scholarly journals Genetic architecture underlying variation in floral meristem termination in Aquilegia

2021 ◽  
Author(s):  
Ya Min ◽  
Evangeline S. Ballerini ◽  
Molly B. Edwards ◽  
Scott A. Hodges ◽  
Elena M. Kramer

Floral organs are produced by floral meristems (FMs), which harbor stem cells in their centers. Since each flower only has a finite number of organs, the stem cell activity of a FM will always terminate at a specific time point, a process termed floral meristem termination (FMT). Variation in the timing of FMT can give rise to floral morphological diversity, but how this process is fine-tuned at a developmental and evolutionary level is poorly understood. Flowers from the genus Aquilegia share identical floral organ arrangement except for stamen whorl numbers (SWN), making Aquilegia a well-suited system for investigation of this process: differences in SWN between species represent differences in the timing of FMT. By crossing A. canadensis and A. brevistyla, quantitative trait locus (QTL) mapping has revealed a complex genetic architecture with seven QTL. We identified potential candidate genes under each QTL and characterized novel expression patterns of select candidate genes using in situ hybridization. To our knowledge, this is the first attempt to dissect the genetic basis of how natural variation in the timing of FMT is regulated and our results provide insight into how floral morphological diversity can be generated at the meristematic level.

2020 ◽  
Vol 7 (11) ◽  
pp. 201081
Author(s):  
Zhenhua Guo ◽  
Lijun Cai ◽  
Zhiqiang Chen ◽  
Ruiying Wang ◽  
Lanming Zhang ◽  
...  

Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.


Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1066
Author(s):  
Gongmin Cheng ◽  
Longyan Zhang ◽  
Hengling Wei ◽  
Hantao Wang ◽  
Jianhua Lu ◽  
...  

Gossypium barbadense is an important source of natural textile fibers, as is Gossypium hirsutum. Cotton fiber development is often affected by various environmental factors, such as abnormal temperature. However, little is known about the underlying mechanisms of temperature regulating the fuzz fiber initiation. In this study, we reveal that high temperatures (HT) accelerate fiber development, improve fiber quality, and induced fuzz initiation of a thermo-sensitive G. barbadense variety L7009. It was proved that fuzz initiation was inhibited by low temperature (LT), and 4 dpa was the stage most susceptible to temperature stress during the fuzz initiation period. A total of 43,826 differentially expressed genes (DEGs) were identified through comparative transcriptome analysis. Of these, 9667 were involved in fiber development and temperature response with 901 transcription factor genes and 189 genes related to plant hormone signal transduction. Further analysis of gene expression patterns revealed that 240 genes were potentially involved in fuzz initiation induced by high temperature. Functional annotation revealed that the candidate genes related to fuzz initiation were significantly involved in the asparagine biosynthetic process, cell wall biosynthesis, and stress response. The expression trends of sixteen genes randomly selected from the RNA-seq data were almost consistent with the results of qRT-PCR. Our study revealed several potential candidate genes and pathways related to fuzz initiation induced by high temperature. This provides a new view of temperature-induced tissue and organ development in Gossypium barbadense.


2020 ◽  
Author(s):  
Nathaly Maldonado-Taipe ◽  
Dilan Sarange ◽  
Sandra Schmöckel ◽  
Christian Jung ◽  
Nazgol Emrani

AbstractQuinoa depicts high nutritional quality and abiotic stress resistance attracting strong interest in the last years. To unravel the function of candidate genes for agronomically relevant traits, studying their transcriptional activities by RT-qPCR is an important experimental approach. The accuracy of such experiments strongly depends on precise data normalization. To date, validation of potential candidate genes for normalization of diurnal expression studies has not been performed in C. quinoa. We selected eight candidate genes based on transcriptome data and literature survey, including conventionally used reference genes. We used three statistical algorithms (BestKeeper, geNorm and NormFinder) to test their stability and added further validation by a simulation-based strategy. We demonstrated that using different reference genes, including those top ranked by stability, causes significant differences among the resulting diurnal expression patterns, and that our novel approach overcomes failures related to stability-based selection of reference genes. Our results show that isocitrate dehydrogenase enzyme (IDH-A) and polypyrimidine tract-binding protein (PTB) are suitable genes to normalize diurnal expression data of two different quinoa accessions. The validated reference genes obtained in this study will improve the accuracy of RT-qPCR data normalization and facilitate gene expression studies in quinoa.


