Single Nucleotide Polymorphic external KASP™ service provider II

GSL has validated two different 10-SNP panel sets from an external KASP™ service provider in Sweden and Australia. The first panel set has SNPs tightly linked with 6 different key trait loci. The second set of SNPs is tightly associated with 10 key traits. Both sets can be run routinely in a high-throughput genotyping platform useful for different markers assisted application strategies.

The 1st 10-SNP panel validated and tested by GSL are associated with the genes:

 SNP Panel   Gene/QTL   Chrom.   Physical position (Mb)   SNP provider ID   Trait
 Panel 1  DTY1.1  1  38.5  snpOS0071  Drought tolerance
 Panel 1  DTY1.1  1  38.9  snpOS0074  Drought tolerance
 Panel 1  DTY3.1  3  30.0  snpOS0085  Drought tolerance
 Panel 1  DTY3.1  3  31.3  snpOS0089  Drought tolerance
 Panel 1  DTY12.1  12  15.3  snpOS0091  Drought tolerance
 Panel 1  DTY12.1  12  17.6  snpOS0095  Drought tolerance
 Panel 1  BPH3  6  1.4  snpOS0065  Brown planthopper
 Panel 1  BPH3  6  1.8  snpOS0067  Brown planthopper
 Panel 1  RTSV1  7  22.1  snpOS0050  Rice tungro spherical virus 
 Panel 1  Xa4  11  27.6  snpOS0052  Bacterial leaf blight

The 2nd 10-SNP panel validated and tested by GSL are associated with the genes:

 SNP Panel   Gene/QTL   Chrom.   Physical position (Mb)   SNP provider ID   Trait
 Panel 2  Pi9  6  10.4  snpOS0007b  Blast
 Panel 2  Pita  12  10.6  snpOS0006  Blast
 Panel 2  xa5  5  0.4  snpOS0054  Bacterial leaf blight
 Panel 2  xa13  8  27.5  snpOS0002  Bacterial leaf blight
 Panel 2  Pi54  11  25.3  snpOS0015  Blast
 Panel 2  Xa21  11  21.3  snpOS0061  Bacterial leaf blight
 Panel 2  sub1  9  6.4  snpOS0040  Submergence
 Panel 2  Chalk5  5  3.3  snpOS0024  Grain chalkiness
 Panel 2  BPH17  4  4.6  snpOS0068  Brown planthopper 
 Panel 2  BADH2  8  20.4  snpOS0022  Fragrance



Add-on SNPs

Any combination of 96 sample batches can be run across any combination of these additional markers, with the cost depending on sample and marker number.

The currently SNPs validated and tested by GSL are associated with the genes:

 Gene/QTL   Trait   Number SNPs 
 Xa4  Bacterial leaf blight  3
 xa5  Bacterial leaf blight  1
 Xa7  Bacterial leaf blight  4
 Xa21  Bacterial leaf blight  1
 xa13  Bacterial leaf blight  1
 Xa23  Bacterial leaf blight  1
 Pi-ta  Blast  1
 Pi9  Blast  3
 Pi2  Blast  1
 Pi54  Blast  3
 BPH3  Brown planthopper  3
 BPH17  Brown planthopper  2
 DTY1.1  Drought tolerance  4
 DTY2.1  Drought tolerance  7
 DTY3.1  Drought tolerance  5
 DTY12.1  Drought tolerance  6
 BADH2  Fragrance  2
 Chalk5  Grain chalkiness  2
 SSIIa  Soluble starch synthases   1
 Wx  Grain quality  1
 GS3  GrainSize  1
 RTSV1  Rice tungro spherical virus   1
 SUB1  Submergence  1



Product highlights

The 20 SNPs have been thoroughly tested and validated for robustness showing high percentage of call rates, precise and accurate SNP call when leaf tissue is provided as instructed by service provider.

The turnaround time may vary between experiments and workload but is relatively fast.