K-mer GWAS for Anthracnose and BCMV Resistance

K-mer GWAS for Anthracnose and BCMV Resistance performs k-mer genome-wide association studies to identify markers associated with anthracnose and bean common mosaic virus resistance in the Andean Diversity Panel of common beans.

Key Features:

• Reference-free k-mer GWAS: Performs reference-free k-mer-based genome-wide association analysis as an alternative to SNP-chip and reference-based whole genome shotgun sequence SNP approaches.
• Three-way comparison framework: Enables comparison between SNP-chip, reference-based WGS-SNP, and reference-free k-mer GWAS results for the same traits.
• Pan-genomic variation detection: Identifies k-mer haplotype variation and structural variation not captured by reference-based methods, including significant k-mers that fail to map to the reference genome.
• High-resolution marker mapping: Provides substantially higher marker resolution than SNP-chip approaches for genome-wide association studies.
• Cis-associated k-mer analysis: Determines genetic context of cis-associated k-mers through whole genome assembly of panel accessions.

Scientific Applications:

• Anthracnose resistance mapping: Identifies genetic associations for resistance to eight races of anthracnose caused by Colletotrichum lindemuthianum in common bean.
• BCMV resistance mapping: Identifies genetic associations for Bean Common Mosaic Virus resistance in the Andean Diversity Panel of Phaseolus vulgaris.
• I-gene and Co-u trait selection analysis: Reveals selection of the linked I-gene and Co-u traits in North American breeding lines and cultivars through k-mer haplotype variation.
• Disease resistance gene repertoire expansion: Identifies expanded local repertoires of disease resistance genes associated with anthracnose and BCMV resistance through whole genome assembly.
• Structural variation assessment: Characterizes the role of structural variation in disease resistance phenotypes, including loci absent from the reference genome.

Methodology:

The tool sequences the P. vulgaris Andean Diversity Panel and performs k-mer GWAS, with historical SNP-chip and phenotypic data enabling three-way comparison between SNP-chip, reference-based WGS-SNP, and reference-free k-mer GWAS. Significantly associated k-mers are mapped to the reference genome, and whole genome assemblies of four ADP accessions are generated to determine the genetic context of cis-associated k-mers.