Genome-wide association analysis of stalk biomass and anatomical traits in maize.

BackgroundMaize stover is an important source of crop residues and a promising sustainable energy source in the United States. Stalk is the main component of stover, representing about half of stover dry weight. Characterization of genetic determinants of stalk traits provide a foundation to optimize maize stover as a biofuel feedstock. We investigated maize natural genetic variation in genome-wide association studies (GWAS) to detect candidate genes associated with traits related to stalk biomass (stalk diameter and plant height) and stalk anatomy (rind thickness, vascular bundle density and area).ResultsUsing a panel of 942 diverse inbred lines, 899,784 RNA-Seq derived single nucleotide polymorphism (SNP) markers were identified. Stalk traits were measured on 800 members of the panel in replicated field trials across years. GWAS revealed 16 candidate genes associated with four stalk traits. Most of the detected candidate genes were involved in fundamental cellular functions, such as regulation of gene expression and cell cycle progression. Two of the regulatory genes (Zmm22 and an ortholog of Fpa) that were associated with plant height were previously shown to be involved in regulating the vegetative to floral transition. The association of Zmm22 with plant height was confirmed using a transgenic approach. Transgenic lines with increased expression of Zmm22 showed a significant decrease in plant height as well as tassel branch number, indicating a pleiotropic effect of Zmm22.ConclusionSubstantial heritable variation was observed in the association panel for stalk traits, indicating a large potential for improving useful stalk traits in breeding programs. Genome-wide association analyses detected several candidate genes associated with multiple traits, suggesting common regulatory elements underlie various stalk traits. Results of this study provide insights into the genetic control of maize stalk anatomy and biomass

Funktionelle Charakterisierung der Arabidopsis thaliana Aquaporine AtPIP1;2 und AtPIP2;3

Die pflanzlichen Aquaporine der Plasmamembran intrinsischen Proteine (PIP) lassen sich in zwei Untergruppen einteilen, die PIP1 und PIP2 Aquaporine. Obwohl diese beiden Gruppen ähnliche Porenregionen aufweisen unterscheiden sie sich in ihrer Leitfähigkeit für Wasser und kleinere Moleküle. Im Vergleich zur hohen Wasser-Leitfähigkeit von PIP2- Aquaporinen, sind PIP1-Aquaporine nahezu wasserundurchlässig. Im Gegensatz dazu können PIP1-Aquaporine die Diffusion von kleinen, ungeladenen Molekülen (Glycerin, Harnstoff, CO2) erleichtern, PIP2-Aquaporine jedoch nicht. Im Rahmen dieser Arbeit sollten die Leitfähigkeitscharakteristika der Aquaporine AtPIP1;2 und AtPIP2;3 aus Arabidopsis thaliana in einem Hefeexpressionssystem mit Hinblick auf ihre Wasser-und Kohlendioxid-Leitfähigkeit untersucht und im Anschluss ihre physiologische Bedeutung für die Pflanze analysiert werden. Es zeigte sich, dass AtPIP2;3 die Membranpermeabilität für Wasser signifikant erhöhen konnte, wohingegen AtPIP1;2 dies nicht vermochte. Im Gegensatz dazu war AtPIP1;2 in der Lage, die Diffusion von CO2 über die Hefe-Plasmamembran zu erleichtern, AtPIP2;3 jedoch nicht. Die physiologische Relevanz dieser verschiedenen Aquaporin-Leitfähigkeiten wurde mit Hilfe von T-DNA-Insertionslinien untersucht. Die verwendeten A. thaliana-Linien atpip1;2-1 und atpip2;3-1, konnten als homozygot charakterisiert werden. Linie atpip1;2-1 enthält lediglich die Insertion im AtPIP1;2-Gen. In Linie atpip2;3-1 findet sich neben der Insertion im AtPIP2;3-Gen eine weitere in einer nicht codierenden Region des 3. Chromosoms. Bei beiden Linien führt die T-DNA-Insertion zum Verlust der entsprechenden Aquaporin-mRNA. Die Untersuchung der hydraulischen Leitfähigkeit von Arabidopsis-Wurzeln der beiden Insertionslinien ergab, dass im Vergleich zur Kontroll-Linie die Abwesenheit von AtPIP2;3 keinen Einfluss auf die hydraulische Leitfähigkeit hat. Dagegen scheint AtPIP1;2 eine Komponente des symplastischen Transportweges von Wasser in der Wurzel zu sein, da atpip1;2-1-Wurzeln eine deutliche Reduktion der hydraulischen Leitfähigkeit aufwiesen. Auch im Blatt konnte eine physiologische Bedeutung von AtPIP1;2 nachgewiesen werden, da Messungen des pflanzlichen Gaswechsels der Linie atpip1;2-1 eine signifikant verringerte photosynthetische Assimilationsrate und stomatäre Leitfähigkeit ergaben. Als Ursache hierfür konnte die starke Reduktion der Mesophyll-Leitfähigkeit für CO2 (gm) identifiziert werden. Hier kommt vermutlich die im heterologen Expressionssystem nachgewiesene molekulare CO2-Leitfähigkeit von AtPIP1;2 zum Tragen. Für Linie atpip2;3-1 konnten bezüglich der Gaswechsel-Analysen keinerlei Unterschiede zu den Kontroll-Pflanzen festgestellt werden. Die Ergebnisse weisen auf eine Funktion von AtPIP1;2 sowohl in der Wasser-Aufnahme durch die Wurzeln als auch in der Erleichterung der CO2-Diffusion im Blatt hin. Hingegen konnte basierend auf den durchgeführten Untersuchungen nicht festgestellt werden, inwieweit AtPIP2;3 von physiologischer Bedeutung ist

