Yant L, Arnold B, DaCosta J, Lahner B, Weisman C, Hollister JD, Salt DE, Bomblies K. Selective sweeps maintained in the face of massive gene flow and hybridization in serpentine-adapted Arabidopsis arenosa. Submitted.
Yant L, Bomblies K. Genome management and mismanagement – cell-level problems and opportunities of whole genome duplication. (Invited review). Genes and Development. 2015.Abstract

Whole genome duplication (WGD) is an enormous mutation that doubles the DNA content in the nucleus. It has occurred in all eukaryotic lineages, and arises in somatic cells of multicellular plants as well as animals. WGD reshapes cellular geometry and physiology, and has important roles in development and stress resilience. It is also associated with aging and disease, and recognized as an engine of dangerous diversity in tumorigenesis. Here we discuss the adaptive potential and problems associated with WGD, focusing primarily on cellular effects and seeing polyploidy as a key player in cell lineage evolution, with strong parallels across kingdoms. 

Yant L, Collani S, Puzey J, Levy C, Kramer EM. Molecular basis for three-dimensional elaboration of the Aquilegia petal spur. Proceedings of the Royal Society B. 2015;282 (1803). Publisher's VersionAbstract

By enforcing specific pollinator interactions, Aquilegia petal nectar spurs maintain reproductive isolation between species. Spur development is the result of three-dimensional elaboration from a comparatively two-dimensional primordium. Initiated by localized, oriented cell divisions surrounding the incipient nectary, this process creates a pouch that is extended by anisotropic cell elongation. We hypothesized that the development of this evolutionary novelty could be promoted by non-mutually exclusive factors, including (i) prolonged, KNOX-dependent cell fate indeterminacy, (ii) localized organ sculpting and/or (iii) redeployment of hormone-signalling modules. Using cell division markers to guide transcriptome analysis of microdissected spur tissue, we present candidate mechanisms underlying spur outgrowth. We see dynamic expression of factors controlling cell proliferation and hormone signalling, but no evidence of contribution from indeterminacy factors. Transcriptome dynamics point to a novel recruitment event in which auxin-related factors that normally function at the organ margin were co-opted to this central structure. Functional perturbation of the transition between cell division and expansion reveals an unexpected asymmetric component of spur development. These findings indicate that the production of this three-dimensional form is an example of organ sculpting via localized cell division with novel contributions from hormone signalling, rather than a product of prolonged indeterminacy.

  • Received November 12, 2014.
  • Accepted January 13, 2015.
Yant L. When two is a crowd: mitochondrial genome merger and its aftermath. New Phytologist. 2015;206 (1) :8. Publisher's Version
Bomblies K, Higgins J, Yant L. Meiosis Evolves -Adaptation to external and internal environments. Tansley Review. New Phytologist. 2015. Publisher's VersionAbstract

Meiosis is essential for the fertility of most eukaryotes and its structures and progression are conserved across kingdoms. Yet many of its core proteins show evidence of rapid or adaptive evolution. What drives the evolution of meiosis proteins? How can constrained meiotic processes be modified in response to challenges without compromising their essential functions? In surveying the literature, we find evidence of two particularly potent challenges to meiotic chromosome segregation that probably necessitate adaptive evolutionary responses: whole genome duplication, and abiotic environment, especially temperature. Evolutionary solutions to both kinds of challenge likely involve modification of homologous recombination and synapsis, probably via adjustments of core structural components important in meiosis I. Synthesizing these findings with broader patterns of the evolution of meiosis genes suggests that the structural components of meiosis co-evolve as adaptive modules and may change in primary sequence and function while maintaining three-dimensional structures and protein interactions. The often sharp divergence of these genes among species likely reflects periodic modification of entire multiprotein complexes driven by genomic or environmental changes. We suggest that the pressures that cause meiosis to evolve to maintain fertility may cause pleiotropic alterations of global crossover rates. We highlight several important areas for future research. 

