Flowering Time Pathways Research Articles

Substitution mapping of yield‐related traits utilizing three Cybonnet rice × wild introgression libraries

AbstractImproving rice (Oryza sativa L.) yields is a major objective of breeding programs worldwide. The Oryza rufipogon species complex (ORSC), which includes the rice ancestral species O. rufipogon Griff. and O. nivara S. D. Sharma & Shastry, is an underutilized resource. Using three phenotypically and genotypically diverse ORSC accessions identified as OrA, OrB, and OrC, three Cybonnet × ORSC chromosome segment substitution line (CSSL) libraries were developed to make this genepool more accessible to breeders. The objective was to characterize these libraries for 20 yield‐related traits to discover genes not currently deployed for rice improvement. Cybonnet and 212 CSSLs from these libraries were evaluated for 2 years in field studies for six agronomic, six panicle architecture, and eight seed traits. Across the three libraries, 62 CSSLs were found to be significantly different from Cybonnet for one or more traits. Of these, 27 CSSLs were significantly different for seed size traits. To ascertain the chromosome region and underlying candidate gene(s) causing these differences, substitution mapping was performed with previously reported genotypes. Mapping with the CSSLs, which had delayed heading under long days, revealed five known genes associated with rice flowering time pathways. The OsMADS50, RFT1, HD3A, SE1, and GHD7 genes were mapped in the OrB and OrC derived CSSLs but only OsMADS50 mapped in the OrA derived CSSLs. Employing this approach for the other 19 traits revealed 28 total candidate genes. A total of 12 of these genes are currently not deployed for yield enhancement. The introgressed ORSC regions associated with these genes are potential sources of novel variation for rice improvement.

High CO2 adaptation mechanisms revealed in the miR156-regulated flowering time pathway.

Elevated CO2 concentrations have been observed to accelerate flowering time in Arabidopsis through the action of a highly conserved regulatory network controlled by miR156 and miR172. However, the network's robustness to the impact of increasing CO2 concentrations on flowering time remains poorly understood. In this study, we investigate this question by conducting a comprehensive analysis of the global landscape of network dynamics, including quantifying the probabilities associated with juvenile and flowering states and assessing the speed of the transition between them. Our findings reveal that a CO2 concentration range of 400-800ppm only mildly advances flowering time, contrasting with the dramatic changes from 200 to 300ppm. Notably, the feedback regulation of miR156 by squamosal promoter binding protein-like proteins (SPLs) plays a substantial role in mitigating the effects of increasing CO2 on flowering time. Intriguingly, we consistently observe a correlation between delayed flowering time and increased variance in flowering time, and vice versa, suggesting that this might be an intrinsic adaptation mechanism embedded within the network. To gain a deeper understanding of this network's dynamics, we identified the sensitive features within the feedback loops of miR156 SPLs and miR172-APETALA2 family proteins (AP2s), with the latter proving to be the most sensitive. Strikingly, our study underscores the indispensability of all feedback regulations in maintaining both juvenile and adult states as well as the transition time between them. Together, our research provides the first physical basis in plant species, aiding in the elucidation of novel regulatory mechanisms and the robustness of the miRNAs-regulated network in response to increasing CO2, therefore influencing the control of flowering time. Moreover, this study provides a promising strategy for engineering plant flowering time to enhance their adaptation and resilience.

Transcriptomic Analysis of Early Flowering Signals in 'Royal' Flax.

Canada is one of the world’s leading producers and exporters of flax seed, with most production occurring in the Prairie Provinces. However, reduced season length and risk of frost restricts production in the northern grain belt of the Canadian Prairies. To expand the growing region of flax and increase production in Canada, flax breeders need to develop earlier-flowering varieties capable of avoiding the risk of abiotic stress. A thorough understanding of flowering control of flax is essential for the efficient breeding of such lines. We identified 722 putative flax flowering genes that span all major flowering-time pathways. Frequently, we found multiple flax homologues for a single Arabidopsis flowering gene. We used RNA sequencing to quantify the expression of genes in the shoot apical meristem (SAM) at 10, 15, 19, and 29 days after planting (dap) using the ‘Royal’ cultivar. We observed the expression of 80% of putative flax flowering genes and the differential expression of only 30%; these included homologues of major flowering regulators, such as SOC1, FUL, and AP1. We also found enrichment of differentially expressed genes (DEGs) in transcription factor (TF) families involved in flowering. Finally, we identified the candidates’ novel flowering genes amongst the uncharacterized flax genes. Our transcriptomic dataset provides a useful resource for investigating the regulatory control of the transition to flowering in flax and for the breeding of northern-adapted varieties.