2018 ◽  
Author(s):  
Josh Strable ◽  
Erik Vollbrecht

AbstractFloret units in cereals produce grain, directly impacting yield. Here we report mutations in the maize CRABS CLAW (CRC) co-orthologs drooping leaf1 (drl1) and drl2 alter the development of ear and tassel florets. Pistillate florets of drl1 ears appear sterile and display ectopic unfused carpels that fail to enclose an expanded nucellus. Staminate florets of drl1 tassels have extra stamens and retain fertile anthers. Natural variation and transposon alleles of drl2 enhance drl1 floret phenotypes by reducing floral meristem (FM) determinacy. The drl paralogs are co-expressed in lateral floral organ primordia, but not within the FM. Together, the expression patterns and indeterminate mutant FMs suggest that the drl genes regulate FM activity and impose meristem determinacy by a non-cell autonomous signal. Genetic interaction analyses of drl mutants with maize floral mutants indicate that the drl genes are required throughout floret development, illustrating their importance for proper floret patterning in maize.


2021 ◽  
Vol 12 ◽  
Author(s):  
Kamila Kwaśniewska ◽  
Caoilfhionn Breathnach ◽  
Christina Fitzsimons ◽  
Kevin Goslin ◽  
Bennett Thomson ◽  
...  

In the model plant Arabidopsis thaliana, the zinc-finger transcription factor KNUCKLES (KNU) plays an important role in the termination of floral meristem activity, a process that is crucial for preventing the overgrowth of flowers. The KNU gene is activated in floral meristems by the floral organ identity factor AGAMOUS (AG), and it has been shown that both AG and KNU act in floral meristem control by directly repressing the stem cell regulator WUSCHEL (WUS), which leads to a loss of stem cell activity. When we re-examined the expression pattern of KNU in floral meristems, we found that KNU is expressed throughout the center of floral meristems, which includes, but is considerably broader than the WUS expression domain. We therefore hypothesized that KNU may have additional functions in the control of floral meristem activity. To test this, we employed a gene perturbation approach and knocked down KNU activity at different times and in different domains of the floral meristem. In these experiments we found that early expression in the stem cell domain, which is characterized by the expression of the key meristem regulatory gene CLAVATA3 (CLV3), is crucial for the establishment of KNU expression. The results of additional genetic and molecular analyses suggest that KNU represses floral meristem activity to a large extent by acting on CLV3. Thus, KNU might need to suppress the expression of several meristem regulators to terminate floral meristem activity efficiently.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 2622-2622
Author(s):  
Esther Natalie Oliva ◽  
Maria Cuzzola ◽  
Roberto Latagliata ◽  
Francesca Ronco ◽  
D'Errigo Maria Grazia ◽  
...  

