AMF

AMF identifies genome-wide SNPs and InDels from restriction-site associated DNA (RAD) sequencing data to support marker-assisted breeding and functional genomics analyses in rice.

Key Features:

• Integrated RAD-Seq analysis: Integrates RAD-Seq data analysis into a single computational workflow for marker discovery in rice.
• High-quality marker detection: Detected 90,743 markers (82,878 SNPs and 7,865 InDels) between rice varieties JP69 and Jiaoyuan5A, with SNP density 0.2 per kilobase and InDel density 0.02 per kilobase.
• Accuracy and validation: Reported a 93% validation accuracy for genome-wide marker detection.
• Linkage to agronomic genes: Linked 82 SNPs and 31 InDels to 117 genes associated with important agronomic traits.
• Variety authentication and linkage-drag minimization: Identified markers for seed authenticity and variety protection (e.g., Jiaoyuanyou69) and supported recombinant selection to minimize linkage drag around the fragrant gene BADH2 in Wuxiang075/Jiachang1 recombinants.
• Large-scale data handling: Handles large-scale RAD-Seq datasets to support marker discovery and marker-assisted selection in rice.

Scientific Applications:

• Marker-assisted selection (MAS): Provides validated SNP and InDel markers for MAS in rice breeding programs.
• Variety identification and protection: Generates diagnostic markers for seed authenticity and legal protection of varieties such as Jiaoyuanyou69.
• Trait–gene association and functional genomics: Associates discovered markers with 117 genes linked to agronomic traits to support functional genomics studies.
• Linkage drag reduction: Supports recombinant selection strategies to minimize linkage drag, exemplified by work on BADH2 in Wuxiang075/Jiachang1 recombinants.
• Genome-wide marker discovery: Enables genome-wide discovery of SNPs and InDels from RAD-Seq in rice varieties including JP69 and Jiaoyuan5A.

Methodology:

Analysis of restriction-site associated DNA (RAD) sequencing data to detect genome-wide SNPs and InDels, compute marker densities, validate markers, and link markers to genes.