scholarly journals Variation in the flowering time orthologsBrFLCandBrSOC1in a natural population ofBrassica rapa

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1339 ◽  
Author(s):  
Steven J. Franks ◽  
Beatriz Perez-Sweeney ◽  
Maya Strahl ◽  
Anna Nowogrodzki ◽  
Jennifer J. Weber ◽  
...  
Keyword(s):  
Flowering Time ◽  
Natural Population ◽  
Regulatory Network ◽  
Genetic Basis ◽  
Allelic Variation ◽  
Flowering Plants ◽  
Promoter Regions ◽  
Late Flowering ◽  
Coding Regions ◽  
The Difference

Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci inBrassica rapaplants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genesFLCandSOC1(BrFLCandBrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, withFLCrepressing andSOC1promoting flowering. InB. rapa, there are four copies ofFLCand three ofSOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression ofBrSOC1paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in theBrSOC1paralogsBr004928, Br00393andBr009324, although the difference was not significant inBr009324. Thus expression of at least 2 of the 3BrSOC1orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of theBrSOC1orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For theBrFLCorthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus theBrFLCorthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of natural variation in such a quantitative trait is challenging.

scholarly journals Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa

2015 ◽  
Author(s):  
Steven J Franks ◽  
Beatriz Perez-Sweeney ◽  
Maya Strahl ◽  
Anna Nowogrodzki ◽  
Jennifer J Weber ◽  
...  
Keyword(s):  
Flowering Time ◽  
Natural Population ◽  
Brassica Rapa ◽  
Regulatory Network ◽  
Genetic Basis ◽  
Allelic Variation ◽  
Flowering Plants ◽  
Promoter Regions ◽  
Late Flowering ◽  
The Difference

Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ~ 30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of natural variation in such a quantitative trait is challenging.

scholarly journals Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa

2015 ◽  
Author(s):  
Steven J Franks ◽  
Beatriz Perez-Sweeney ◽  
Maya Strahl ◽  
Anna Nowogrodzki ◽  
Jennifer J Weber ◽  
...  
Keyword(s):  
Flowering Time ◽  
Natural Population ◽  
Brassica Rapa ◽  
Regulatory Network ◽  
Genetic Basis ◽  
Allelic Variation ◽  
Flowering Plants ◽  
Promoter Regions ◽  
Late Flowering ◽  
The Difference

Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ~ 30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of natural variation in such a quantitative trait is challenging.

scholarly journals Revisiting a GWAS peak in Arabidopsis thaliana reveals possible confounding by genetic heterogeneity

2021 ◽  
Author(s):  
Eriko Sasaki ◽  
Thomas Köcher ◽  
Danièle L Filiault ◽  
Magnus Nordborg
Keyword(s):  
Arabidopsis Thaliana ◽  
Flowering Time ◽  
Genetic Basis ◽  
Allelic Variation ◽  
Alternative Hypothesis ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Locus Model ◽  
Genome Wide ◽  
Causal Variants

AbstractGenome-wide association studies (GWAS) have become a standard approach for exploring the genetic basis of phenotypic variation. However, correlation is not causation, and only a tiny fraction of all associations have been experimentally confirmed. One practical problem is that a peak of association does not always pinpoint a causal gene, but may instead be tagging multiple causal variants. In this study, we reanalyze a previously reported peak associated with flowering time traits in Swedish in Arabidopsis thaliana. The peak appeared to pinpoint the AOP2/AOP3 cluster of glucosinolate biosynthesis genes, which is known to be responsible for natural variation in herbivore resistance. Here we propose an alternative hypothesis, by demonstrating that the AOP2/AOP3 flowering association can be wholly accounted for by allelic variation in two flanking genes with clear roles in regulating flowering: NDX1, a regulator of the main flowering time controller FLC, and GA1, which plays a central role in gibberellin synthesis and is required for flowering under some conditions. In other words, we propose that the AOP2/AOP3 flowering-time association is yet another example of a spurious, “synthetic” association, arising from trying to fit a single-locus model in the presence of two statistically associated causative loci.

scholarly journals ZmCOL3, a CCT-domain containing gene affects maize adaptation as a repressor and upstream of ZmCCT

2017 ◽  
Author(s):  
Minliang Jin ◽  
Xiangguo Liu ◽  
Wei Jia ◽  
Haijun Liu ◽  
Wenqiang Li ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Gene ◽  
Flowering Time ◽  
Flowering Plants ◽  
Promoter Regions ◽  
Modified Model ◽  
Long Day ◽  
Mapping Analysis ◽  
Photoperiod Pathway ◽  
Key Genes

