CYTOGENETIC STUDIES IN CLARKIA,SECTION PRIMIGENIA. IV. A CYTOLOGICAL SURVEY OF CLARKIA GRACILIS

Clarkia gracilis (2n = 28) is an allotetraploid which combines genomes from two subsections of section Primigenia. Natural populations consist of plants homozygous for a single chromosome arrangement, which may differ from the arrangements in other populations by one or more reciprocal translocations. One arrangement, the “standard,” was widespread. Cytological observations on plants derived from crosses between populations of C. gracilis, and on triploid plants derived from crosses with C. amoena subsp. huntiana, one of the parents of the tetraploid, were used to determine the end arrangements present. Ten arrangements were identified, and it was found that the standard amoena subgenome of C. gracilis is identical in end arrangement to the previously defined standard arrangement of the diploid C. amoena. Hence a race of C. amoena with this arrangement was involved in the hybridization which gave rise to C. gracilis. Evidence was found that other arrangements of C. amoena have probably been introduced into C. gracilis by subsequent introgressive hybridization. Cytological differences, coupled with differences in morphology, ecology, and distribution indicate that C. gracilis should be subdivided into four subspecies instead of the three presently recognized.     

DEVELOPMENT OF FLOWER FORM IN AN ALLOTETRAPLOID CLARKIA AND ITS PARENTAL DIPLOID SPECIES

The allotetraploid Clarkia delicata possesses a floral phenotype and breeding system intermediate to its diploid progenitors. Three patterns were observed in a comparative study of anther, sepal, and petal development using allometry and scanning electron micrographs. In Pattern 1 (e.g., anther), all three species are similar at inception and in subsequent development. Anthers of the allotetraploid mature at a size intermediate to both diploids. In Pattern 2 (e.g., sepal and petal limb), diploids exhibit divergent developmental patterns, and the allotetraploid develops similarly to one diploid. In Pattern 3 (e.g., petal size and shape), diploids exhibit divergent developmental patterns, and the allotetraploid is variously intermediate to both. In petal size (length vs. width), the diploid developmental pathways are parallel, and the allotetraploid is intermediate at all points of development. In petal shape (limb length above widest point/length below widest point vs. petal width), diploid developmental pathways intersect, and the allotetraploid is similar to one diploid at inception and the other in subsequent development.     

Constitutive Activation of an Anthocyanin Regulatory Gene PcMYB10.6 Is Related to Red Coloration in Purple-Foliage Plum

Cherry plum is a popular ornamental tree worldwide and most cultivars are selected for purple foliage. Here, we report the investigation of molecular mechanism underlying red pigmentation in purple-leaf plum ‘Ziyeli’ (Prunus cerasifera Ehrhar f. atropurpurea (Jacq.) Rehd.), which shows red color pigmentation in fruit (flesh and skin) and foliage. Six anthocyanin-activating MYB genes, designated PcMYB10.1 to PcMYB10.6, were isolated based on RNA-Seq data from leaves of cv. Ziyeli. Of these PcMYB10 genes, five (PcMYB10.1 through PcMYB10.5) show distinct spatial and temporal expression patterns, while the PcMYB10.6 gene is highly expressed in all the purple-coloured organs of cv. Ziyeli. Constitutive activation of PcMYB10.6 is closely related to red pigmentation in the leaf, fruit (flesh and skin), and sepal. However, the PcMYB10.6 activation cannot induce red pigmentation in the petal of cv. Ziyeli during late stages of flower development due to due to a lack of expression of PcUFGT. The inhibition of red pigmentation in the petal of cherry plum could be attributed to the high-level expression of PcANR that directs anthocyanidin flux to proanthocyanidin biosynthesis. In addition, PcMYB10.2 is highly expressed in fruit and sepal, but its expression cannot induce red pigmentation. This suggests the PcMYB10 gene family in cherry plum may have diverged in function and PcMYB10.2 plays little role in the regulation of red pigmentation. Our study provides for the first time an example of constitutive activation of an anthocyanin-activating MYB gene in Prunus although its underlying mechanism remains unclear.     

FERTILITY SELECTION ON A DISCRETE FLORAL POLYMORPHISM IN CLARKIA (ONAGRACEAE)

This study investigated fertility selection on a flower petal pigmentation polymorphism in Clarkia gracilis ssp. sonomensis. Natural populations are typically composed of nearly 100% spotted-petal plants, although rare populations contain a majority of unspotted plants. I compared fitness values for the two morphs using a simple fertility model to estimate selection for experimental arrays of plants placed into existing populations of different phenotypic frequencies. Both male and female reproductive success were estimated as well as the pattern of mating among phenotypes. Although the separate fitness components varied from no differences to a strong advantage for spotted plants, for every situation the selection calculations predicted an increase in the frequency of the spotted allele. Pollinator behavior and postpollination mechanisms may be responsible for the fitness differences. The apparent inability of the unspotted allele to spread though most natural populations is consistent with its selective disadvantage in this study.     