Posé D, Yant L. DNA-binding Factor Target Identification by Chromatin Immunoprecipitation (ChIP) in Plants. In: Methods in Molecular Biology, Vol. 1363, Plant Signal Transduction. Vol. 1363. Springer ; 2015. Publisher's VersionAbstract

Chromatin immunoprecipitation (ChIP) allows the precise identification of genomic loci that physically interact with a protein of interest, whether that protein is a transcription factor, a core polymerase, a his- tone, or other chromatin-associated protein. In short, tissue is first cross-linked to freeze a population of DNA-protein interactions at a stage of interest. Chromatin is then extracted, fragmented, and incubated with a specific antibody against the protein of interest. Next, the resultant DNA-protein complexes are immunoprecipitated and captured using beads that bind to the antibody constant region. Samples are finally reverse cross-linked to separate the bound fragments and the DNA is purified. This DNA is analyzed by quantitative PCR for enrichment of genomic regions expected to be bound by the protein under study. The protocol detailed in this chapter has been successfully applied in the identification of target genes for seven transcriptional regulators of diverse classes involved in Arabidopsis thaliana floral transition. 

Sharma B, Yant L, Hodges SA, Kramer EM. Understanding the development and evolution of novel floral form in Aquilegia. Current opinion in plant biology. 2014;17 :22-27. Publisher's VersionAbstract

Flowers of the lower eudicot Aquilegia (columbine) possess morphological innovations, namely elaborate petal spurs and a fifth distinct organ identity, the staminodium, that are well suited to the investigation of key questions in developmental evolution. The recent evolution of these characteristics combined with a growing set of genetic and genomic resources has provided insight into how the traits arose and diversified. The petal spur appears to represent a key innovation that diversified largely via modification of specific aspects of cell expansion. In the case of the staminodium, gene duplication has played a role in allowing a novel organ identity to be carved out of the traditional ABC program.

Yant L, Hollister JD, Wright KM, Arnold BJ, Higgins JD, Franklin CFH, Bomblies K. Meiotic Adaptation to Genome Duplication in Arabidopsis arenosa. Current Biology. 2013;23 (21) :2151-2156. pdf at PMCAbstract

Whole genome duplication (WGD) is a major factor in the evolution of multicellular eukaryotes, yet by doubling the number of homologs, WGD severely challenges reliable chromosome segregation [ 1–3 ], a process conserved across kingdoms [ 4 ]. Despite this, numerous genome-duplicated (polyploid) species persist in nature, indicating early problems can be overcome [ 1, 2 ]. Little is known about which genes are involved—only one has been molecularly characterized [ 5 ]. To gain new insights into the molecular basis of adaptation to polyploidy, we investigated genome-wide patterns of differentiation between natural diploids and tetraploids of Arabidopsis arenosa, an outcrossing relative of A. thaliana [ 6, 7 ]. We first show that diploids are not preadapted to polyploid meiosis. We then use a genome scanning approach to show that although polymorphism is extensively shared across ploidy levels, there is strong ploidy-specific differentiation in 39 regions spanning 44 genes. These are discrete, mostly single-gene peaks of sharply elevated differentiation. Among these peaks are eight meiosis genes whose encoded proteins coordinate a specific subset of early meiotic functions, suggesting these genes comprise a polygenic solution to WGD-associated chromosome segregation challenges. Our findings indicate that even conserved meiotic processes can be capable of nimble evolutionary shifts when required.

Posé D, Verhage L, Ott F, Yant L, Mathieu J, Angenent GC, Immink RGH, Schmid M. Temperature-dependent regulation of flowering by antagonistic FLM variants. Nature. 2013. Publisher's VersionAbstract

The appropriate timing of flowering is crucial for plant reproductive success. It is therefore not surprising that intricate genetic networks have evolved to perceive and integrate both endogenous and environmental signals, such as carbohydrate and hormonal status, photoperiod and temperature. In contrast to our detailed understanding of the vernalization pathway, little is known about how flowering time is controlled in response to changes in the ambient growth temperature. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing. Here we report that the two main FLM protein splice variants, FLM-beta and FLM-delta, compete for interaction with the floral repressor SVP. The SVP-FLM-beta complex is predominately formed at low temperatures and prevents precocious flowering. By contrast, the competing SVP-FLM-delta complex is impaired in DNA binding and acts as a dominant-negative activator of flowering at higher temperatures. Our results show a new mechanism that controls the timing of the floral transition in response to changes in ambient temperature. A better understanding of how temperature controls the molecular mechanisms of flowering will be important to cope with current changes in global climate.