AbstractFlowering time is a vital trait to control the adaptation of flowering plants to different environments. CCT-domain containing genes are considered to play an important role in plants flowering. Among 53 maize CCT family genes, 28 of them were located in the flowering time QTL regions and 16 genes were significant associated with flowering time based on candidate gene-based association mapping analysis. Furthermore, a CCT gene named as ZmCOL3 was validated to be a flowering repressor upstream of ZmCCT which is one of the key genes regulating maize flowering. The overexpressed ZmCOL3 could delay flowering time about 4 days whether in long day or short day conditions. The absent of one cytosine in 3’UTR and the present of 551bp fragment in promoter regions are likely the causal polymorphisms which may contribute to the maize adaptation from tropical to temperate regions. ZmCOL3 could transactivate ZmCCT transcription or interfere circadian clock to inhibit flowering which was integrated in the modified model of maize photoperiod pathway.HighlightMaize CCT genes influence flowering time in different latitude environments and one of them named ZmCOL3 is a flowering time repressor which could transactivate ZmCCT transcription to delay flowering.

Optimization of the Expression of 1,3-1,4-β-glucanase Gene from Rhizomucor miehei in the Komagataella kurtzmanii yeast

2019 ◽  
Vol 35 (5) ◽  
pp. 3-11 ◽  
Author(s):  
I.I. Gubaidullin ◽  
A.S. Fedorov ◽  
D.G. Kozlov
Keyword(s):  
Target Gene ◽  
Rhizomucor Miehei ◽  
Leader Peptide ◽  
Promoter Regions ◽  
Functional Elements ◽  
Resource Center ◽  
The Status ◽  
Pichia Pastoris Yeast ◽  
The Difference ◽  
Genetic Constructs

Key functional elements of the vector (promoter, leader and terminator regions) that provide the expression of a target l,3-l,4-(3-glucanase gene from Rhizomucor miehei in the Komagataella kurtzmanii yeast have been optimized. It was shown that the promoter regions of the gene AOX1 from the Pichia pastoris yeast currently reclassified as Komagataella phaffti and from К. kurtzmanii yeast as parts of a vector provided equal levels of expression of the target gene in the cells of the recipient strain К. kurtzmanii Y727his4, i.e. they were completely interchangeable. This means that genetic constructs that were previously developed for the biosynthesis of recombinant proteins in К. phajfii are able to provide an effective expression in the К kurtzmanii yeast. The leader peptide MF4I (used as a variant of mif4I containing one amino acid substitution) and the leader peptide maxHH (containing the double proregion of the Hspl50 protein from Saccharomyces cerevisiae) confirmed the status of the most powerful elements among the five leader sequences analyzed. Their efficiency was 1.7 times higher than that of the standard leader from the yeast alpha-factor, and by 20% higher than the characteristics of the second group of artificial leaders. At the same time, it was found that, the choice of the terminator region had the strongest influence on the expression of the target gene among all of the vector functional elements. The best terminator elements were variants derived from the transcription termination region of the AOX1 gene, and the difference in the expression level of the target gene using different terminators was approximately 4.5 times. Based on the analysis of the obtained data, the optimal composition of the key functional elements of the expression vector was determined ; it included the promoter and terminator regions of the AOX1 yeast gene and one of the artificial leaders, mif4I or maxHH. β-glucanase, Komagataella kurtzmanii, yeast, secretion, strain producer The work was financially supported by the Ministry of Science and Higher education of the Russian Federation (Unique Project Identifier RFMEFI60717X0179) using the Unique Scientific Facility of the National Bio-Resource Center «All-Russian Collection of Industrial Microorganisms», NRC «Kurchatov Institute» - GOSNIIGENETIKA

Novel Loci Control Variation in Reproductive Timing inArabidopsis thalianain Natural Environments

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1875-1884 ◽  
Author(s):  
Cynthia Weinig ◽  
Mark C Ungerer ◽  
Lisa A Dorn ◽  
Nolan C Kane ◽  
Yuko Toyonaga ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Allelic Variation ◽  
Developmental Pathways ◽  
Natural Environments ◽  
Reproductive Timing ◽  
Controlled Environments ◽  
Photoperiod Pathway ◽  
Differential Involvement ◽  
Short Days ◽  
Transition To Flowering

