Dataset Information

Combination of RNA-Seq transcriptomics and iTRAQ proteomics reveal the mechanism involved in fresh-cut yam yellowing.

ABSTRACT: The aim of this study was to examine the regulation of transcriptomics and proteomics related to the yellowing of fresh-cut yams after storage. The comparison of yellow fresh-cut yam (YFY) vs. white fresh-cut yam (control) revealed 6894 upregulated and 6800 downregulated differentially expressed genes along with 1277 upregulated and 677 downregulated differentially expressed proteins. The results showed that the total carotenoids, flavonoids, and bisdemethoxycurcumin in YFY were higher than in the control due to the significant up-regulation of critical genes in the carotenoid biosynthesis pathway, flavonoid biosynthesis pathway, and stilbenoid, diarylheptanoid, and gingerol biosynthesis pathway. In addition, the tricarboxylic acid cycle and phenylpropanoid biosynthesis were both enhanced in YFY compared to the control, providing energy and precursors for the formation of yellow pigments. The results suggest that the synthesis of yellow pigments is regulated by critical genes, which might explain the yellowing of fresh-cut yam after storage.

SUBMITTER: Guo S

PROVIDER: S-EPMC8032744 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Combination of RNA-Seq transcriptomics and iTRAQ proteomics reveal the mechanism involved in fresh-cut yam yellowing.

Guo Shuang S Wang Dan D Ma Yue Y Zhang Yan Y Zhao Xiaoyan X

Scientific reports 20210408 1

The aim of this study was to examine the regulation of transcriptomics and proteomics related to the yellowing of fresh-cut yams after storage. The comparison of yellow fresh-cut yam (YFY) vs. white fresh-cut yam (control) revealed 6894 upregulated and 6800 downregulated differentially expressed genes along with 1277 upregulated and 677 downregulated differentially expressed proteins. The results showed that the total carotenoids, flavonoids, and bisdemethoxycurcumin in YFY were higher than in t ...[more]

PMID: 33833352

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Project description:Egg production performance is an important economic trait in the poultry industry. In previous studies, attention has often been paid to the growth and development of the ovaries, while there has been less research on the testicular tissue of male goose. Due to various factors, there are usually significant differences in the process of testicular spermatogenesis among different goose breeds. The Jilin white goose (JL) is a high-production local goose species in China, domesticated from Anser cygnoides, which has a high egg-laying performance and the egg-laying period can last from February to July. In the production of goose within Jilin Province, the female goose of Jilin White goose is considered as an important maternal parent of synthetic lines, and ganders from Hungarian white goose (HU), Wanxi white goose (WX) and Jilin white goose are the main male parents. Each year, all 3 gander species begin to exhibit breeding capacity in February and reach the peak of reproductive capacity by April, marked by high fertilization rates. With the gradual increase in temperature, the testicular tissue of Hungarian and Wanxi goose gradually diminishes in its ability to produce sperm. the testicular tissue undergoes significant shrinkage by the end of June, resulting in a near loss of sperm production capability, thereby yielding low fertilization rates. However, the Jilin White goose demonstrates the ability to maintain a stable sperm production capacity. Individuals with low sperm motility contribute to increased seed production costs and pose constraints on the industrial development of livestock and poultry varieties. In this study, transcriptomics and proteomics data from gooses testicular of 3 different goose breeds inclouding Jilin white goose, Wanxi white gooseand Hungary white goose sampled in 2 stages, peak of laying cycle (PLC) and end of laying cycle (ELC). In a comparative analysis between PLC and ELC groups (ELC vs. PLC) of 3 breeds, we identified 401,340,6651 differentially expressed genes (DEGs) and 18,225,323 differentially expressed proteins (DEPs), respectively. Differentially expressed genes and proteins were significantly enriched in Gene Ontology (GO) terms such as phosphotransferase activity, cytoskeletal protein binding, microtubule motor activity, channel activity and carbohydrate metabolic process. The KEGG enrichment analysis of the DEGs in testicular showed that most differentially expressed mRNAs participate in the KEGG pathways, including ECM-receptor interaction, MAPK signaling pathway, carbon metabolism, Cell cycle, VEGF signaling pathway, Lipoic acid metabolism and p53 signaling pathway. The differential expression of 4 selected DEGs (SPAG6, NEK2, HSPA4L, SERF1A) was verified by qRT-PCR, and the results were consistent with RNA-seq data. In conclusion, this study reveals the differences in gene expression regulation in testicular tissues of different goose species, and screening candidate genes and proteins related to spermatogenesis.

Dataset Information

Combination of RNA-Seq transcriptomics and iTRAQ proteomics reveal the mechanism involved in fresh-cut yam yellowing.

Publications

Combination of RNA-Seq transcriptomics and iTRAQ proteomics reveal the mechanism involved in fresh-cut yam yellowing.

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