Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 May 5;15(5):587.
doi: 10.3390/genes15050587.

Genome-Wide Analysis of Transcription Factor R2R3-MYB Gene Family and Gene Expression Profiles during Anthocyanin Synthesis in Common Walnut (Juglans regia L.)

Dongjun Zuo  1 , Yujie Yan  1 , Jiayu Ma  1 , Peng Zhao  1
Affiliations

Genome-Wide Analysis of Transcription Factor R2R3-MYB Gene Family and Gene Expression Profiles during Anthocyanin Synthesis in Common Walnut (Juglans regia L.)

Dongjun Zuo et al. Genes (Basel). .

Abstract

The R2R3-MYB gene family, encoding plant transcriptional regulators, participates in many metabolic pathways of plant physiology and development, including flavonoid metabolism and anthocyanin synthesis. This study proceeded as follows: the JrR2R3-MYB gene family was analyzed genome-wide, and the family members were identified and characterized using the high-quality walnut reference genome "Chandler 2.0". All 204 JrR2R3-MYBs were established and categorized into 30 subgroups via phylogenetic analysis. JrR2R3-MYBs were unevenly distributed over 16 chromosomes. Most JrR2R3-MYBs had similar structures and conservative motifs. The cis-acting elements exhibit multiple functions of JrR2R3-MYBs such as light response, metabolite response, and stress response. We found that the expansion of JrR2R3-MYBs was mainly caused by WGD or segmental duplication events. Ka/Ks analysis indicated that these genes were in a state of negative purifying selection. Transcriptome results suggested that JrR2R3-MYBs were widely entangled in the process of walnut organ development and differentially expressed in different colored varieties of walnuts. Subsequently, we identified 17 differentially expressed JrR2R3-MYBs, 9 of which may regulate anthocyanin biosynthesis based on the results of a phylogenetic analysis. These genes were present in greater expression levels in 'Zijing' leaves than in 'Lvling' leaves, as revealed by the results of qRT-PCR experiments. These results contributed to the elucidation of the functions of JrR2R3-MYBs in walnut coloration. Collectively, this work provides a foundation for exploring the functional characteristics of the JrR2R3-MYBs in walnuts and improving the nutritional value and appearance quality of walnuts.

Keywords: JrR2R3-MYB; Juglans; transcriptome anthocyanin biosynthesis.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Chromosomal distribution of JrMYB genes.
Figure 2
Figure 2
Phylogenetic relationships of R2R3-MYB proteins between J. regia, O.sativa, and Arabidopsis.
Figure 3
Figure 3
Collinearity analyses of JrR2R3-MYB genes. Different color lines indicate paralogous gene pairs.
Figure 4
Figure 4
The collinearity relationships of R2R3-MYB genes. (A) Collinearity relationships of R2R3-MYB genes among J. regia and Arabidopsis; (B) collinearity relationships of R2R3-MYB genes among J. regia and J. mandshurica; (C) collinearity relationships of R2R3-MYB genes among J. regia and J. nigra. Grey lines indicate orthologous gene pairs and red lines indicate orthologous R2R3-MYB gene pairs.
Figure 5
Figure 5
The analysis of all JrR2R3-MYB cis-acting elements. The colored numbers indicate the number of cis-acting elements.
Figure 6
Figure 6
Gene expression levels of JrR2R3-MYBs in different organs.
Figure 7
Figure 7
Gene expression patterns of JrR2R3-MYBs in different organs in red walnut and green walnut.
Figure 8
Figure 8
The DEGs in ‘Zijing’ and ‘Lvling’ walnut varieties. (A) A heat map of 17 differentially expressed JrR2R3-MYBs in differently colored leaves of two walnut varieties ‘Zijing’ and ‘Lvling’ obtained using RNA-seq. (B) Phylogenetic analysis of the discrepancy-expressed JrR2R3-MYBs in ‘Zijing’ walnut and anthocyanin-related R2R3-MYBs. Red fronts represent JrR2R3-MYBs, and circles represent JrR2R3-MYBs in ‘Zijing’ walnut.
Figure 9
Figure 9
Relative expression of 9 JrR2R3-MYBs in ‘Zijing’ and ‘Lvling’ leaves. LL represents ‘Lvling’, ZJ represents ‘Zijing’. The yellow bars represent qRT-PCR results, while the bule lines represent FPKM value. ns = no significant different, * = p < 0.05, ** = p < 0.01, and *** = p < 0.001.
Figure 10
Figure 10
Network analysis of JrR2R3-MYB members. (A) Protein–protein interactions of the nine JrR2R3-MYB proteins related to ‘Zijing’ walnut color regulation JrR2R3-MYB proteins. Red font indicates JrR2R3-MYB proteins. (B) MiRNA targeting of the nine JrR2R3-MYB genes related to ‘Zijing’ walnut color regulation. The blue circle and orange circle represent miRNAs and JrR2R3-MYBs, respectively. Blue lines represent cleavage, and orange lines represent translation.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. McGranahan G., Leslie C. Walnut. In: Badenes M.L., Byrne D.H., editors. Fruit Breeding. Springer; Boston, MA, USA: 2012. pp. 827–846.
    1. Martínez-García P.J., Crepeau M.W., Puiu D., Gonzalez-Ibeas D., Whalen J., Stevens K.A., Paul R., Butterfield T.S., Britton M.T., Reagan R.L., et al. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols. Plant J. 2016;87:507–532. doi: 10.1111/tpj.13207. - DOI - PubMed
    1. Zhang J.P., Zhang W.T., Ji F.F., Qiu J., Song X.B., Bu D.C., Pan G., Ma Q.G., Chen J.X., Huang R.M., et al. A high-quality walnut genome assembly reveals extensive gene expression divergences after whole-genome duplication. Plant Biotechnol. J. 2020;18:1848–1850. doi: 10.1111/pbi.13350. - DOI - PMC - PubMed
    1. Feldman E.B. The scientific evidence for a beneficial health relationship between walnuts and coronary heart disease. J. Nutr. 2002;132:1062S–1101S. doi: 10.1093/jn/132.5.1062S. - DOI - PubMed
    1. Sideli G.M., McAtee P., Marrano A., Allen B.J., Brown P.J., Butterfield T.S., Dandekar A.M., Leslie C.A., Neale D.B. Genetic analysis of walnut (Juglans regia L.) pellicle pigment variation through a novel, high-throughput phenotyping platform. G3-Genes. Genom. Genet. 2020;10:4411–4424. doi: 10.1534/g3.120.401580. - DOI - PMC - PubMed

Publication types

LinkOut - more resources