The First Comprehensive Phylogeny of Coptis (Ranunculaceae) and Its Implications for Character Evolution and Classification

Coptis (Ranunculaceae) contains 15 species and is one of the pharmaceutically most important plant genera in eastern Asia. Understanding of the evolution of morphological characters and phylogenetic relationships within the genus is very limited. Here, we present the first comprehensive phylogenetic analysis of the genus based on two plastid and one nuclear markers. The phylogeny was reconstructed using Bayesian inference, as well as maximum parsimony and maximum likelihood methods. The Swofford-Olsen-Waddell-Hillis and Bayesian tests were used to assess the strength of the conflicts between traditional taxonomic units and those suggested by the phylogenetic inferences. Evolution of morphological characters was inferred using Bayesian method to identify synapomorphies for the infrageneric lineages. Our data recognize two strongly supported clades within Coptis. The first clade contains subgenus Coptis and section Japonocoptis of subgenus Metacoptis, supported by morphological characters, such as traits of the central leaflet base, petal color, and petal shape. The second clade consists of section Japonocoptis of subgenus Metacoptis. Coptis morii is not united with C. quinquefolia, in contrast with the view that C. morii is a synonym of C. quinquefolia. Two varieties of C. chinensis do not cluster together. Coptis groenlandica and C. lutescens are reduced to C. trifolia and C. japonica, respectively. Central leaflet base, sepal shape, and petal blade carry a strong phylogenetic signal in Coptis, while leaf type, sepal and petal color, and petal shape exhibit relatively higher levels of evolutionary flexibility.     

Differential expression of duplicated peroxidase genes in the allotetraploid Brassica napus

Gene redundancy due to polyploidization provides a selective advantage for plant adaptation. We examined the expression patterns of two peroxidase genes (BnPOX1 and BnPOX2) in the natural allotetraploid Brassica napus and the model diploid progenitors Brassica rapa (Br) and Brassica oleracea (Bo) in response to the fungal pathogen Sclerotinia sclerotiorum. We demonstrated that the Bo homeolog of BnPOX1 was up-regulated after infection, while both BnPOX2 homeologs were down-regulated. A bias toward reciprocal expression of the homeologs of BnPOX1 in different organs in the natural allotetraploid of B. napus was also observed. These results suggest that subfunctionalization of the duplicated BnPOX genes after B. napus polyploidization as well as subneofunctionalization of the homeologs in response to this specific biotic stress has occurred. Retention of expression patterns in the diploid progenitors and the natural allotetraploid in some organs indicates that the function of peroxidase genes has been conserved during evolution.     

Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis

Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism.     

Cbf14 copy number variation in the A, B, and D genomes of diploid and polyploid wheat

Freezing tolerance and winter hardiness are complex traits. In the Triticeae, two loci on the group 5 chromosome homoeologs are repeatedly identified as having major effects on these traits. Recently, we found that segments of the genomic region at one of these loci, Frost resistance-2 (Fr-2) is copy number variable in barley. Freezing-tolerant winter-hardy genotypes have greater tandem copy numbers of the genomic region encompassing the C-repeat binding factor genes Cbf2A and Cbf4B at Fr-H2 than the less freezing-tolerant nonwinter-hardy genotypes. Here we report that in wheat the Cbf14 gene at Fr-2 is copy number variable. Using DNA blot hybridizations, we estimated copy numbers of Cbf14 across the different genomes of diploid and polyploid wheat. Copy numbers of Cbf14 are lower in the B genome than in the A and D genomes across all ploidy levels. Among hexaploid red wheats, winter genotypes harbor greater Cbf14 copy numbers than spring genotypes. Cbf14 copy numbers also vary across the red winter wheats such that hard wheats harbor greater copy numbers than soft wheats. Analysis of hexaploid wheat chromosome 5 substitution lines indicates that Cbf14 copy numbers in the introgressions are stable in the different backgrounds. Taken together our data suggest that higher copy number states existed in the diploid wild ancestors prior to the polyploidization events and that the loss of Cbf14 copies occurred in the cultivated germplasm.     

Bulk Segregant Analysis of an Induced Floral Mutant Identifies a MIXTA-Like R2R3 MYB Controlling Nectar Guide Formation in Mimulus lewisii

The genetic and developmental basis of many ecologically important floral traits (e.g., carotenoid pigmentation, corolla tube structure, nectar volume, pistil and stamen length) remains poorly understood. Here we analyze a chemically induced floral mutant of Mimulus lewisii through bulk segregant analysis and transgenic experiments and identify a MIXTA-like R2R3 MYB gene that controls nectar guide formation in M. lewisii flowers, which involves epidermal cell development and carotenoid pigmentation.     

