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.

scholarly journals Characterization of Mungbean CONSTANS-LIKE Genes and Functional Analysis of CONSTANS-LIKE 2 in the Regulation of Flowering Time in Arabidopsis

2021 ◽  
Vol 12 ◽  
Author(s):  
Chenyang Liu ◽  
Qianqian Zhang ◽  
Hong Zhu ◽  
Chunmei Cai ◽  
Shuai Li
Keyword(s):  
Flowering Time ◽  
Expression Patterns ◽  
Plant Growth And Development ◽  
Promoter Regions ◽  
Short Day ◽  
Long Day ◽  
Close Phylogenetic Relationship ◽  
Gene Functions ◽  
Gene Structures

CONSTANS-LIKE (COL) genes play important roles in the regulation of plant growth and development, and they have been analyzed in many plant species. However, few studies have examined COL genes in mungbean (Vigna radiata). In this study, we identified and characterized 31 mungbean genes whose proteins contained B-Box domains. Fourteen were designated as VrCOL genes and were distributed on 7 of the 11 mungbean chromosomes. Based on their phylogenetic relationships, VrCOLs were clustered into three groups (I, II, and III), which contained 4, 6, and 4 members, respectively. The gene structures and conserved motifs of the VrCOL genes were analyzed, and two duplicated gene pairs, VrCOL1/VrCOL2 and VrCOL8/VrCOL9, were identified. A total of 82 cis-acting elements were found in the VrCOL promoter regions, and the numbers and types of cis-acting elements in each VrCOL promoter region differed. As a result, the expression patterns of VrCOLs varied in different tissues and throughout the day under long-day and short-day conditions. Among these VrCOL genes, VrCOL2 showed a close phylogenetic relationship with Arabidopsis thaliana CO and displayed daily oscillations in expression under short-day conditions but not long-day conditions. In addition, overexpression of VrCOL2 accelerated flowering in Arabidopsis under short-day conditions by affecting the expression of the flowering time genes AtFT and AtTSF. Our study lays the foundation for further investigation of VrCOL gene functions.

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 Functional characterization of mungbean CONSTANS-LIKE genes reveals a key role for CONSTANS-LIKE 2 in the control of flowering time in A. thaliana under short-day conditions

2020 ◽  
Author(s):  
Chenyang Liu ◽  
Qianqian Zhang ◽  
Hong Zhu ◽  
Chunmei Cai ◽  
Shuai Li
Keyword(s):  
Plant Growth ◽  
Flowering Time ◽  
Growth And Development ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Plant Growth And Development ◽  
Promoter Regions ◽  
Short Day ◽  
Long Day ◽  
Close Phylogenetic Relationship

Abstract Background: CONSTANS-LIKE (COL) genes play important roles in the regulation of plant growth and development, and they have been analyzed in many plant species. However, few investigations have examined COL genes in mungbean (Vigna radiata).Results: In this study, we identified and characterized a total 14 of VrCOL genes from mungbean, which distributed on 7 of the 11 mungbean chromosomes. Based on their conserved domains, VrCOLs were clustered into three groups (I, II and III), which contained 4, 5 and 5 members, respectively. The gene structures and conserved motifs of the VrCOL genes were analyzed, and two duplicated gene pairs, VrCOL1/VrCOL2 and VrCOL8/VrCOL9, were identified. A total of 82 cis-acting elements were found in the VrCOL promoter regions, and the numbers and types of cis-acting elements in each VrCOL promoter region differed. As a result, the expression patterns of VrCOLs varied in different tissues, and under long day and short day conations throughout the day. Among these VrCOL genes, VrCOL2 showed a close phylogenetic relationship with Arabidopsis thaliana (A. thaliana) CO and displayed daily oscillations in expression under short day conditions but not long day conditions. In addition, overexpression of VrCOL2 accelerated flowering in A. thaliana under short day conditions by activating the expression of flowering time gene AtFT and AtTSF.Conclusion: Overall, we identified 14 VrCOL genes from mungbean using genome-wide identification. Characteristics and transcription pattern analysis of VrCOL genes revealed their important roles in plant growth and development, and our results suggested that VrCOL2 regulate flowering time under short day conditions in A. thaliana. Our study lays the foundation for further dissection of VrCOL gene functions.