Robustification of GWAS to explore effective SNPs addressing the challenges of hidden population stratification and polygenic effects

Genome-wide association studies (GWAS) play a vital role in identifying important genes those is associated with the phenotypic variations of living organisms. There are several statistical methods for GWAS including the linear mixed model (LMM) which is popular for addressing the challenges of hidden population stratification and polygenic effects. However, most of these methods including LMM are sensitive to phenotypic outliers that may lead the misleading results. To overcome this problem, in this paper, we proposed a way to robustify the LMM approach for reducing the influence of outlying observations using the β-divergence method. The performance of the proposed method was investigated using both synthetic and real data analysis. Simulation results showed that the proposed method performs better than both linear regression model (LRM) and LMM approaches in terms of powers and false discovery rates in presence of phenotypic outliers. On the other hand, the proposed method performed almost similar to LMM approach but much better than LRM approach in absence of outliers. In the case of real data analysis, our proposed method identified 11 SNPs that are significantly associated with the rice flowering time. Among the identified candidate SNPs, some were involved in seed development and flowering time pathways, and some were connected with flower and other developmental processes. These identified candidate SNPs could assist rice breeding programs effectively. Thus, our findings highlighted the importance of robust GWAS in identifying candidate genes.

Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces.

Convergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal substantial evidence of parallel adaptation at the level of individual single-nucleotide polymorphism (SNPs), genes, and pathways in four independent highland maize populations. The majority of convergently selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands, while standing variation introduced by ancient gene flow was also a contributor. Polygenic adaptation analyses of quantitative traits reveal that alleles affecting flowering time are significantly associated with elevation, indicating the flowering time pathway was targeted by highland adaptation. In addition, repeatedly selected genes were significantly enriched in the flowering time pathway, indicating their significance in adapting to highland conditions. Overall, our study system represents a promising model to study convergent evolution in plants with potential applications to crop adaptation across environmental gradients.

Characterization of QTL and Environmental Interactions Controlling Flowering Time in Andean Common Bean (Phaseolus vulgaris L.)

Genetic variation for response of flowering time to photoperiod plays an important role in adaptation to environments with different photoperiods, and as consequence is an important contributor to plant productivity and yield. To elucidate the genetic control of flowering time [days to flowering (DTF); growing degree days (GDD)] in common bean, a facultative short-day plant, a quantitative trait loci (QTL) analysis was performed in a recombinant inbred mapping population derived from a cultivated accession and a photoperiod sensitive landrace, grown in different long-day (LD) and short-day (SD) environments by using a multiple-environment QTL model approach. A total of 37 QTL across 17 chromosome regions and 36 QTL-by-QTL interactions were identified for six traits associated with time to flowering and response to photoperiod. The DTF QTL accounted for 28 and 11% on average of the phenotypic variation in the population across LD and SD environments, respectively. Of these, a genomic region on chromosome 4 harboring the major DTF QTL was associated with both flowering time in LD and photoperiod response traits, controlling more than 60% of phenotypic variance, whereas a major QTL on chromosome 9 explained up to 32% of flowering time phenotypic variation in SD. Different epistatic interactions were found in LD and SD environments, and the presence of significant QTL × environment (QE) and epistasis × environment interactions implies that flowering time control may rely on different genes and genetic pathways under inductive and non-inductive conditions. Here, we report the identification of a novel major locus controlling photoperiod sensitivity on chromosome 4, which might interact with other loci for controlling common bean flowering time and photoperiod response. Our results have also demonstrated the importance of these interactions for flowering time control in common bean, and point to the likely complexity of flowering time pathways. This knowledge will help to identify and develop opportunities for adaptation and breeding of this legume crop.

Candidate genes underlying QTL for flowering time and their interactions in a wide spring barley (Hordeum vulgare L.) cross

Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant’s response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka × Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL co-locating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley.

