Extensive nrDNA Polymorphism in Morus L. and Its Application

Area of Science:

• Genomics
• Plant Taxonomy
• Molecular Evolution

Background:

• The internal transcribed spacer (ITS) is crucial for Morus genus taxonomy, but genome-wide nuclear ribosomal DNA (nrDNA) characteristics are not well understood.
• While ITS evolution is generally concerted, exceptions exist, suggesting potential complexities in nrDNA evolution within Morus.

Purpose of the Study:

• To investigate genome-wide nrDNA characteristics in the genus Morus.
• To assess the extent of concerted evolution of nrDNA in Morus species.
• To develop novel molecular markers for Morus species identification and phylogenetic analysis.

Main Methods:

• Identification and analysis of single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) within nrDNA regions of 542 mulberry accessions.
• Validation of ITS polymorphism using cloning and Sanger sequencing.
• Development of a cleaved amplified polymorphic sequence (CAPS) marker for species differentiation.

Main Results:

• 158 SNPs and 15 InDels were identified across sixteen Morus species, revealing significant intra-individual polymorphism and incomplete nrDNA concerted evolution.
• The ITS regions (ITS1-5.8S-ITS2) exhibited high polymorphism, with 66 SNPs and 13 InDels.
• A novel CAPS marker was developed using a 13/16 bp InDel in ITS1, enabling rapid discrimination of M. alba and M. notabilis.

Conclusions:

• nrDNA in Morus exhibits incomplete concerted evolution, with substantial intra-individual polymorphism, particularly in the ITS regions.
• The developed CAPS marker provides an efficient tool for distinguishing key Morus species, bypassing traditional sequencing or phenotypic analysis.
• Findings enhance understanding of Morus taxonomy, supporting conservation efforts and breeding programs for mulberry.