V. Akech, M. Nyine, T. Shah, R. Swennen
The 4K Musa DArTAG panel v.01 is a mid-density SNP genotyping panel for banana and plantain, developed at the International Institute of Tropical Agriculture (IITA). The panel is designed to provide an affordable and efficient tool for genotyping in diversity analyses, quality control/quality assurance (QC/QA), marker assisted selection, and genomic selection programs.
This first version of the Musa panel includes 4,065 SNP markers distributed across the 11 Musa chromosomes (Figure 1; Table 1).
Figure 1. SNP density plot for 4065 SNPs in the current Musa DArTAG panel v.01 aligned to the DH Pahang reference genome version4.
The sequences included in this panel are primarily derived from IITA genomic resources, based on large genotypic datasets generated using DArTseq genotyping platform. This 4K DArTag panel is based on existing DarTSeq (4000 SNPs) and KASP data (65 SNPs). The 65 KASP markers are associated with several traits i.e., resistance to banana bacterial wilt (Xanthomonas vasicola pv. musacearum), Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), banana weevils (Cosmopolites sordidus); quality, and as well as markers linked to fruit-filling QTL.
| Table 1. Distribution of SNPs across genomes and chromosome of Musa. | ||||||||||||||
| Chromosome → | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | Un | Total Genome | |
| Genome ↓ | ||||||||||||||
| A | 303 | 278 | 415 | 407 | 356 | 410 | 348 | 450 | 407 | 385 | 289 | 3 | 4051 | |
| Plantain-specific | 1 | 1 | - | - | 1 | 2 | 2 | 3 | 2 | 2 | - | - | 14 | |
| Total Chromosome | 304 | 279 | 415 | 407 | 357 | 412 | 350 | 453 | 409 | 387 | 289 | 3 | 4065 | |
The SNP markers were selected based on their overall polymorphism, minor allele frequency, genome and chromosome allocation and overall genome distribution. Fourteen of these markers are plantain-specific markers. The panel has been validated in the Matooke background.
