelowskia. Furthermore, 15 previously developed microsatellites were tested for amplification in these three genera. The microsatellite markers that amplify across these genera may be useful for other genera in the Brassicaceae as well.     

Comparative mapping and rapid karyotypic evolution in the genus helianthus

Comparative genetic linkage maps provide a powerful tool for the study of karyotypic evolution. We constructed a joint SSR/RAPD genetic linkage map of the Helianthus petiolaris genome and used it, along with an integrated SSR genetic linkage map derived from four independent H. annuus mapping populations, to examine the evolution of genome structure between these two annual sunflower species. The results of this work indicate the presence of 27 colinear segments resulting from a minimum of eight translocations and three inversions. These 11 rearrangements are more than previously suspected on the basis of either cytological or genetic map-based analyses. Taken together, these rearrangements required a minimum of 20 chromosomal breakages/fusions. On the basis of estimates of the time since divergence of these two species (750,000-1,000,000 years), this translates into an estimated rate of 5.5-7.3 chromosomal rearrangements per million years of evolution, the highest rate reported for any taxonomic group to date.     

Genetic analysis of sunflower domestication

Quantitative trait loci (QTL) controlling phenotypic differences between cultivated sunflower and its wild progenitor were investigated in an F(3) mapping population. Composite interval mapping revealed the presence of 78 QTL affecting the 18 quantitative traits of interest, with 2-10 QTL per trait. Each QTL explained 3.0-68.0% of the phenotypic variance, although only 4 (corresponding to 3 of 18 traits) had effects >25%. Overall, 51 of the 78 QTL produced phenotypic effects in the expected direction, and for 13 of 18 traits the majority of QTL had the expected effect. Despite being distributed across 15 of the 17 linkage groups, there was a substantial amount of clustering among QTL controlling different traits. In several cases, regions influencing multiple traits harbored QTL with antagonistic effects, producing a cultivar-like phenotype for some traits and a wild-like phenotype for others. On the basis of the directionality of QTL, strong directional selection for increased achene size appears to have played a central role in sunflower domestication. None of the other traits show similar evidence of selection. The occurrence of numerous wild alleles with cultivar-like effects, combined with the lack of major QTL, suggests that sunflower was readily domesticated.     

GENETIC SIMILARITY IS HIGH BETWEEN INTERCONTINENTAL DISJUNCT SPECIES OF SENECIO (ASTERACEAE)

Senecio flavus (Decne.) Schultz-Bip. of the Saharo-Arabian and Namibian deserts and Senecio mohavensis Gray of the Mojave and Sonoran deserts form a pair of closely related disjunct annual taxa. The two species exhibit slight morphological differences and have different ploidy levels: all North American populations examined are tetraploid, while African and Asian populations are diploid. Senecio flavus comprises two morphologically and geographically distinct subspecies, subsp. flavus and subsp. breviflorus Kadereit. Electrophoretic examination of 13 enzymes revealed that the subsp. breviflorus has two additional isozymes relative to subsp. flavus, and that 5. mohavensis has four additional isozymes relative to subsp. breviflorus. Senecio flavus subsp. breviflorus and S. mohavensis are identical at 20 of the 21 (I = 0.952) remaining homologous loci. This value is much higher than the genetic identity values observed in other taxa with disjunct intercontinental distributions such as members of Agastache, Datisca, Liriodendron, and Styrax. This suggests that the Senecio disjunction may be of recent origin. Senecio flavus subsp. flavus from North Africa and Namibia has lower genetic identity values with S. mohavensis (0.857 and 0.805, respectively), implicating S. flavus subsp. breviflorus as the progenitor of 5. mohavensis. The complete lack of heterozygosity confirms that the plants are highly autogamous, and thus could have attained their disjunct distribution through long distance dispersal.     

Molecular Data and the Dynamic Nature of Polyploidy

During the past decade, molecular techniques have provided a wealth of data that have facilitated the resolution of several controversial questions in polyploid evolution. Herein we have focused on several of these issues: (1) the frequency of recurrent formation of polyploid species; (2) the genetic consequences of multiple polyploidizations within a species; (3) the prevalence and genetic attributes of autopolyploids; and (4) the genetic changes that occur in polyploid genomes following their formation.

Molecular data provide a more dynamic picture of polyploid evolution than has been traditionally espoused. Numerous studies have demonstrated multiple origins of both allopolyploids and autopolyploids. In several polyploid species studied in detail, multiple origins were found to be frequent on a local geographic scale, as well as during a short span of time. Molecular data strongly suggest that recurrent formation of polyploid species is the rule, rather than the exception. In addition, molecular data indicate that recurrent formation of polyploids has important genetic consequences, introducing considerable genetic variation from diploid progenitors into polyploid derivatives.

Molecular data also suggest a much more important role for natural autopolyploids than has been historically envisioned. In contrast to the longstanding view of autopolyploidy as being rare, molecular data continue to reveal steadily increasing numbers of well-documented autoploids having tetrasomic or higher-level polysomic inheritance. Although autopolyploidy undoubtedly occurs much less frequently than allopolyploidy in natural populations, it nonetheless has been a significant evolutionary mechanism. Molecular data also provide compelling genetic evidence that contradicts the traditional view of autopolyploidy as being maladaptive. Electrophoretic studies have revealed three important attributes of autopolyploids compared to their diploid progenitors: (1) enzyme multiplicity, (2) increased heterozygosity, and (3) increased allelic diversity. Genetic variability is, in fact, typically substantially higher in autopoloids than in their diploid progenitors. These genetic attributes of autopolyploids are due to polysomic inheritance and provide strong genetic arguments for the potential success of autopolyploids in nature.

