How Apple Skin Color Changes: Gene Study and Expression Analysis

Jenn Hoskins
9th May, 2024

How Apple Skin Color Changes: Gene Study and Expression Analysis

Image Source: Natural Science News, 2024

Key Findings

  • Researchers at Gansu Agricultural University identified 59 phytocyanin genes in apples, important for fruit development
  • These apple genes were grouped into four subfamilies based on their structures and functions
  • The study suggests these genes help regulate apple color and could improve fruit quality
In the realm of plant biology, the role of phytocyanins (PCs) has been a subject of interest due to their involvement in vital processes such as photosynthesis, development, and stress responses. PCs are a family of copper-containing proteins that facilitate electron transport, a crucial component in the energy conversion processes of plants. Recently, researchers at Gansu Agricultural University have made a significant leap in understanding PCs in apples, a crop of global economic importance[1]. The study embarked on a comprehensive exploration of the PC gene family in apple, scientifically known as Malus domestica. The team successfully identified 59 distinct members of the MdPC gene family distributed across 12 chromosomes. This discovery is not only a milestone in apple genomics but also enriches the existing knowledge of PC gene families in other plants, such as rice and Chinese cabbage, where 62 and 84 PC genes were previously identified, respectively[2][3]. Phytocyanins in apple were categorized into four subfamilies: MdENODLs (Apple Early nodulin-like proteins), MdUCLs (Apple Uclacyanin-like proteins), MdSCLs (Apple Stellacyanin-like proteins), and MdPLCLs (Apple Plantacyanin-like proteins). This classification was based on the unique structural features of these proteins, including copper binding sites and glycosylation sites, which are modifications that can influence a protein's function and stability. Intriguingly, the study revealed that MdPC genes with similar structures and motifs tend to cluster within the same subfamily, suggesting that these genes may have evolved from common ancestors. This is consistent with previous findings in other plants that showed gene duplications as a driving force in the diversification of the PC gene family[2][3][4]. The research further delved into the evolutionary relationships of apple PCs, uncovering 14 gene pairs with shared collinearity, which implies a shared evolutionary history. Additionally, apple PCs displayed homology with those in strawberry and grape, indicating that these gene families may have a common lineage that predates the divergence of these fruit species. A key aspect of the study was the examination of selection pressures, which revealed that the MdPC gene family is under purifying selection, a process that tends to eliminate deleterious mutations, thereby preserving the functional integrity of these proteins over time. Protein interaction predictions highlighted the potential partnership between MdPC family members and the Nad3 protein, which is involved in the mitochondrial respiratory chain, hinting at a broader role for PCs in energy metabolism. Of particular note is the involvement of MdPC genes in the biosynthesis of phenylpropanoids, a group of compounds that contribute to the color, flavor, and nutritional value of fruits. The study's gene expression analysis, supported by Chip data, showed that certain MdPC genes were highly expressed in mature fruits and peels, which are critical stages for fruit color development. The researchers also identified numerous cis-regulatory elements in the promoter regions of MdPC genes, which are DNA sequences that influence the expression of genes. These elements are associated with responses to light, phytohormones, and abiotic stresses, as well as the regulation of flavonoid biosynthesis, a pathway involved in pigment formation in fruits. Quantitative real-time PCR (qRT-PCR) results provided insights into the expression patterns of MdPC genes during the apple coloring process. Notably, members of Group IV were up-regulated at all stages of apple coloring, with the highest expression at the DAF13 stage, while Group II members showed varied expression patterns, with a notable increase at the DAF21 stage. The findings from Gansu Agricultural University's study offer a foundational understanding of the structure and evolutionary trajectory of the MdPC gene family in apple. More importantly, this work paves the way for further research into the molecular mechanisms by which these genes regulate apple fruit coloration, with potential applications in improving fruit quality and developing new varieties.

GeneticsPlant ScienceEvolution

References

Main Study

1) Molecular evolution of Phytocyanin gene and analysis of expression at different coloring periods in apple (Malus domestica).

Published 8th May, 2024

https://doi.org/10.1186/s12870-024-05069-6

Related Studies

2) The putative phytocyanin genes in Chinese cabbage (Brassica rapa L.): genome-wide identification, classification and expression analysis.

https://doi.org/10.1007/s00438-012-0726-4

3) The phytocyanin gene family in rice (Oryza sativa L.): genome-wide identification, classification and transcriptional analysis.

https://doi.org/10.1371/journal.pone.0025184

4) The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins.

Journal: Structure (London, England : 1993), Issue: Vol 12, Issue 6, Jun 2004


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