Rapid Genome-Wide Location-Specific Polymorphic SSR Marker Discovery in Black Pepper by GBS Approach

Area of Science:

• Genomics
• Plant Science
• Bioinformatics

Background:

• Black pepper (Piper nigrum) is a vital spice crop with significant medicinal and cultural importance.
• Simple sequence repeats (SSRs) are crucial genetic markers for population structure, gene discovery, and diversity analysis.
• Existing SSR databases lack chromosomal location specificity, hindering advanced genetic applications.

Purpose of the Study:

• To develop a comprehensive, chromosome-specific SSR database for black pepper.
• To identify polymorphic and hypervariable SSR markers for genetic diversity and breeding applications.
• To establish a web-based genomic resource for black pepper research.

Main Methods:

• Generated ddRAD sequence data for 29 black pepper genotypes.
• Utilized the latest black pepper genome assembly to mine genome-wide SSRs.
• Integrated ddRAD and genome assembly data to identify polymorphic SSRs.

Main Results:

• Mined 276,230 genome-wide SSRs distributed across 26 chromosomes.
• Identified 3,176 polymorphic SSRs, with 2,015 found to be hypervariable.
• Developed BlackP2MSATdb (http://webtom.cabgrid.res.in/blackp2msatdb/), the first web resource for black pepper genomic and polymorphic SSRs.

Conclusions:

• The study successfully mapped SSRs to specific chromosomes in black pepper.
• The developed BlackP2MSATdb resource significantly enhances capabilities for black pepper genetic research and breeding.
• This resource is instrumental for varietal signature development, physical mapping, and marker-assisted selection (MAS).