Identification,isolation and expression analysis of eight stress-related <Emphasis Type="Italic">R2R3</Emphasis>-<Emphasis Type="Italic">MYB</Emphasis> genes in tartary buckwheat (<Emphasis Type="Italic">Fagopyrum tataricum</Emphasis>)

Key message

Eight R2R3 - MYB genes in tartary buckwheat were identified, and their expression patterns were comprehensively analyzed, which reveals role in plant response to abiotic stresses.

Abstract

The proteins of the R2R3-MYB superfamily play key roles in the growth and development processes as well as defense responses in plants. However, their characteristics and functions have not been fully investigated in tartary buckwheat (Fagopyrum tataricum), a strongly abiotic resistant coarse cereal. In this article, eight tartary buckwheat R2R3-MYB genes were isolated with full-length cDNA and DNA sequences. Phylogenetic analysis of the members of the R2R3-MYB superfamily between Arabidopsis and tartary buckwheat revealed that the assumed functions of the eight tartary buckwheat R2R3-MYB proteins are divided into five Arabidopsis functional subgroups that are involved in abiotic stress. Expression analysis during abiotic stress and exogenous phytohormone treatments identified that the eight R2R3-MYB genes responded to one or more treatments. This study is the first comprehensive analysis of the R2R3-MYB gene family in tartary buckwheat under abiotic stress.

     

A quantitative trait locus involved in maize yield is tightly associated to the r1 gene on the long arm of chromosome 10

We produced and studied for 3?years two synthetic populations of maize differing in their constitution only for the selected alleles present at the red color 1 (r1) locus (R-sc vs. r?Cr). r1 is a regulatory gene conferring anthocyanin pigmentation in different tissues: the R-sc allele confers pigmentation only in the aleurone seed layer, while the r?Cr allele confers pigmentation in several tissues such as root, silk and anther but the seed is colourless. The colourless population (r?Cr/r?Cr) was characterized by improved agronomic features, such as ear weight and plant height, compared with the R-sc/R-sc coloured population. This finding was confirmed by studying single F4 R/r families where the presence of the r?Cr allele conferred positive features, acting as a dominant trait. Quantitative trait locus (QTL) analysis performed using molecular markers on the long arm of chromosome 10 (bin 10.06), where the r1 gene maps, identified a QTL map position for plant height tightly associated to the r1 gene. Thus the r1 gene may represent a major QTL or it could be closely linked to another gene involved in the agronomic performance of the two populations studied.     

Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes

Whole-genome duplication (polyploidization) is among the most dramatic mutational processes in nature, so understanding how natural selection differs in polyploids relative to diploids is an important goal. Population genetics theory predicts that recessive deleterious mutations accumulate faster in allopolyploids than diploids due to the masking effect of redundant gene copies, but this prediction is hitherto unconfirmed. Here, we use the cotton genus (Gossypium), which contains seven allopolyploids derived from a single polyploidization event 1–2 Million years ago, to investigate deleterious mutation accumulation. We use two methods of identifying deleterious mutations at the nucleotide and amino acid level, along with whole-genome resequencing of 43 individuals spanning six allopolyploid species and their two diploid progenitors, to demonstrate that deleterious mutations accumulate faster in allopolyploids than in their diploid progenitors. We find that, unlike what would be expected under models of demographic changes alone, strongly deleterious mutations show the biggest difference between ploidy levels, and this effect diminishes for moderately and mildly deleterious mutations. We further show that the proportion of nonsynonymous mutations that are deleterious differs between the two coresident subgenomes in the allopolyploids, suggesting that homoeologous masking acts unequally between subgenomes. Our results provide a genome-wide perspective on classic notions of the significance of gene duplication that likely are broadly applicable to allopolyploids, with implications for our understanding of the evolutionary fate of deleterious mutations. Finally, we note that some measures of selection (e.g., dN/dS, π_N/π_S) may be biased when species of different ploidy levels are compared.     

Genome size variation and polyploidy in the resurrection plant genus Ramonda: Cytogeography of living fossils

The genus Ramonda includes three preglacial paleoendemic species surviving as the rare resurrection angiosperms of the Northern hemisphere in refugia habitats in the Balkan (Ramonda nathaliae and Ramonda serbica) and Iberian Peninsulas (Ramonda myconi). This study focuses on: assessing genome size and base composition, determining chromosome number and ploidy level in several populations, evaluating inter- and intra-specific variations in DNA content and chromosome number as well as looking for the possible hybridization in the sympatric zones of Balkan species. R. nathaliae and R. myconi are diploid species (2n = 2x = 48) while R. serbica is hexaploid (2n = 6x = 144). The mean 2C DNA values ranged from 2.30 pg for R. nathaliae to 2.59 pg for R. myconi compared to 7.91 pg for R. serbica. The base composition for R. nathaliae was 42.1% GC, for R. myconi 39.9% and for R. serbica 41.2%. In one population of R. serbica the DNA content ranged from 2C = 7.65 to 11.82 pg, revealing different ploidy levels among its individuals. In sympatric populations genome size was intermediary (～5 pg) between the diploid and hexaploid classes which indicates the hybridization ability between R. serbica and R. nathaliae. It appears that polyploidization is the major evolutionary mechanism in the genus Ramonda.     

