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RNA-seq analysis of the most basal half centimeter (dividing cells) of the fourth leaf of maize RIL89 plants, profiled at different time points after leaf appearance and with different watering conditions

ABSTRACT: RNA-seq analysis of the most basal half centimeter (dividing cells) of the fourth leaf of maize RIL89 plants, profiled at different time points after leaf appearance and with different watering conditions

PROVIDER: PRJEB31651 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3212270_1.fastq.gz	Fastqsanger.gz
	ERR3212270_2.fastq.gz	Fastqsanger.gz
	ERR3212280_1.fastq.gz	Fastqsanger.gz
	ERR3212280_2.fastq.gz	Fastqsanger.gz
	ERR3212290_1.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of the most basal half centimeter (dividing cells) of the fourth leaf of maize RIL89 plants, profiled at different time points after leaf appearance and with different watering conditions

Project description:Transcriptome of the most basal half centimeter (dividing cells) of the fourth leaf of maize RIL89 plants was profiled at different days after leaf appearance (DALA). Leaf samples were taken for well-watered and water deficit plants at 4, 5, 6 and 7 days after the appearance of leaf four and at day 5 and 7, samples were harvested from the plants re-watered (RW) at day 4 (RW5) and day 6 (RW7), respectively. RIL89 is derived from a cross between parental lines B73 and H99.

2023-03-01 | E-MTAB-7749 | biostudies-arrayexpress

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Project description:Plants require a distinctive cohort of enzymes to coordinate division and cell expansion. Proteomic analysis now enables interrogation of immature leaf bases where these processes occur. Hence we investigated proteins in tissues sampled from leaves of a drought-tolerant rice (IAC1131) to provide insights into the effect of soil drying on gene expression when compared with the drought-sensitive Nipponbare. Shoot growth zones were dissected to count dividing cells and extract protein for subsequent Tandem Mass Tags (TMT) quantitative proteomic analysis. Gene Ontology (GO) annotations of differentially expressed proteins provided insights into responses of Nipponbare and IAC1131 to drought. Soil drying did not affect the proportion of mitotic cells in IAC1131. More than 800 proteins across most functional categories were up-regulated in drought (and down-regulated on re-watering) in IAC1131, including those involved in organization of the meristem and subsequent cell formation. On the other hand, the proportion of dividing cells in Nipponbare was severely impaired during drought and fewer than 200 proteins responded in abundance when the growing zones underwent a drying cycle. However, those proteins involved in oxidation state and response to external stimuli were more likely to be upregulated by drought, even in Nipponbare.

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Project description:Transcriptome of three zones (from the base to 3.5 cm, from 3.5 to 7.0 cm and from 7.0 to 10.5 cm) of the developing fourth leaf of maize B104 plants was profiled at two days after leaf appearance (DALA). Only leaf samples were taken for well-watered plants.

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Transcriptomic analysis of three Sorghum bicolor landraces following progressive water stress and re-watering

Project description:Background: Sorghum bicolor is a remarkably drought tolerant cereal crop. Its natural biodiversity that enables this tolerance has developed in sub-Saharan Africa. The sequencing of the sorghum genome in 2009 has expedited research of this crop which has also been proposed as a model C4 cereal crop for genomics. In this study, the genetic response mechanisms involved in sorghums’ tolerance to progressive water deficit and moderate re-watering were investigated in three previously uncharacterized South African landraces (designated: LR5, LR6 and LR35) using cDNA microarrays comprising 35 899 transcript probes. Results: Across the three landraces, significant differential expression of 1 797 genes, including 264 genes with currently unknown functions, were altered in response to progressive water stress and re-watering. The modulated sorghum genes had homology to proteins involved in growth, regulation, and protection. Gene ontology analysis identified significant enrichment of 26 genes involved in the ‘response to abiotic stimulus’ GO category in LR6 during severe stress. The expression of USP responded to progressive water stress and moderate re-watering in LR6 and LR35. Moreover, our results indicate a putative role for β-alanine betaine biosynthesis in drought tolerance of sorghum. Conclusions: This study identified the drought responsive gene complement of three previously uncharacterized South African sorghum landraces. Each landrace is a distinct genotype and similar responses to water deficit and re-watering were not expected. Functional characterizations of some of the differentially expressed genes found in this study may be used as possible targets for marker-assisted breeding or transgenic initiatives for sorghum and, other closely related crop species.

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The basal cm of leaf 4 of GA2OX::PLA1 (193-01) versus wild type in the growth chamber and the field (May-June 2016)

Project description:GA2OX::PLA1 transgenic plants and their none-transgenic siblings were grown in the field in Wetteren and in the growth chamber. In the field, we sampled three plants per plot (three plots were sown per genotype), resulting in three pools each consisting of three plants. Every pool represented a different subplot. In the growth chamber, the plants were sampled randomly across the population, with three pools, each consisting of three plants. For each plant, the day of leaf 4 appearance was marked and the samples were taken two days after leaf 4 appeared. The seedlings were cut just above soil level and the growing fourth leaf was dissected out and the younger leaves inside leaf 4 were removed. Using a ruler we sampled the basal cm of leaf 4 (division zone) for RNA preparation. The samples were snap frozen and transported to the lab for storage at -80 degrees and further processing. Two time points were sampled, two days after leaf 4 appearance as well as six days after leaf appearance.

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