Linkage mapping evidence for a syntenic QTL associated with flowering time in perennial C4 rhizomatous grasses Miscanthus and switchgrass.

Flowering in perennial species is directed via complex signalling pathways that adjust to developmental regulations and environmental cues. Synchronized flowering in certain environments is a prerequisite to commercial seed production, and so the elucidation of the genetic architecture of flowering time in Miscanthus and switchgrass could aid breeding in these underdeveloped species. In this context, we assessed a mapping population in Miscanthus and two ecologically diverse switchgrass mapping populations over 3 years from planting. Multiple flowering time quantitative trait loci (QTL) were identified in both species. Remarkably, the most significant Miscanthus and switchgrass QTL proved to be syntenic, located on linkage groups 4 and 2, with logarithm of odds scores of 17.05 and 21.8 respectively. These QTL regions contained three flowering time transcription factors: Squamosa Promoter‐binding protein‐Like, MADS‐box SEPELLATA2 and gibberellin‐responsive bHLH137. The former is emerging as a key component of the age‐related flowering time pathway.

Medicago PHYA promotes flowering, primary stem elongation and expression of flowering time genes in long days

BackgroundFlowering time is an important trait for productivity in legumes, which include many food and fodder plants. Medicago truncatula (Medicago) is a model temperate legume used to study flowering time pathways. Like Arabidopsis thaliana (Arabidopsis), its flowering is promoted by extended periods of cold (vernalization, V), followed by warm long day (LD) photoperiods. However, Arabidopsis flowering-time genes such as the FLOWERING LOCUS C (FLC)/ MADS AFFECTING FLOWERING (MAF) clade are missing and CONSTANS-LIKE (CO-LIKE) genes do not appear to have a role in Medicago or Pisum sativum (pea). Another photoperiodic regulator, the red/far red photoreceptor PHYTOCHROME A (PHYA), promotes Arabidopsis flowering by stabilizing the CO protein in LD. Interestingly, despite the absence of CO-LIKE function in pea, PsPHYA plays a key role in promoting LD photoperiodic flowering and plant architecture. Medicago has one homolog of PHYA, MtPHYA, but its function is not known.ResultsGenetic analysis of two MtPHYA Tnt1 insertion mutant alleles indicates that MtPHYA has an important role in promoting Medicago flowering and primary stem elongation in VLD and LD and in perception of far-red wavelengths in seedlings. MtPHYA positively regulates the expression of MtE1-like (MtE1L), a homologue of an important legume-specific flowering time gene, E1 in soybean and other Medicago LD-regulated flowering-time gene homologues, including the three FLOWERING LOCUS T-LIKE (FT-LIKE) genes, MtFTa1, MtFTb1 and MtFTb2 and the two FRUITFULL-LIKE (FUL-LIKE) genes MtFULa and MtFULb. MtPHYA also modulates the expression of the circadian clock genes, GIGANTEA (GI) and TIMING OF CAB EXPRESSION 1a (TOC1a). Genetic analyses indicate that Mtphya-1 Mte1l double mutants flowered at the same time as the single mutants. However, Mtphya-1 Mtfta1 double mutants had a weak additive effect in delaying flowering and in reduction of primary axis lengths beyond what was conferred by either of the single mutants.ConclusionMtPHYA has an important role in LD photoperiodic control of flowering, plant architecture and seedling de-etiolation under far-red wavelengths in Medicago. It promotes the expression of LD-induced flowering time genes and modulates clock-related genes. In addition to MtFTa1, MtPHYA likely regulates other targets during LD floral induction in Medicago.

Genome-wide identification of lncRNAs during hickory (Carya cathayensis) flowering.