Yant L. Genome-wide mapping of transcription factor binding reveals developmental process integration and a fresh look at evolutionary dynamics. American Journal of Botany. 2012. publisher's versionAbstract

How does evolution forge adaptive responses? Are many changes required or few? Just how complex are the transcriptional networks that control development? Diverse questions like these are being newly addressed by next-generation sequencing-based techniques. Facilitating a mechanistic understanding, these approaches reveal the direct in vivo interactions between transcription factors and their physical targets, combined with genome-scale readouts to comprehensively map adaptive gene regulatory networks (GRNs). Here I focus on pioneering work from the last 3 years that has leveraged these data to investigate diverse aspects of GRN circuitry controlling the reproductive transition in plants. These approaches have revealed surprising new functions for long-investigated key players in developmental programs and laid bare the basis for pleiotropy in many others, suggesting widespread process integration at the transcriptional level. Evolutionary questions begged by the recent deluge of GRN mapping data are being assessed anew, both by emerging work outside Arabidopsis thaliana and novel analyses within. These studies have swiftly exposed the distinctive power and adaptability of genome-wide GRN mapping and illustrate that this unique data type holds tremendous promise for plant biology.

Dinh TT, Girke T, Liu X, Yant L, Schmid M, Chen X. The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element. Development. 2012;139 (11) :1978-1986. full-text on PMCAbstract

Cell fate specification in development requires transcription factors for proper regulation of gene expression. In Arabidopsis, transcription factors encoded by four classes of homeotic genes, A, B, C and E, act in a combinatorial manner to control proper floral organ identity. The A-class gene APETALA2 (AP2) promotes sepal and petal identities in whorls 1 and 2 and restricts the expression of the C-class gene AGAMOUS (AG) from whorls 1 and 2. However, it is unknown how AP2 performs these functions. Unlike the other highly characterized floral homeotic proteins containing MADS domains, AP2 has two DNA-binding domains referred to as the AP2 domains and its DNA recognition sequence is still unknown. Here, we show that the second AP2 domain in AP2 binds a non-canonical AT-rich target sequence, and, using a GUS reporter system, we demonstrate that the presence of this sequence in the AG second intron is important for the restriction of AG expression in vivo. Furthermore, we show that AP2 binds the AG second intron and directly regulates AG expression through this sequence element. Computational analysis reveals that the binding site is highly conserved in the second intron of AG orthologs throughout Brassicaceae. By uncovering a biologically relevant AT-rich target sequence, this work shows that AP2 domains have wide-ranging target specificities and provides a missing link in the mechanisms that underlie flower development. It also sets the foundation for understanding the basis of the broad biological functions of AP2 in Arabidopsis, as well as the divergent biological functions of AP2 orthologs in dicotyledonous plants.

Posé D, Yant L, Schmid M. The end of innocence: flowering networks explode in complexity. Current Opinion in Plant Biology. 2011.
Salomé PA, Bomblies K, Laitinen RAE, Yant L, Mott R, Weigel D. Genetic architecture of flowering-time variation in Arabidopsis thaliana. Genetics. 2011;188 (2) :421-433. pdf on PMCAbstract

The onset of flowering is an important adaptive trait in plants. The small ephemeral species Arabidopsis thaliana grows under a wide range of temperature and day-length conditions across much of the Northern hemisphere, and a number of flowering-time loci that vary between different accessions have been identified before. However, only few studies have addressed the species-wide genetic architecture of flowering time control. We have taken advantage of a set of 18 distinct accessions that present much of the common genetic diversity of A. thaliana and mapped quantitative trait loci (QTL) for flowering time in 17 F2 populations derived from these parents. We found that the majority of flowering-time QTL cluster in as few as five genomic regions, which include the locations of the entire FLC/MAF clade of transcription factor genes. By comparing effects across shared parents, we conclude that in several cases there might be an allelic series caused by rare alleles. While this finding parallels results obtained for maize, in contrast to maize much of the variation in flowering time in A. thaliana appears to be due to large-effect alleles.