In addition to providing numerous important insights into the formation of polyploids and the immediate genetic consequences of polyploidy, molecular data also have been used to study the subsequent evolution of polyploid genomes. Common hypotheses on the subsequent evolution of polyploid genomes include (1) gene silencing, eventually leading to extensively diploidized polyploid genomes; (2) gene diversification, resulting in regulatory or functional divergence of duplicate genes; and (3) genome diversification, resulting in chromosomal repatterning. Compelling, but limited, genetic evidence for all of these factors has been obtained in molecular analyses of polyploid species. The occurrence of these processes in polyploid genomes indicates that polyploid genomes are plastic and susceptible to evolutionary change.

In summary, molecular data continue to demonstrate that polyploidization and the subsequent evolution of polyploid genomes are very dynamic processes.     

What Can Molecular and Morphological Markers Tell Us About Plant Hybridization?

The study of hybrids and their evolutionary significance is often based on a number of tacit assumptions regarding character expression in hybrids. This article examines morphological, chemical, and molecular character expression in hybrids to determine whether traditionally recognized properties of hybrid plants, such as hybrid intermediacy and character coherence, are actually supported by empirical evidence, and also examines the impact of hybrids on phylogenetic analyses. We show that hybrids are a mosaic of both parental and intermediate morphological characters rather than just intermediate ones, and that a large proportion of first (64%) and later generation hybrids (89%) exhibit extreme or novel characters. Chemical character expression in hybrids is more predictable, with predominantly additive or complementary expression for both first generation hybrids (68%) and hybrid taxa (54%). Likewise, the genetic basis, and thus the expression of molecular characters, is well-worked out and predictable, although non-Mendelian inheritance has been reported in a few instances for molecular markers as well.

There is even less empirical support for the concept of character coherence than hybrid intermediacy. Although morphological character coherence has been reported in both artificial and natural hybrid populations, it appears to be the exception rather than the rule. This idiosyncratic relationship among morphological characters is shown to be the norm for the relationship of morphological to molecular characters, as well as for the relationship among molecular characters.

Hybrids are shown to have little impact on the topology of nonhybrid taxa in phylogenetic trees. However, the expression of primitive vs. derived character states, the placement of hybrids in cladograms, the number of equally parsimonious trees produced, and the effects of hybrids on phylogenetic topology do not appear to be predictable. Thus, cladistic identification of hybrid taxa is difficult and may not be possible based on phenotypic data, regardless of the analytical tools used.     

Molecular Evidence and the Origin and Development of the Domesticated Sunflower (Helianthus annum, Asteraceae)

The domesticated sunflower,Helianthus annuus, is an important economic crop, yet molecular data regarding its evolution are limited. Here we review morphological, geographical, archaeological, and molecular evidence pertaining to its origin and development. New isozyme and chloroplast DNA (cpDNA) evidence is also presented. Morphological, geographical, and archaeological evidence has led to the hypothesis that the domesticated sunflower was derived from a wild/weedy form ofH. annuus possibly in the Midwest. Molecular evidence was concordant with this hypothesis. A high degree of enzymatic and cpDNA sequence similarity was observed between wild and domesticatedH. annuus, and domesticatedH. annuus contained a subset of the alleles and cpDNAs found in wildH. annuus. The extensive polymorphism in the wild plants and the virtual monomorphism in cultivated lines for both isozyme and cpDNA phenotypes further suggest a single origin of the domesticated sunflower from a very limited gene pool. In addition, Native American varieties of the domesticated sunflower were genetically more variable than other cultivated lines, possibly indicating that they gave rise to the other cultivated stocks. Molecular evidence did not, however, allow conclusions as to the exact geographic origin of the domesticated sunflower.     

Genetic consequences of selection during the evolution of cultivated sunflower

We mapped quantitative trait loci (QTL) controlling differences in seed oil content and composition between cultivated and wild sunflower and used the results, along with those of a previous study of domestication-related QTL, to guide a genome-wide analysis of genetic variation for evidence of past selection. The effects of the seed oil QTL were almost exclusively in the expected direction with respect to the parental phenotypes. A major, oil-related QTL cluster mapped near a cluster of domestication-related QTL on linkage group six (LG06), the majority of which have previously been shown to have effects that are inconsistent with the parental phenotypes. To test the hypothesis that this region was the target of a past selective sweep, perhaps resulting in the fixation of the antagonistic domestication-related QTL, we analyzed simple sequence repeat (SSR) diversity from 102 markers dispersed throughout the sunflower genome. Our results indicate that LG06 was most likely the target of multiple selective sweeps during the postdomestication era. Strong directional selection in concert with genetic hitchhiking therefore offers a possible explanation for the occurrence of numerous domestication-related QTL with apparently maladaptive phenotypic effects.