Non-coding RNAs with lengths greater than 200bp are known as long non-coding RNAs (lncRNAs), and these RNAs play important role in gene regulation and plant development. However, to date, little is known regarding the role played by lncRNAs during flowering in hickory (Carya cathayensis). Here, we performed whole transcriptome RNA-sequencing of samples from hickory female and male floral buds, in which three samples (H0311PF, H0318PF, and H0402PF) represent pre-flowering, flowering, and post-flowering, respectively, while eight male samples collected from May 8th to June 13th as this time course are the key stage for male floral bud differentiation. We identified 2163 lncRNAs in hickory during flowering, containing 213 intronic, 1488 intergenic, and 462 antisense lncRNAs. We noticed that 510 and 648 lncRNAs were differentially expressed corresponding to female and male floral buds, respectively. And some of the lncRNAs were in a tightly tissue-specific or stage-specific manner. To further understand the roles of the lncRNAs, we predicted the function of the lncRNAs in cis- and trans-acting modes. The results showed that 924 lncRNAs were cis-correlated with 1536 protein-coding genes, while 1207 lncRNAs co-expressed (trans-acting) with 7432 protein-coding genes (R > 0.95 or R < - 0.95). These lncRNAs were all enriched in flower development-associated biological processes, i.e., circadian rhythm, vernalization response, response to gibberellin, inflorescence development, floral organ development, etc. To further understand the relationships between lncRNAs and floral-core genes, we build a co-expressing lncRNA-mRNA flowering network. We classified these floral genes into different pathway (photoperiod, vernalization, gibberellin, autonomous, and sucrose pathway) according to their particular functions. We found a set of lncRNAs that preferentially expressed in these pathways. The network showed that some lncRNAs (i.e., XLOC_038669, XLOC_017938) functioned in a particular flowering time pathway, while others (i.e., XLOC_011251, XLOC_04110) were involved in multiple pathway. Furthermore, some lncRNAs (i.e., XLOC_038669, XLOC_009597, and XLOC_049539) played roles in single or multiple pathways via interaction with each other. This study provides a genome-wide survey of hickory flower-related lncRNAs and will contribute to further understanding of the molecular mechanism underpinning flowering in hickory.

The florigen interactor BdES43 represses flowering in the model temperate grass Brachypodium distachyon.

FLOWERING LOCUS T (FT) protein, physiologically florigen, has been identified as a system integrator of numerous flowering time pathways in many studies, and its homologs are found throughout the plant lineage. It is important to uncover how precisely florigenic homologs contribute to flowering initiation and how these factors interact genetically. Here we dissected the function of Brachypodium FT orthologs BdFTL1 and BdFTL2 using overexpression and gene-editing experiments. Transgenic assays showed that both BdFTL1 and BdFTL2 could promote flowering, whereas BdFTL2 was essential for flowering initiation. Notably, BdFTL1 is subject to alternative splicing (AS), and its transcriptional level and AS are significantly affected by BdFTL2. Additionally, BdFTL2 could bind with the PHD-containing protein BdES43, an H3K4me3 reader. Furthermore, BdES43 was antagonistic to BdFTL2 in flowering initiation in a transcription-dependent manner and significantly affected BdFTL1 expression. BdFTL2, BdES43 and H3K4me3 also had highly similar distribution patterns within the BdFTL1 locus, indicating their interplay in regulating target genes. Taken together, florigen BdFTL2 functions as a potential epigenetic effector of BdFTL1 by interacting with a BdES43-H3K4me3 complex. This finding provides an additional insight for the regulatory mechanism underlying the multifaceted roles of florigen.

Adaptive signals of flowering time pathways in wild barley from Israel over 28 generations

Flowering time is one of the most critical traits for plants’ life cycles, which is influenced by various environment changes, such as global warming. Previous studies have suggested that to guarantee reproductive success, plants have shifted flowering times to adapt to global warming. Although many studies focused on the molecular mechanisms of early flowering, little was supported by the repeated sampling at different time points through the changing climate. To fully dissect the temporal and spatial evolutionary genetics of flowering time, we investigated nucleotide variation in ten flowering time candidate genes and nine reference genes for the same ten wild-barley populations sampled 28 years apart (1980–2008). The overall genetic differentiation was significantly greater in the descendant populations (2008) compared with the ancestral populations (1980); however, local adaptation tests failed to detect any single-nucleotide polymorphism (SNP)/indel under spatial-diversifying selection at either time point. By contrast, the WFABC (Wright–Fisher ABC-based approach) that detected 54 SNPs/indels was under strong selection during the past 28 generations. Moreover, all these 54 alleles were segregated in the ancestral populations, but fixed in the descendent populations. Among the top ten SNPs/indels, seven were located in genes of FT1 (FLOWERING TIME LOCUS T 1), CO1 (CONSTANS-LIKE PROTEIN 1), and VRN-H2 (VERNALIZATION-H2), which have been documented to be associated with flowering time regulation in barley cultivars. This study might suggest that all ten populations have undergone parallel evolution over the past few decades in response to global warming, and even an overwhelming local adaptation and ecological differentiation.