AbstractMolecular biologists are rapidly characterizing the genetic basis of flowering in model species such as Arabidopsis thaliana. However, it is not clear how the developmental pathways identified in controlled environments contribute to variation in reproductive timing in natural ecological settings. Here we report the first study of quantitative trait loci (QTL) for date of bolting (the transition from vegetative to reproductive growth) in A. thaliana in natural seasonal field environments and compare the results with those obtained under typical growth-chamber conditions. Two QTL specific to long days in the chamber were expressed only in spring-germinating cohorts in the field, and two loci specific to short days in the chamber were expressed only in fall-germinating cohorts, suggesting differential involvement of the photoperiod pathway in different seasonal environments. However, several other photoperiod-specific QTL with large effects in controlled conditions were undetectable in natural environments, indicating that expression of allelic variation at these loci was overridden by environmental factors specific to the field. Moreover, a substantial number of QTL with major effects on bolting date in one or more field environments were undetectable under controlled environment conditions. These novel loci suggest the involvement of additional genes in the transition to flowering under ecologically relevant conditions.

scholarly journals Inter-species functional compatibility of the Theobroma cacao and Arabidopsis FT orthologs: 90 million years of functional conservation of meristem identity genes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
S. F. Prewitt ◽  
A. Shalit-Kaneh ◽  
S. N. Maximova ◽  
M. J. Guiltinan
Keyword(s):  
Gene Expression ◽  
Tissue Culture ◽  
Gene Family ◽  
Flowering Time ◽  
Molecular Mechanisms ◽  
Regulatory Pathways ◽  
Late Flowering ◽  
Precocious Flowering ◽  
Transition To Flowering

Abstract Background In angiosperms the transition to flowering is controlled by a complex set of interacting networks integrating a range of developmental, physiological, and environmental factors optimizing transition time for maximal reproductive efficiency. The molecular mechanisms comprising these networks have been partially characterized and include both transcriptional and post-transcriptional regulatory pathways. Florigen, encoded by FLOWERING LOCUS T (FT) orthologs, is a conserved central integrator of several flowering time regulatory pathways. To characterize the molecular mechanisms involved in controlling cacao flowering time, we have characterized a cacao candidate florigen gene, TcFLOWERING LOCUS T (TcFT). Understanding how this conserved flowering time regulator affects cacao plant’s transition to flowering could lead to strategies to accelerate cacao breeding. Results BLAST searches of cacao genome reference assemblies identified seven candidate members of the CENTRORADIALIS/TERMINAL FLOWER1/SELF PRUNING gene family including a single florigen candidate. cDNA encoding the predicted cacao florigen was cloned and functionally tested by transgenic genetic complementation in the Arabidopsis ft-10 mutant. Transgenic expression of the candidate TcFT cDNA in late flowering Arabidopsis ft-10 partially rescues the mutant to wild-type flowering time. Gene expression studies reveal that TcFT is spatially and temporally expressed in a manner similar to that found in Arabidopsis, specifically, TcFT mRNA is shown to be both developmentally and diurnally regulated in leaves and is most abundant in floral tissues. Finally, to test interspecies compatibility of florigens, we transformed cacao tissues with AtFT resulting in the remarkable formation of flowers in tissue culture. The morphology of these in vitro flowers is normal, and they produce pollen that germinates in vitro with high rates. Conclusion We have identified the cacao CETS gene family, central to developmental regulation in angiosperms. The role of the cacao’s single FT-like gene (TcFT) as a general regulator of determinate growth in cacao was demonstrated by functional complementation of Arabidopsis ft-10 late-flowering mutant and through gene expression analysis. In addition, overexpression of AtFT in cacao resulted in precocious flowering in cacao tissue culture demonstrating the highly conserved function of FT and the mechanisms controlling flowering in cacao.

scholarly journals Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zheng Ma ◽  
Na Luo ◽  
Lu Liu ◽  
Huanxian Cui ◽  
Jing Li ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Lipid Metabolism ◽  
Lipid Content ◽  
Regulatory Network ◽  
Total Lipid Content ◽  
Fatty Acid Transport ◽  
Lipid Deposition ◽  
Ppar Signaling ◽  
The Difference