Local adaptation for body color in Drosophila americana

Pigmentation is one of the most variable traits within and between Drosophila species. Much of this diversity appears to be adaptive, with environmental factors often invoked as selective forces. Here, we describe the geographic structure of pigmentation in Drosophila americana and evaluate the hypothesis that it is a locally adapted trait. Body pigmentation was quantified using digital images and spectrometry in up to 10 flies from each of 93 isofemale lines collected from 17 locations across the United States and found to correlate most strongly with longitude. Sequence variation at putatively neutral loci showed no evidence of population structure and was inconsistent with an isolation-by-distance model, suggesting that the pigmentation cline exists despite extensive gene flow throughout the species range, and is most likely the product of natural selection. In all other Drosophila species examined to date, dark pigmentation is associated with arid habitats; however, in D. americana, the darkest flies were collected from the most humid regions. To investigate this relationship further, we examined desiccation resistance attributable to an allele that darkens pigmentation in D. americana. We found no significant effect of pigmentation on desiccation resistance in this experiment, suggesting that pigmentation and desiccation resistance are not unequivocally linked in all Drosophila species.     

Evidence for duplication and divergence of the structural gene for phosphoglucoisomerase in diploid species of clarkia

Formal genetic analysis of the mode of inheritance of the electrophoretic phenotypes for phosphoglucoisomerase (PGI) in the annual plants Clarkia rubicunda and C. xantiana showed that these diploid species have two and three genes, respectively, that specify PGI subunits. Electrophoretic examination of seven other diploid species of Clarkia revealed that species assigned to ancestral sections in the current taxonomy have two PGI genes, whereas more specialized species have three PGI genes. Together with evidence that diploid species in two closely related genera have two PGI genes, this suggests the third PGI gene arose within Clarkia. Intergenic heterodimers are formed between polypeptides specified by the third gene and one of the other PGI genes, indicating they have a high degree of structural similarity. The combined genetic, biochemical, and phylogenetic evidence suggests that the third PGI gene resulted from a process of gene duplication. The apparent Michaelis constants (F6P to G6P) of the most common electrophoretic variants of the ancestral gene in C. xantiana and in C. rubicunda are closely similar, but that of the duplicate enzyme is much higher. The intergenic heteromer has an intermediate value. Four alleles have been identified for the duplicate PGI gene in C. xantiana, including a null allele which eliminates the activity of its product. This allele is one of the few examples of a "silenced" duplicate gene. The ancestral and duplicate genes assort independently in C. xantiana. In conjunction with the substantial chromosomal rearrangements that characterize species of Clarkia, this may mean that the duplicate PGI marks a duplicated chromosomal segment that originated from a cross between partially overlapping reciprocal translocations rather than from unequal crossing over.     

Physical mapping of rDNA sites in possible diploid progenitors of polyploid Festuca species

Festuca species form a polyploid series but only two of the diploid species have been firmly proposed as progenitors of any polyploid. The number and distribution of rDNA sites on the chromosomes of F. scariosa (section Scariosae) and the four diploid species that comprise section Montanae are presented with their relative DNA amounts and key morphological features. Comparisons of the results with those of some polyploid Festuca species from section Bovinae published previously indicate that F. scariosa and F. altissima could be diploid progenitors of the polyploids. It is unlikely that any one of the other three Montanae species is a progenitor of these polyploids.     

Polyphyletic allopolyploid origin ofRanunculus cantoniensis (4x) fromR. silerifolius (2x) ×R. chinensis (2x)

Both diploid and tetraploid experimental interspecific hybrids betweenRanunculus silerifolius (2x) andR. chinensis (2x) exhibit normal bivalent pairing. However, microspores of diploid hybrids do not undergo mitosis and their pollen grains are highly sterile, whereas tetraploid hybrids form good pollen grains after microspore division. Evidence is forwarded for the assumption thatR. cantoniensis (4x) has originated by hybridization between these two diploid parental species and by polyploidization of the diploid hybrids. Parallelisms between the different karyotypes ofR. cantoniensis (4x) andR. silerifolius (2x) suggest that the former is a species of polyphyletic origin.