Heterologous expression of ELF4 from Chlamydomonas reinhardtii and Physcomitrella patens delays flowering in Arabidopsis thaliana

The circadian clock perceives seasonal changes in day length and temperature and then regulates numerous internal cellular processes. Arabidopsis thaliana EARLY FLOWERING4 (ELF4) is a key circadian clock component that is involved in transcriptional regulation of the central oscillator and multiple output pathways. However, the functions of ELF4 orthologues in other organisms are poorly understood. Here, we identified ELF4 orthologous genes in two non-flowering organisms, the unicellular green alga Chlamydomonas (CrELF4) and the moss Physcomitrella patens (PpELF4). Constitutive expression of CrELF4 and PpELF4 in the Arabidopsis elf4 mutant not only completely rescued its early flowering phenotype, but also induced late flowering. This was associated with decreased transcript levels of CONSTANS (CO) and FLOWERING LOCUS T (FT), two key positive regulators of flowering-time pathways. In addition, expression of CrELF4 and PpELF4 in the Arabidopsis elf4 mutant inhibited hypocotyl elongation and altered the expression of circadian clock-related genes. Taken together, these data suggest that ELF4 orthologous genes in Chlamydomonas and Physcomitrella share an evolutionary conserved role with Arabidopsis ELF4 and indicate that the plant clock component ELF4 is functionally conserved from basal plants to angiosperms.

Flowering-time Genes and Flowering-time Pathways in Wheat (Triticum aestivum L.)

Flowering-time Genes and Flowering-time Pathways in Wheat (<i>Triticum aestivum</i> L.)

Translating Flowering Time From Arabidopsis thaliana to Brassicaceae and Asteraceae Crop Species.

Flowering and seed set are essential for plant species to survive, hence plants need to adapt to highly variable environments to flower in the most favorable conditions. Endogenous cues such as plant age and hormones coordinate with the environmental cues like temperature and day length to determine optimal time for the transition from vegetative to reproductive growth. In a breeding context, controlling flowering time would help to speed up the production of new hybrids and produce high yield throughout the year. The flowering time genetic network is extensively studied in the plant model species Arabidopsis thaliana, however this knowledge is still limited in most crops. This article reviews evidence of conservation and divergence of flowering time regulation in A. thaliana with its related crop species in the Brassicaceae and with more distant vegetable crops within the Asteraceae family. Despite the overall conservation of most flowering time pathways in these families, many genes controlling this trait remain elusive, and the function of most Arabidopsis homologs in these crops are yet to be determined. However, the knowledge gathered so far in both model and crop species can be already exploited in vegetable crop breeding for flowering time control.

P-236 - Unravelling the role of DRIF transcription factors in Arabidopsis thaliana

Transcriptions factors play a pivotal role in the regulation of gene expression and in the control of several developmental processes. A new sub-family of transcriptional regulators, called DIV-and-RAD-interacting-factors (DRIFs) participate in an antagonistic module of interactions regulated by a small interfering peptide, and have been co-opted to regulate different developmental processes in plants. It is still unknown what molecular and cellular processes this module controls in Arabidopsis thaliana. Single knockout lines for five DRIF homologs do not show any obvious phenotypes, suggesting genetic redundancy. Double and triple mutants were obtained and are currently being analysed. One phenotype displayed by a triple mutant is late flowering under long days with no observable difference from wild-type plants under short days, suggesting that the DRIFs may be involved in the long-day flowering time pathway. The expression of genes controlling this pathway will be analysed in the triple mutant. Other phenotypes displayed by double and triple mutants are currently being explored and will be presented.

The autonomous flowering-time pathway pleiotropically regulates seed germination in Arabidopsis thaliana.