Moyroud E, Minguet EG, Ott F, Yant L, Posé D, Monniaux M, Blanchet S, Bastien O, Thévenon E, Weigel D. Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor. The Plant Cell. 2011;23 (4) :1293-1306. pdf on PMC
Salomé PA, Bomblies K, Fitz J, Laitinen RAE, Warthmann N, Yant L, Weigel D. The recombination landscape in Arabidopsis thaliana F2 populations. Heredity. 2011;108 (4) :447-455. pdf on PMC
Bomblies K, Yant L, Laitinen RA, Kim S-T, Hollister JD, Warthmann N, Fitz J, Weigel D. Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana. PLoS genetics. 2010;6 (3) :e1000890. pdf on PMCAbstract

As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies, it is essential to understand patterns of natural genetic variation and the forces that shape them. Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such as long-distance migration and colonization. Far less is known about the role of contemporary factors or environmental heterogeneity in generating diversity patterns at local scales. We sampled 1,005 individuals from 77 closely spaced stands in diverse settings around Tübingen, Germany. A set of 436 SNP markers was used to characterize genome-wide patterns of relatedness and recombination. Neighboring genotypes often shared mosaic blocks of alternating marker identity and divergence. We detected recent outcrossing as well as stretches of residual heterozygosity in largely homozygous recombinants. As has been observed for several other selfing species, there was considerable heterogeneity among sites in diversity and outcrossing, with rural stands exhibiting greater diversity and heterozygosity than urban stands. Fine-scale spatial structure was evident as well. Within stands, spatial structure correlated negatively with observed heterozygosity, suggesting that the high homozygosity of natural A. thaliana may be partially attributable to nearest-neighbor mating of related individuals. The large number of markers and extensive local sampling employed here afforded unusual power to characterize local genetic patterns. Contemporary processes such as ongoing outcrossing play an important role in determining distribution of genetic diversity at this scale. Local “outcrossing hotspots” appear to reshuffle genetic information at surprising rates, while other stands contribute comparatively little. Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions.

Yant L, Mathieu J, Dinh TT, Ott F, Lanz C, Wollmann H, Chen X, Schmid M. Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2. The Plant Cell. 2010;22 (7) :2156-2170. pdf on PMCAbstract

The Arabidopsis thaliana transcription factor APETALA2 (AP2) has numerous functions, including roles in seed development, stem cell maintenance, and specification of floral organ identity. To understand the relationship between these different roles, we mapped direct targets of AP2 on a genome-wide scale in two tissue types. We find that AP2 binds to thousands of loci in the developing flower, many of which exhibit AP2-dependent transcription. Opposing, logical effects are evident in AP2 binding to two microRNA genes that influence AP2 expression, with AP2 positively regulating miR156 and negatively regulating miR172, forming a complex direct feedback loop, which also included all but one of the AP2-like miR172 target clade members. We compare the genome-wide direct target repertoire of AP2 with that of SCHLAFMUTZE, a closely related transcription factor that also represses the transition to flowering. We detect clear similarities and important differences in the direct target repertoires that are also tissue specific. Finally, using an inducible expression system, we demonstrate that AP2 has dual molecular roles. It functions as both a transcriptional activator and repressor, directly inducing the expression of the floral repressor AGAMOUS-LIKE15 and directly repressing the transcription of floral activators like SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1.

Yant L, Mathieu J, Schmid M. Just say no: floral repressors help Arabidopsis bide the time. Current opinion in plant biology. 2009;12 (5) :580-586.
Mathieu J, Yant LJ, Mürdter F, Küttner F, Schmid M. Repression of flowering by the miR172 target SMZ. PLoS biology. 2009;7 (7) :e1000148. pdf on PMC
Maness NJ, Yant LJ, Chung C, Loffredo JT, Friedrich TC, Piaskowski SM, Furlott J, May GE, Soma T, León EJ. Comprehensive immunological evaluation reveals surprisingly few differences between elite controller and progressor Mamu-B* 17-positive Simian immunodeficiency virus-infected rhesus macaques. Journal of virology. 2008;82 (11) :5245-5254.