T-DNA insertion in aquaporin gene AtPIP1;2 generates transcription profiles reminiscent of a low CO2 response.

Results from CO2 diffusion studies and characterization of Arabidopsis thaliana aquaporin AtPIP1;2 T-DNA insertion lines support the idea that specific aquaporins facilitate the diffusion of CO2 through biological membranes. However, their function as CO2 diffusion facilitators in plant physiology is still a matter of debate. Assuming that a lack of AtPIP1;2 causes a characteristic transcriptional response, we compared data from a AtPIP1;2 T-DNA insertion line obtained by Illumina sequencing, Affymetrix chip analysis and quantitative real time PCR to the transcriptome of plants grown under drought stress or under low CO2 conditions. The plant reaction to the deficit of AtPIP1;2 was unlike drought stress responses but comparable to that of low CO2 conditions. In addition, we observed a phenotype characteristic to plants grown under low CO2 . The findings support the hypothesis that AtPIP1;2 function in plant physiology is not to facilitate water but CO2 diffusion

Transcriptome analysis of the aquaporin AtPIP1;2 deficient line in Arabidopsis thaliana.

Atmospheric CO2 impacts all aspects of plant development. It has changed in the past and is predicted to change further on. Studies on the response of crop plants to low and elevated CO2 concerning growth, productivity and physiological processes are intense. In contrast, the molecular mechanisms of cellular CO2 exchange are still under discussion. At the same time it becomes more and more accepted that carbon dioxide is transported across cellular biomembranes by CO2 conducting aquaporins. Our recent study (Boudichevskaia et al., 2015) demonstrates that the lack of a single gene product - aquaporin AtPIP1;2 - resulted in massive transcriptional reprogramming in Arabidopsis as a consequence of reduced tissue CO2 diffusion rates. Therefore, the transcriptome data of the aquaporin AtPIP1;2 deficient line can be used in the comparative expression analyses for better understanding the role of aquaporins with regard to CO2 and water transport in plants. Here we describe a gene expression dataset generated for three biological replicates per genotype on Affymetrix platform. We provide detailed methods and analysis on microarray data which has been deposited in Gene Expression Omnibus (GEO): GSE62167. Additionally, we provide the R code for data preprocessing and quality control

Transcriptome analysis of the aquaporin AtPIP1;2 deficient line in Arabidopsis thaliana