Two critical developmental transitions in plants are seed germination and flowering, and the timing of these transitions has strong fitness consequences. How genetically independent the regulation of these transitions is can influence the expression of life cycles. This study tested whether genes in the autonomous flowering-time pathway pleiotropically regulate flowering time and seed germination in the genetic model Arabidopsis thaliana, and tested whether the interactions among those genes are concordant between flowering and germination stages. Several autonomous-pathway genes promote flowering and impede germination. Moreover, the interactions among those genes were highly concordant between the regulation of flowering and germination. Despite some degree of functional divergence between the regulation of flowering and germination by autonomous-pathway genes, the autonomous pathway is highly functionally conserved across life stages. Therefore, genes in the autonomous flowering-time pathway are likely to contribute to genetic correlations between flowering and seed germination, possibly contributing to the winter-annual life history.

Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana.

FLOWERING LOCUS M (FLM), a component of the thermosensory flowering time pathway in Arabidopsis thaliana, is regulated by temperature-dependent alternative splicing (AS). The main splicing variant, FLM-β, is a well-documented floral repressor that is down-regulated in response to increasing ambient growth temperature. Two hypotheses have been formulated to explain how flowering time is modulated by AS of FLM. In the first model a second splice variant, FLM-δ, acts as a dominant negative isoform that competes with FLM-β at elevated ambient temperatures, thereby indirectly promoting flowering. Alternatively, it has been suggested that the induction of flowering at elevated temperatures is caused only by reduced FLM-β expression. To better understand the role of the two FLM splice forms, we employed CRISPR/Cas9 technology to specifically delete the exons that characterize each splice variant. Lines that produced repressive FLM-β but were incapable of producing FLM-δ were late flowering. In contrast, FLM-β knockout lines that still produced FLM-δ flowered early, but not earlier than the flm-3 loss of function mutant, as would be expected if FLM-δ had a dominant-negative effect on flowering. Our data support the role of FLM-β as a flower repressor and provide evidence that a contribution of FLM-δ to the regulation of flowering time in wild-type A. thaliana seems unlikely.

De novo transcriptome sequencing of Camellia sasanqua and the analysis of major candidate genes related to floral traits

Camellia sasanqua is one of the most famous horticultural plants in Camellia (Theaceae) due to its aesthetic appeal as landscape plant. Knowledge regarding the genetic basis of flowering time, floral aroma and color in C. sasanqua is limited, but is essential to breed new varieties with desired floral traits. Here, we described the de novo transcriptome of young leaves, flower buds and flowers of C. sasanqua. A total of 60,127 unigenes were functionally annotated based on the sequence similarity. After analysis, we found that two floral integrator genes, SOC1 and AP1, in flowering time pathway showed evidence of gene family expansion. Compared with 1-deoxy-D-xylulose-5-phosphate pathway, some genes in the mevalonate pathway were most highly expressed, suggesting that this might represent the major pathway for terpenoid biosynthesis related to floral aroma in C. sasanqua. In flavonoid biosynthesis pathway, PAL, CHI, DFR and ANS showing significantly higher expression levels in flowers and flower buds might have important role in regulation of floral color. The top five most transcription factors (TFs) families in C. sasanqua transcriptome were MYB, MIKC, C3H, FAR1 and HD-ZIP, many of which have a direct relationship with floral traits. In addition, we also identified 33,540 simple sequence repeats (SSRs) in the C. sasanqua transcriptome. Collectively, the C. sasanqua transcriptome dataset generated from this study along with the SSR markers provide a new resource for the identification of novel regulatory transcripts and will accelerate the genetic improvement of C. sasanqua breeding programs.

The Genomic Architecture of Flowering Time Varies Across Space and Time in Mimulus guttatus.

The degree to which genomic architecture varies across space and time is central to the evolution of genomes in response to natural selection. Bulked-segregant mapping combined with pooled sequencing provides an efficient means to estimate the effect of genetic variants on quantitative traits. We develop a novel likelihood framework to identify segregating variation within multiple populations and generations while accommodating estimation error on a sample- and SNP-specific basis. We use this method to map loci for flowering time within natural populations of Mimulus guttatus, collecting the early- and late-flowering plants from each of three neighboring populations and two consecutive generations. Structural variants, such as inversions, and genes from multiple flowering-time pathways exhibit the strongest associations with flowering time. We find appreciable variation in genetic effects on flowering time across both time and space; the greatest differences evident between populations, where numerous factors (environmental variation, genomic background, and private polymorphisms) likely contribute to heterogeneity. However, the changes across years within populations clearly identify genotype-by-environment interactions as an important influence on flowering time variation.