Genome-wide Analysis of MYB Gene Family in Potato Provides Insights into Tissue-specific Regulation of Anthocyanin Biosynthesis

The MYB transcription factor is one of the largest gene families in plants,playing an important role in regulating plant growth,development,response to stress,senescence,and especially the anthocyanin biosynthesis.In this study,A total of 217 MYB genes,including 901R-MYBs,124 R2R3-MYBs,and 3 R1R2R3-MYBs have been identified from the potato genome.The 1R-MYB and R2R3-MYB family members could be divided into 20 and 35 subgroups respectively.Analysis of gene structure and protein motifs revealed that members within the same subgroup presented similar exon/intron and motif organization,further supporting the results of phylogenetic analysis.Potato is an ideal plant to reveal the tissue-specific anthocyanins biosynthesis regulated by MYB,as the anthocyanins could be accumulated in different tissues,showing colorful phenotypes.Five pairs of colored and colorless tissues,stigma,petal,stem,leaf,and tuber flesh,were applied to the transcriptomic analysis.A total of 70 MYB genes were found to be differentially expressed between colored and colorless tissues,and these differentially expressed genes were suspected to regulate the biosynthesis of anthocyanin of different tissues.Co-expression analysis identified numerous potential interactive regulators of anthocyanins biosynthesis,involving 39 MYBs,24 bHLHs,2 WD-repeats,and 29 biosynthesis genes.Genome-wide association study(GWAS)of tuber flesh color revealed amajor signal at the end of Chromosome 10,which was co-localized with reported I gene(StMYB88),controlling tuber peel color.Analyses of DEGs(Differentially Expression Genes)revealed that both StMYB88 and StMYB89 were closely related to regulating anthocyanin biosynthesis of tuber flesh.This work offers a comprehensive overview of the MYB family in potato and will lay a foundation for the functional validation of these genes in the tissue-specific regulation of anthocyanin biosynthesis.

Inheritance of steroidal glycoalkaloids in potato tuber flesh

Potato (Solanum tuberosum L.) is the third most important food crop worldwide after wheat and rice in terms of human consumption. A critical domestication trait for potato was the decrease of toxic steroidal glycoalkaloids (SGAs) in tuber flesh. Here, we used a diploid F2 segregating population derived from a cross between S. tuberosum and the wild potato species Solanum chacoense to map the quantitative trait loci (QTLs) associated with the regulation of SGAs content in tuber flesh. In a three-year study, we identified two QTLs on chromosomes 2 and 8 affecting SGAs content in tuber flesh. The QTL on chromosome 8 harbors 38 genes that are co-expressed with the GLYCOALKALOID METABOLISM genes. These findings lay the foundation for exploiting the genes controlling SGAs content in tuber flesh and they provide a theoretical basis for the use of wild germplasm in potato breeding.

Genomics Approaches to Domestication Studies of Horticultural Crops

The majority of crops we eat today are derived from the domestication of their wild progenitors. Crop domestication satisfies the human need for food and nutrition. Characterization of the history and genetic basis of crop domestication is essential for us to conduct modern breeding practices. Genomics provide unprecedented opportunities for us to study domestication. In this review, the typical domestication syndromes of horticultural crops will be introduced. Using the tomato as a typical example, we will discuss how genetic and genomic data were used to decipher the origins, progenitors, and domestication processes of this crop. In the domestication exploration of the genetic basis especially,genome-scaled diversity scanning approaches have gained great popularity. Combining these approaches with QTL(Quantitative trait locus)-mapping, GWAS(Genome wide association study), metabolomics and homology-based searches as well as pan-genomics have demonstrated tremendous advantages and significantly contribute to our understanding of domestication. Genomics studies will accelerate domestication research and further breeding of crops.