The pearl millet SNP mid-density genotyping panel is comprised of 3501 markers distributed across all the 7 chromosomes, including 5 that were derived from an unanchored scaffold, designed on the 843B Cenchrus americanus reference genome (figshare.com/ndownloader/files/37686405). Over 63% of the SNPs (2218) are within genic regions, of which 613 are in coding regions spread over 2096 genes, showing good functional potential.
The pearl millet panel was validated using 470 lines from both the global (PMiGAP) collection as well as a diverse West African germplasm set (WCA), ensuring robust capture across breeding-relevant populations. WCA samples reveal more informativeness of the markers relative to the PMiGAP set, which as expected, recorded a relatively lower heterozygosity. Overall, ~74% of the markers (2582) perform well in both populations, with 315 and 18 markers performing well exclusively in the WCA and PMiGAP populations, respectively.
Table1: Overall marker performance
|
|
Overall |
PMiGAP |
WCA |
|
Mean Call Rate |
0.88 |
0.86 |
0.89 |
|
Median Call Rate |
0.96 |
0.94 |
0.97 |
|
Mean MAF |
0.12 |
0.11 |
0.12 |
|
Mean Heterozygosity |
0.11 |
0.07 |
0.13 |
|
Mean Genetic Diversity (GD) |
0.175 |
0.167 |
0.176 |
|
Mean Polymorphism Information Content (PIC) |
0.146 |
0.140 |
0.147 |
Fig 2. Pearl Millet panel validation performance summary from 470 samples from WCA (282) and PMiGAP (188) populations
Table 2: Tiered quality metrics across the whole panel
|
|
Quality Tiers |
|
|---|---|---|
|
Call Rate >= 95% |
1,844 |
53% |
|
Call Rate >= 80% |
2,798 |
80% |
|
Polymorphic (MAF > 5%) |
1,991 |
57% |
|
High Quality (CR>=80% & MAF>5%) |
1,803 |
52% |
|
Failed (CR = 0%) |
14 |
0.4% |