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 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 Candidate Gene Association Mapping of Arabidopsis Flowering Time

Genetics ◽  
2009 ◽  
Vol 183 (1) ◽  
pp. 325-335 ◽  
Author(s):  
Ian M. Ehrenreich ◽  
Yoshie Hanzawa ◽  
Lucy Chou ◽  
Judith L. Roe ◽  
Paula X. Kover ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Gene ◽  
Flowering Time ◽  
Gene Association ◽  
Candidate Gene Association

scholarly journals A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape

2021 ◽  
Author(s):  
Paul Vollrath ◽  
Harmeet S. Chawla ◽  
Sarah V. Schiessl ◽  
Iulian Gabur ◽  
HueyTyng Lee ◽  
...  
Keyword(s):  
Association Mapping ◽  
Flowering Time ◽  
Oilseed Rape ◽  
Major Effect ◽  
Structural Variants ◽  
Winter Oilseed Rape ◽  
Flowering Locus T ◽  
Winter Type ◽  
Long Read ◽  
Flowering Locus

Abstract Key message A novel structural variant was discovered in the FLOWERING LOCUS T orthologue BnaFT.A02 by long-read sequencing. Nested association mapping in an elite winter oilseed rape population revealed that this 288 bp deletion associates with early flowering, putatively by modification of binding-sites for important flowering regulation genes. Abstract Perfect timing of flowering is crucial for optimal pollination and high seed yield. Extensive previous studies of flowering behavior in Brassica napus (canola, rapeseed) identified mutations in key flowering regulators which differentiate winter, semi-winter and spring ecotypes. However, because these are generally fixed in locally adapted genotypes, they have only limited relevance for fine adjustment of flowering time in elite cultivar gene pools. In crosses between ecotypes, the ecotype-specific major-effect mutations mask minor-effect loci of interest for breeding. Here, we investigated flowering time in a multiparental mapping population derived from seven elite winter oilseed rape cultivars which are fixed for major-effect mutations separating winter-type rapeseed from other ecotypes. Association mapping revealed eight genomic regions on chromosomes A02, C02 and C03 associating with fine modulation of flowering time. Long-read genomic resequencing of the seven parental lines identified seven structural variants coinciding with candidate genes for flowering time within chromosome regions associated with flowering time. Segregation patterns for these variants in the elite multiparental population and a diversity set of winter types using locus-specific assays revealed significant associations with flowering time for three deletions on chromosome A02. One of these was a previously undescribed 288 bp deletion within the second intron of FLOWERING LOCUS T on chromosome A02, emphasizing the advantage of long-read sequencing for detection of structural variants in this size range. Detailed analysis revealed the impact of this specific deletion on flowering-time modulation under extreme environments and varying day lengths in elite, winter-type oilseed rape.

Design of a Brassica rapa core collection for association mapping studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 884-898 ◽  
Author(s):  
Jianjun Zhao ◽  
Anna Artemyeva ◽  
Dunia Pino Del Carpio ◽  
Ram Kumar Basnet ◽  
Ningwen Zhang ◽  
...  
Keyword(s):  
Association Mapping ◽  
Flowering Time ◽  
Brassica Rapa ◽  
Core Collection ◽  
Field Experiments ◽  
Research Centre ◽  
Candidate Gene Approach ◽  
Core Collections ◽  
Genome Wide ◽  
Using Data

A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.

scholarly journals Association mapping reveals gene action and interactions in the determination of flowering time in barley

2008 ◽  
Vol 118 (2) ◽  
pp. 259-273 ◽  
Author(s):  
Silke Stracke ◽  
Grit Haseneyer ◽  
Jean-Baptiste Veyrieras ◽  
Hartwig H. Geiger ◽  
Sascha Sauer ◽  
...  
Keyword(s):  
Association Mapping ◽  
Flowering Time ◽  
Gene Action
Sign in / Sign up

Export Citation Format

Share Document