Discovering candidate genes related to flowering time in the spring panel of Camelina sativa

Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 367 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

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Overexpression of AtAHL20 causes delayed flowering in Arabidopsis via repression of FT expression

BMC Plant Biology ◽

10.1186/s12870-020-02733-5 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Reuben Tayengwa ◽

Pushpa Sharma Koirala ◽

Courtney F. Pierce ◽

Breanna E. Werner ◽

Michael M. Neff

Keyword(s):

Transgenic Plants ◽

Gene Family ◽

Flowering Time ◽

Camelina Sativa ◽

Negative Regulator ◽

Peptide Sequence ◽

Type I ◽

Mrna Levels ◽

Core Motif ◽

Late Flowering

Abstract Background The 29-member Arabidopsis AHL gene family is classified into three main classes based on nucleotide and protein sequence evolutionary differences. These differences include the presence or absence of introns, type and/or number of conserved AT-hook and PPC domains. AHL gene family members are divided into two phylogenetic clades, Clade-A and Clade-B. A majority of the 29 members remain functionally uncharacterized. Furthermore, the biological significance of the DNA and peptide sequence diversity, observed in the conserved motifs and domains found in the different AHL types, is a subject area that remains largely unexplored. Results Transgenic plants overexpressing AtAHL20 flowered later than the wild type under both short and long days. Transcript accumulation analyses showed that 35S:AtAHL20 plants contained reduced FT, TSF, AGL8 and SPL3 mRNA levels. Similarly, overexpression of AtAHL20’s orthologue in Camelina sativa, Arabidopsis’ closely related Brassicaceae family member species, conferred a late-flowering phenotype via suppression of CsFT expression. However, overexpression of an aberrant AtAHL20 gene harboring a missense mutation in the AT-hook domain’s highly conserved R-G-R core motif abolished the late-flowering phenotype. Data from targeted yeast-two-hybrid assays showed that AtAHL20 interacted with itself and several other Clade-A Type-I AHLs which have been previously implicated in flowering-time regulation: AtAHL19, AtAHL22 and AtAHL29. Conclusion We showed via gain-of-function analysis that AtAHL20 is a negative regulator of FT expression, as well as other downstream flowering time regulating genes. A similar outcome in Camelina sativa transgenic plants overexpressing CsAHL20 suggest that this is a conserved function. Our results demonstrate that AtAHL20 acts as a photoperiod-independent negative regulator of transition to flowering.

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Identification of early and late flowering time candidate genes in endodormant and ecodormant almond flower buds

Tree Physiology ◽

10.1093/treephys/tpaa151 ◽

2020 ◽

Author(s):

Ángela S Prudencio ◽

Frank A Hoeberichts ◽

Federico Dicenta ◽

Pedro Martínez-Gómez ◽

Raquel Sánchez-Pérez

Keyword(s):

Flowering Time ◽

Candidate Genes ◽

Weather Conditions ◽

Tree Breeding ◽

Prunus Dulcis ◽

Fruit Tree ◽

Flower Buds ◽

Flower Bud ◽

Late Flowering ◽

Chilling Requirements

Abstract Flower bud dormancy in temperate fruit tree species, like almond [Prunus dulcis (Mill.) D.A. Webb], is a survival mechanism that ensures flowering will occur under suitable weather conditions for successful flower development, pollination and fruit set. Dormancy is divided into three sequential phases: paradormancy, endodormancy and ecodormancy. During the winter, buds need cultivar-specific chilling requirements to overcome endodormancy and heat requirements to activate the machinery to flower in the ecodormancy phase. One of the main factors that enables the transition from endodormancy to ecodormancy is transcriptome reprogramming. In this work, we therefore monitored three almond cultivars with different chilling requirements and flowering times by RNA sequencing during the endodormancy release of flower buds and validated the data by qRT-PCR in two consecutive seasons. We were thus able to identify early and late flowering time candidate genes in endodormant and ecodormant almond flower buds associated with metabolic switches, transmembrane transport, cell wall remodeling, phytohormone signaling and pollen development. These candidate genes were indeed involved in the overcoming of the endodormancy in almond. This information may be used for the development of dormancy molecular markers, increasing the efficiency of temperate fruit tree breeding programs in a climate-change context.

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

The Crop Journal ◽

10.1016/j.cj.2020.07.008 ◽

2020 ◽

Author(s):

Ana M. Casas ◽

Carlota R. Gazulla ◽

Arantxa Monteagudo ◽

Carlos P. Cantalapiedra ◽

Marian Moralejo ◽

...