Abstract Abstract 2622 Poster Board II-598 Introduction: Genetic alterations reported in myelodysplastic syndromes (MDS) are not disease-specific and the underlying molecular causes of the disease remain poorly understood. It has been suggested that one or more of the genes mapping within the commonly deleted region of the 5q syndrome, together with other distant genes, may be critical to the development of the 5q syndrome. Potential candidate genes have been identified including the tumor suppressor gene SPARC, and the ribosomial protein gene, RPS14. Haploinsufficiency of RPS14 has been demonstrated and recent evidence indicates RPS14 as a causal gene for the 5q syndrome. Lenalidomide has proven efficacy in MDS patients with del(5q). Rapid and durable responses include transfusion-independence, with a rise in Hb, suppression of the 5q-deletion clone and improvement in bone marrow morphologic features. Methods: In a multicenter Italian phase II trial to evaluate safety, changes in quality of life and efficacy of lenalidomide in primary MDS patients with del(5q) and low or Int-1 risk IPSS, we investigate changes in bone marrow cytogenetics and gene expression patterns during treatment. The starting dose of lenalidomide is 10 mg p.o once daily on a continuous daily schedule for a maximum of 12 months. Dosing is based upon clinical and laboratory findings. Bone marrow cytogenetics and gene expression profiling are performed on study entry and every 12 weeks up to end of study (week 52). Gene expression assays of 51 candidate genes from the published literature and genomic databases have been selected and are carried out with TaqMan® Low Density Array Fluidic card (TaqMan® Human Array, Applied Biosystems, Foster City, CA, USA) based on Applied Biosystems PRISM® 7900HT comparative dd CT method, according to manufacturer's instructions. Using an 18S mRNA gene pre-designed assay from Applied Biosystems to detect the expression of the housekeeping gene 18S in each sample, target gene expression is normalized with 18S gene expression derived from a bone marrow pool of normal healthy subjects and for each sample the ratio between the target and 18S are expressed. Results: Baseline values for 23 patients (mean age 73 ± 10 years) are available and 16 have been re-evaluated after 12 weeks. Mean Hb was 8.6 ± 0.9 g/dL and 20 patients were transfusion-dependent. Seven patients had additional cytogenetic abnormalities. At baseline, RPS14 was under-expressed in 19 out of 21 patients evaluated. After 12 weeks RPS14 was re-evaluated in 13 patients: all had erythroid responses and RPS14 increased significantly from 0.07 (IQ Range 0.03–0.13) to 76.1 (0.73– 304.0, p=0.002). SPARC expression was under-expressed in 15/23 patients and variations during treatment were not significant. Baseline FAS gene was under-expressed in all patients and increased above reference values (p=0,006) after 12 weeks in 7/14 cases. IL7R was over-expressed in all patients at baseline (median 3263.3, IQ range 1998.3–5027.1) and was significantly reduced after 12 weeks (median 0.17, IQ range 0.05–2.20, p<0.0001). TINAGL1 gene expression was very high at baseline (mean 5214 ± 3661) and significantly reduced below normal values during treatment (0.63±0.87, p<0.0001). WTI was over-expressed in almost all patients (median 3246, IQ range 1590–7785) and, though reduced during treatment, still remained highly over reference values at 12 weeks (p=0.148). The expression of the other genes did not vary significantly during treatment. Conclusions: A preliminary study evaluating short-term effects of lenalidomide in low and Int-1 IPSS risk MDS and del(5q) demonstrates that gene expression is abnormal and varies during treatment. RPS14 is down-expressed and a significant increase in its expression is observed during treatment with lenalidomide in responsive patients. There is also an increase in FAS expression; the protein encoded by FAS gene is a member of the TNF-receptor superfamily and its interaction with its ligand leads to apoptosis.The IL7R gene on chromosome 5 (5p13) codifies for the IL7 receptor, which blocks apoptosis during differentiation and activation of T lymphocytes. TINAGL1 gene on chromosome 1 codifies for a Cathepsin B-like protein implicated in a number of human diseases such as cancer. During lenalidomide treatment, the expression of IL7R and TINAGL1 are reduced. Further results and repeated testing during this trial may develop new insights in the pathogenesis of MDS with del(5q) and in long-term effects of lenalidomide on bone marrow changes. Disclosures: Oliva: Celgene: Consultancy. Balleari:Celgene: Consultancy. Finelli:Celgene: Consultancy.


2021 ◽  
Vol 23 (1) ◽  
pp. 454
Author(s):  
Qin Di ◽  
Angela Piersanti ◽  
Qi Zhang ◽  
Cristina Miceli ◽  
Hui Li ◽  
...  