Abstract Background A body distribution with high intramuscular fat and low abdominal fat is the ideal goal for broiler breeding. Preadipocytes with different origins have differences in terms of metabolism and gene expression. The transcriptome analysis performed in this study of intramuscular preadipocytes (DIMFPs) and adipose tissue-derived preadipocytes (DAFPs) aimed to explore the characteristics of lipid deposition in different chicken preadipocytes by dedifferentiation in vitro. Results Compared with DAFPs, the total lipid content in DIMFPs was reduced (P < 0.05). Moreover, 72 DEGs related to lipid metabolism were screened, which were involved in adipocyte differentiation, fatty acid transport and fatty acid synthesis, lipid stabilization, and lipolysis. Among the 72 DEGs, 19 DEGs were enriched in the PPAR signaling pathway, indicating its main contribution to the regulation of the difference in lipid deposition between DAFPs and DIMFPs. Among these 19 genes, the representative APOA1, ADIPOQ, FABP3, FABP4, FABP7, HMGCS2, LPL and RXRG genes were downregulated, but the ACSL1, FABP5, PCK2, PDPK1, PPARG, SCD, SCD5, and SLC27A6 genes were upregulated (P < 0.05 or P < 0.01) in the DIMFPs. In addition, the well-known pathways affecting lipid metabolism (MAPK, TGF-beta and calcium) and the pathways related to cell communication were enriched, which may also contribute to the regulation of lipid deposition. Finally, the regulatory network for the difference in lipid deposition between chicken DAFPs and DIMFPs was proposed based on the above information. Conclusions Our data suggested a difference in lipid deposition between DIMFPs and DAFPs of chickens in vitro and proposed a molecular regulatory network for the difference in lipid deposition between chicken DAFPs and DIMFPs. The lipid content was significantly increased in DAFPs by the direct mediation of PPAR signaling pathways. These findings provide new insights into the regulation of tissue-specific fat deposition and the optimization of body fat distribution in broilers.

Distribution and variability in development of the genus Trigonella in Asia Minor and its possible use in Australian environments

1981 ◽  
Vol 32 (5) ◽  
pp. 793 ◽  
Author(s):  
GM Halloran ◽  
AL Pennell
Keyword(s):  
Flowering Time ◽  
Subterranean Clover ◽  
Asia Minor ◽  
Vernalization Response ◽  
Developmental Patterns ◽  
Late Flowering ◽  
Commercial Cultivars ◽  
Wide Variability ◽  
Upper Level ◽  
Autumn Sowing

A number of Trigonella species were examined for their possible use in Australian environments. There was a wide variability in flowering time in Trigonella. Under an outdoor autumn sowing the range in flowering time was comparable with that found within early- to late-flowering Australian commercial cultivars of subterranean clover. The upper level of vernalization response was much lower in Trigonella than in subterranean clover. Good prospects exist within Trigonella for selecting genotypes with close adaptation (in terms of appropriate developmental patterns) to a range of Australian environments, a range at least as wide as that now occupied by subterranean clover and annual medic.

scholarly journals The molecular through ecological genetics of abnormal abdomen. IV. Components of genetic variation in a natural population of Drosophila mercatorum.

Genetics ◽  
1992 ◽  
Vol 130 (2) ◽  
pp. 355-366
Author(s):  
H Hollocher ◽  
A R Templeton ◽  
R DeSalle ◽  
J S Johnston
Keyword(s):  
Genetic Variation ◽  
Natural Population ◽  
Allelic Variation ◽  
Natural Populations ◽  
Developmental Time ◽  
Ecological Genetics ◽  
Adult Longevity ◽  
Genetic Determinants ◽  
Drosophila Mercatorum ◽  
Y Chromosomes

Abstract Natural populations of Drosophila mercatorum are polymorphic for a phenotypic syndrome known as abnormal abdomen (aa). This syndrome is characterized by a slow-down in egg-to-adult developmental time, retention of juvenile abdominal cuticle in the adult, increased early female fecundity, and decreased adult longevity. Previous studies revealed that the expression of this syndrome in females is controlled by two closely linked X chromosomal elements: the occurrence of an R1 insert in a third or more of the X-linked 28S ribosomal genes (rDNA), and the failure of replicative selection favoring uninserted 28S genes in larval polytene tissues. The expression of this syndrome in males in a laboratory stock was associated with the deletion of the rDNA normally found on the Y chromosome. In this paper we quantify the levels of genetic variation for these three components in a natural population of Drosophila mercatorum found near Kamuela, Hawaii. Extensive variation is found in the natural population for both of the X-linked components. Moreover, there is a significant association between variation in the proportion of R1 inserted 28S genes with allelic variation at the underreplication (ur) locus such that both of the necessary components for aa expression in females tend to cosegregate in the natural population. Accordingly, these two closely linked X chromosomal elements are behaving as a supergene in the natural population. Because of this association, we do not believe the R1 insert to be actively transposing to an appreciable extent. The Y chromosomes extracted from nature are also polymorphic, with 16% of the Ys lacking the Y-specific rDNA marker. The absence of this marker is significantly associated with the expression of aa in males. Hence, all three of the major genetic determinants of the abnormal abdomen syndrome are polymorphic in this natural population.

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