Keyword(s):

Hordeum Vulgare ◽

Flowering Time ◽

Candidate Genes ◽

Spring Barley ◽

Hordeum Vulgare L

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Overexpression of AtAHL20 causes delayed flowering in Arabidopsis via repression of FT expression

10.21203/rs.3.rs-38575/v1 ◽

2020 ◽

Author(s):

Reuben Tayengwa ◽

Pushpa Sharma-Koirala ◽

Courtney F. Pierce ◽

Breanna E Werner ◽

Michael M Neff

Keyword(s):

Drought Stress ◽

Transgenic Plants ◽

Gene Family ◽

Stress Tolerance ◽

Flowering Time ◽

Camelina Sativa ◽

Negative Regulator ◽

Wild Type ◽

Late Flowering ◽

Drought Stress Tolerance

Abstract Background The 29-member Arabidopsis AHL gene family is classified into three main classes based on nucleotide and protein sequence evolutionary differences. These differences include the presence or absence of introns, type and/or number of conserved AT-hook and PPC domains. AHL gene family members are divided into two phylogenetic clades, Clade-A and Clade-B. A majority of the 29 members remain functionally uncharacterized. Furthermore, the biological significance of the DNA and peptide sequence diversity, observed in the conserved motifs and domains found in the different AHL types, is a subject area that remains largely unexplored. Results Transgenic plants overexpressing AtAHL20 flowered later than the wild type. Transcript accumulation analyses showed that 35S:AtAHL20 plants contained reduced FT, TSF, AGL8 and SPL3 mRNA levels. Similarly, overexpression of AtAHL20’s orthologue in Camelina sativa, Arabidopsis’ closely related Brassicaceae family member species, conferred a late-flowering phenotype via suppression of CsFT expression. In addition, 35S:AtAHL20 seedlings exhibited suppressed hypocotyl length and enhanced water stress tolerance. However, overexpression of an aberrant AtAHL20 gene harboring a missense mutation in the AT-hook domain’s highly conserved R-G-R core motif abolished the late-flowering phenotype. Data from targeted yeast-two-hybrid assays showed that AtAHL20 interacted with itself and several other Clade-A Type-I AHLs which have been previously implicated in flowering-time regulation: AtAHL22, AtAHL27 and AtAHL29. Conclusion We showed via gain-function analysis that AtAHL20 is a negative regulator of FT expression, as well as other downstream flowering time regulating genes. A similar outcome in Camelina sativa transgenic plants overexpressing CsAHL20 suggest that this is a conserved function. Additionally, overexpression of AtAHL20 resulted in shorter hypocotyls and enhanced drought stress tolerance compared to wild-type plants. Our results demonstrate that AtAHL20 is a negative regulator of transition to flowering and hypocotyl elongation, but a positive regulator of drought stress tolerance.

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Evaluating Population Genomic Candidate Genes Underlying Flowering Time in Arabidopsis thaliana Using T-DNA Insertion Lines

Journal of Heredity ◽

10.1093/jhered/esz026 ◽

2019 ◽

Vol 110 (4) ◽

pp. 445-454 ◽

Cited By ~ 2

Author(s):

Veronica K Chong ◽

John R Stinchcombe

Keyword(s):

Arabidopsis Thaliana ◽

Flowering Time ◽

Candidate Genes ◽

Insertional Mutagenesis ◽

Knock Out ◽

Population Genomic ◽

Outlier Loci ◽

Genomic Studies ◽

Dna Insertion ◽

Genomic Scans

Abstract Population genomic scans have emerged as a powerful tool to detect regions of the genome that are potential targets of selection. Despite the success of genomic scans in identifying novel lists of loci potentially underlying adaptation, few studies proceed to validate the function of these candidate genes. In this study, we used transfer-DNA (T-DNA) insertion lines to evaluate the effects of 27 candidate genes on flowering time in North American accessions of Arabidopsis thaliana. We compared the flowering time of T-DNA insertion lines that knock out the function of a candidate gene obtained from population genomic studies to a wild type under long- and short-day conditions. We also did the same for a collection of randomly chosen genes that had not been identified as candidates. We validated the well-known effect of long-day conditions in accelerating flowering time and found that gene disruption caused by insertional mutagenesis tends to delay flowering. Surprisingly, we found that knockouts in random genes were just as likely to produce significant phenotypic effects as knockouts in candidate genes. T-DNA insertions at a handful of candidate genes that had previously been identified as outlier loci showed significant delays in flowering time under both long and short days, suggesting that they are promising candidates for future investigation.

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