Soybean (Glycine max (L.) Merrill) oil is a complex mixture of five fatty acids (palmitic, stearic, oleic, linoleic, and linolenic). The high content of linoleic acid (LA) contributes to the oil having poor oxidative stability. Therefore, soybean seed with a lower LA content is desirable. To investigate the genetic architecture of LA, we performed a genome-wide association study (GWAS) using 510 soybean cultivars collected from China. The phenotypic identification results showed that the content of LA varied from 36.22% to 72.18%. The GWAS analysis showed that there were 37 genes related to oleic acid content, with a contribution rate of 7%. The candidate gene Glyma.04G116500.1 (GmWRI14) on chromosome 4 was detected in three consecutive years. The GmWRI14 showed a negative correlation with the LA content and the correlation coefficient was −0.912. To test whether GmWRI14 can lead to a lower LA content in soybean, we introduced GmWRI14 into the soybean genome. Matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-TOF IMS) showed that the overexpression of GmWRI14 leads to a lower LA content in soybean seeds. Meanwhile, RNA-seq verified that GmWRI14-overexpressed soybean lines showed a lower accumulation of GmFAD2-1A and GmFAD2-1B than control lines. Our results indicate that the down-regulation of the FAD2 gene triggered by the transcription factor GmWRI14 is the underlying mechanism reducing the LA level of seed. Our results provide novel insights into the genetic architecture of LA and pinpoint potential candidate genes for further in-depth studies.


2020 ◽  
Author(s):  
Gongmin Cheng ◽  
Longyan Zhang ◽  
Hengling Wei ◽  
Hantao Wang ◽  
Jianhua Lu ◽  
...  

Abstract Background: Gossypium barbadense L. is the most important renewable source of textile fiber. Cotton fiber cell initiation and elongation are often affected by various environmental stimulus, such as high temperature. However, little is known about the underlying mechanisms of temperature regulating the fuzz fiber initiation.Results: In the present study, phenotypic observation revealed that high temperature (HT) accelerated the fiber development, improved fiber quality and induced fuzz fiber initiation. It has been proved that the fuzz fiber initiation was inhibited by low temperature (LT), and 4 days post-anthesis (DPA) was the key stage for fuzz fiber initiation. Based on comparative transcriptome analysis, a total of 43,826 differentially expressed genes (DEGs) were identified, of which 9,667 were involved in both fiber development and temperature response with 901 transcription factor genes and 189 genes related to plant hormone signal transduction. Further analysis of gene expression patterns revealed that 240 genes were involved in fuzz fiber initiation. Functional annotation revealed that the candidate genes related to fuzz initiation were significantly involved in asparagine biosynthetic process, cell wall biosynthesis and stress response. Furthermore, the expression trends of sixteen selected genes from the RNA-seq data were almost consistent with the results of qRT-PCR results.Conclusions: Our study revealed several potential candidate genes and pathways that related to fuzz fiber initiation induced by high-temperature and provided a new view of temperature-induced tissue and organ development in Gossypium barbadense.


2019 ◽  
Author(s):  
Ellen Freebern ◽  
Daniel JA Santos ◽  
Lingzhao Fang ◽  
Jicai Jiang ◽  
Kristen L. Parker Gaddis ◽  
...  

AbstractBackgroundHealth traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to identify associated genomic variants and thus reveal insights into the genetic architecture of complex traits and diseases. The objective of this study is to investigate the genetic basis of seven health traits in dairy cattle and to identify potential candidate genes associated with cattle health using GWAS, fine mapping, and analyses of multitissue transcriptome data.ResultsWe studied cow livability and six direct disease traits, mastitis, ketosis, hypocalcemia, displaced abomasum, metritis, and retained placenta, using de-regressed breeding values and more than three million imputed DNA sequence variants. After data edits and filtering on reliability, phenotypes for 11,880 to 24,699 Holstein bulls were included in the analyses of the seven traits. GWAS was performed using a mixed-model association test, and a Bayesian fine-mapping procedure was conducted to calculate a posterior probability of causality to each variant and gene in the candidate regions. The GWAS results detected a total of eight genome-wide significant associations for three traits, cow livability, ketosis, and hypocalcemia, including the bovine MHC region associated with livability. Our fine-mapping of associated regions reported 20 candidate genes with the highest posterior probabilities of causality for cattle health. Combined with transcriptome data across multiple tissues in cattle, we further exploited these candidate genes to identify specific expression patterns in disease-related tissues and relevant biological explanations such as the expression of GC in the liver and association with mastitis as well as the CCDC88C expression in CD8 cells and association with cow livability.ConclusionsCollectively, our analyses report six significant associations and 20 candidate genes of cattle health. With the integration of multi-tissue transcriptome data, our results provide useful information for future functional studies and better understanding of the biological relationship between genetics and disease susceptibility in cattle.


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