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Genomic methylation variation during grape genome duplication

ABSTRACT: WGBS was used to assess gene expression variation between 2X and 4X grape

ORGANISM(S): Vitis vinifera

PROVIDER: GSE119632 | GEO | 2020/06/10

REPOSITORIES: GEO

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Project description:Polyploidization is one of the effective ways to improve plant height and yield of rice (Oryza sativa L.). However, the molecular mechanism of regulation is not yet fully understood. Here, we investigated the agronomic traits of diploid (Balilla-2x) and tetraploid (Balilla-4x) of japonica rice variety Balilla. Compared with Balilla-2x, Balilla-4x exhibited significantly increased plant height, spike length and yield per plant. RNA-seq analysis of the leaves of Balilla-2x and Balilla-4x was performed and the results showed that the expression levels of yield related genes (e.g., STH1, OsYUC9, and OsDEP1) were significantly upregulated in Balilla-4x rice plants, these genes are related to plant height and panicle development. These results indicated that polyploidization changed the expression of genes related to agronomic traits such as plant height and spike length, thereby increasing rice yield. This study provides a further basis for understanding the yield of rice after polyploidization, and can serve as a new theoretical reference for breeding high-yielding rice varieties achieved.

2024-01-30 | GSE254291 | GEO

The acute milk yield response to frequent milking in early lactation is mediated by genes transiently regulated by milk removal.

Project description:Milking dairy cows four times daily (4X) instead of twice daily (2X) during early lactation stimulates an increase in milk yield that partly persists through late lactation; however, the mechanisms behind this response are unknown. We hypothesized that the acute mammary response to regular milkings would be transient and would involve different genes from those that may be specifically regulated in response to 4X. Nine multiparous cows were assigned at parturition to unilateral frequent milking (UFM; 2X of the left udder half, 4X of the right udder half). Mammary biopsies were obtained from both rear quarters at 5 days in milk (DIM), immediately after 4X glands had been milked (Experiment 1; n = 4 cows), or 2.5 h after both udder halves had last been milked (Experiment 2; n = 5 cows). Affymetrix GeneChip® Bovine Genome Arrays were used to measure gene expression. Eight hundred and fifty five genes were differentially expressed in mammary tissue between 2X vs. 4X glands of cows in experiment 1 (FDR ≤ 0.05), whereas none were differentially expressed in experiment 2 using the same criterion. We conclude that there is an acute transcriptional response to milk removal, but 4X milking did not elicit differential expression of unique genes. Therefore, there does not appear to be a sustained transcriptional response to 4X milking on day 5 of lactation. Using a differential expression plot of data from both experiments, as well as qRT-PCR, we identified at least two genes that may be responsive to both milk removal and to 4X milking. Therefore, the milk yield response to 4X milking may be mediated by genes that are acutely regulated by removal of milk from the mammary gland.

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Transcriptome response to change in ploidy level in Arabidopsis

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