Atmospheric CO2 impacts all aspects of plant development. It has changed in the past and is predicted to change further on. Studies on the response of crop plants to low and elevated CO2 concerning growth, productivity and physiological processes are intense. In contrast, the molecular mechanisms of cellular CO2 exchange are still under discussion. At the same time it becomes more and more accepted that carbon dioxide is transported across cellular biomembranes by CO2 conducting aquaporins. Our recent study (Boudichevskaia et al., 2015) demonstrates that the lack of a single gene product – aquaporin AtPIP1;2 – resulted in massive transcriptional reprogramming in Arabidopsis as a consequence of reduced tissue CO2 diffusion rates. Therefore, the transcriptome data of the aquaporin AtPIP1;2 deficient line can be used in the comparative expression analyses for better understanding the role of aquaporins with regard to CO2 and water transport in plants. Here we describe a gene expression dataset generated for three biological replicates per genotype on Affymetrix platform. We provide detailed methods and analysis on microarray data which has been deposited in Gene Expression Omnibus (GEO): GSE62167. Additionally, we provide the R code for data preprocessing and quality control

The Arabidopsis thaliana aquaporin AtPIP1;2 is a physiologically relevant CO(2) transport facilitator.

Cellular exchange of carbon dioxide (CO(2) ) is of extraordinary importance for life. Despite this significance, its molecular mechanisms are still unclear and a matter of controversy. In contrast to other living organisms, plants are physiologically limited by the availability of CO(2) . In most plants, net photosynthesis is directly dependent on CO(2) diffusion from the atmosphere to the chloroplast. Thus, it is important to analyze CO(2) transport with regards to its effect on photosynthesis. A mutation of the Arabidopsis thaliana AtPIP1;2 gene, which was characterized as a non-water transporting but CO(2) transport-facilitating aquaporin in heterologous expression systems, correlated with a reduction in photosynthesis under a wide range of atmospheric CO(2) concentrations. Here, we could demonstrate that the effect was caused by reduced CO(2) conductivity in leaf tissue. It is concluded that the AtPIP1;2 gene product limits CO(2) diffusion and photosynthesis in leaves

The Arabidopsis aquaporin PIP1;2 rules cellular CO(2) uptake.

The membrane CO(2) flux into Arabidopsis mesophyll cells was studied using a scanning pH microelectrode. Arabidopsis thaliana mesophyll cells were exposed to photosynthesis-triggering light intensities, which induced cellular CO(2) uptake. Data obtained on a AtPIP1;2 T-DNA insertion line indicated that under these conditions, cellular CO(2) transport was not limited by unstirred layer effects but was dependent on the expression of the aquaporin AtPIP1;2. Complementation of the AtPIP1;2 knockout restored membrane CO(2) transport levels to that of controls. The results provide new arguments for the ongoing debate about the validity of the lipid bilayer model system and the Meyer-Overton rule for cellular gas transport. In conclusion, we suggest a modified model of molecular gas transport mechanisms in living cells. © 2011 Blackwell Publishing Ltd

Genome-wide association analysis of stalk biomass and anatomical traits in maize.

BackgroundMaize stover is an important source of crop residues and a promising sustainable energy source in the United States. Stalk is the main component of stover, representing about half of stover dry weight. Characterization of genetic determinants of stalk traits provide a foundation to optimize maize stover as a biofuel feedstock. We investigated maize natural genetic variation in genome-wide association studies (GWAS) to detect candidate genes associated with traits related to stalk biomass (stalk diameter and plant height) and stalk anatomy (rind thickness, vascular bundle density and area).ResultsUsing a panel of 942 diverse inbred lines, 899,784 RNA-Seq derived single nucleotide polymorphism (SNP) markers were identified. Stalk traits were measured on 800 members of the panel in replicated field trials across years. GWAS revealed 16 candidate genes associated with four stalk traits. Most of the detected candidate genes were involved in fundamental cellular functions, such as regulation of gene expression and cell cycle progression. Two of the regulatory genes (Zmm22 and an ortholog of Fpa) that were associated with plant height were previously shown to be involved in regulating the vegetative to floral transition. The association of Zmm22 with plant height was confirmed using a transgenic approach. Transgenic lines with increased expression of Zmm22 showed a significant decrease in plant height as well as tassel branch number, indicating a pleiotropic effect of Zmm22.ConclusionSubstantial heritable variation was observed in the association panel for stalk traits, indicating a large potential for improving useful stalk traits in breeding programs. Genome-wide association analyses detected several candidate genes associated with multiple traits, suggesting common regulatory elements underlie various stalk traits. Results of this study provide insights into the genetic control of maize stalk anatomy and biomass