The sorghum SNP mid-density panel (MDP) comprises 3,491 genome wide markers, including 42 QC and 50 trait markers used currently in a great number of sorghum breeding programs.
Distribution of the 3,491 DArTag SNP markers along the 10 sorghum chromosomes.
The genome-wide SNPs were called following the whole genome re-sequencing of the sorghum reference panel and can be used for QTL mapping, Genome-Wide Association Studies (GWAS), Genomic Selection, fingerprinting of breeding material, variety tracking and genetic diversity studies. The trait markers include polymorphic SNPs for shootfly resistance (10), staygreen trait (9), Striga resistance (8), sugar cane aphid resistance (2), fertility restoration (20) and aluminium (Al) tolerance.
This panel was verified in a diverse set of sorghum breeding lines from the ICRISAT Asia and Africa breeding programs in addition to Brazilian sorghum lines with the SbMATE locus incorporated. Overall, the utility of the panel is demonstrated by its diversity metrics (Table 1), and high polymorphism (89%) across the material tested.
Table 1: Summary of the MDP performance across ICRISAT genotypes
|Metric||Eastern and Southern Africa||West and Central Africa||Asia|
|Mean Genetic Diversity||0.38||0.38||0.42|
|Mean Polymorphism Information Content||0.30||0.30||0.33|
|Mean Marker Allele Frequency||0.28||0.29||0.33|
The mid-density panel is a useful and globally accessible resource for genomic profiling of sorghum germplasm by breeders.
In this panel, molecular markers tagging the aluminium (Al) tolerance gene, SbMATE were also included (Magalhaes et al., 2007). The expected effect of favorable alleles of SbMATE in field conditions can reach 1 ton/ha, depending on many factors such as Al saturation in the soil, occurrence of drought stress and the nature of the SbMATE allele being used. Provided they are polymorphic, all SbMATE markers included in the panel are adequate for marker assisted backcrossing approaches. For allele mining, these markers lead to differential recovery of Al tolerant accessions (Hufnagel et al., 2018).
To understand about the recovery of Al tolerant accessions using SbMATE in sorghum please refer to Table 2 of Caniato et al. (2014).
- FAOSTAT, 2022. Food and Agriculture Organization of the United Nations. FAOSTAT Statistical Database. URL https://www.fao.org/faostat/en/#data/QI
- Caniato FF, Hamblin MT, Guimaraes CT, Zhang Z, Schaffert RE, Kochian LV, Magalhaes JV (2014) Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB, PlosOne9: e87438
- Hufnagel B, Guimaraes CT, Craft EJ, Shaff JE, Schaffert RE, Kochian LV, Magalhaes JV (2018). Exploiting sorghum genetic diversity for enhanced aluminum tolerance: Allele mining based on the AltSB locus, Scientific Reports, 8:1-13
- Magalhaes JV, Liu J, Guimarães CT, Lana UGP, Alves VMC, Wang Y-H, Schaffert RE, Hoekenga OA, Piñeros MA, Shaff JE, Klein PE, Carneiro NP, Coelho CM, Trick HN, Kochian LV (2007) A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum, Nature Genetics, 39: 1156-1161.