External service provider II KASP™ SNP genotyping 

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  Favorable allele   Unfavorable allele 
 Panel 1  DTY1.1  1  38.5  snpOS0071  Drought tolerance  A  G
 Panel 1  DTY1.1  1  38.9  snpOS0074  Drought tolerance  G  T
 Panel 1  DTY3.1  3  30.0  snpOS0085  Drought tolerance  G  A
 Panel 1  DTY3.1  3  31.3  snpOS0089  Drought tolerance  C  G
 Panel 1  DTY12.1  12  15.3  snpOS0091  Drought tolerance  T  C
 Panel 1  DTY12.1  12  17.6  snpOS0095  Drought tolerance  A  G
 Panel 1  BPH3  6  1.4  snpOS0065  Brown planthopper  T  C
 Panel 1  BPH3  6  1.8  snpOS0067  Brown planthopper  A  T
 Panel 1  RTSV1  7  22.1  snpOS0050  Rice tungro spherical virus   GTGCT  ATGTT
 Panel 1  Xa4  11  27.6  snpOS0052  Bacterial leaf blight  A  C

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  Favorable allele   Unfavorable allele 
 Panel 2  Pi9  6  10.4  snpOS0007b  Blast  -  CGATGGTTTC
 Panel 2  Pita  12  10.6  snpOS0006  Blast  C  A
 Panel 2  xa5  5  0.4  snpOS0054  Bacterial leaf blight  AG  TC
 Panel 2  xa13  8  27.5  snpOS0002  Bacterial leaf blight  G  A
 Panel 2  Pi54  11  25.3  snpOS0015  Blast  T  C
 Panel 2  Xa21  11  21.3  snpOS0061  Bacterial leaf blight  C  G
 Panel 2  sub1  9  6.4  snpOS0040  Submergence  T  C
 Panel 2  Chalk5  5  3.3  snpOS0024  Grain chalkiness  G  A
 Panel 2  BPH17  4  4.6  snpOS0068  Brown planthopper   For review  For review
 Panel 2  BADH2  8  20.4  snpOS0022  Fragrance  TATAT  AAAAGATTATGGC

The 3rd 10-SNP Hybrid panel validated and tested by GSL are associated with the genes:

 SNP Panel   Gene/QTL   Chrom.   Physical position (Mb)   SNP provider ID   Trait  Favorable allele   Unfavorable allele 
 Panel 3  Rf4  10  18.8  snpOS0320  Restorer factor  C  T
 Panel 3  Rf3  1  4.94  snpOS0328  Restorer factor  G  A
 Panel 3  WA-CMS  Mt    snpOS0334  Cytoplasmic male sterility   TGTAG  -
 Panel 3  Xa23  11  23.4  snpOS0048  Bacterial leaf blight  T  C
 Panel 3  SSIIa  6  6.75  snpOS0036  Grain quality  For review  For review
 Panel 3  Pi9  6  10.3  snpOS0007b  Blast  -  CGATGGTTTC
 Panel 3  Pita  12  10.6  snpOS0006  Blast  C  A
 Panel 3  Submergence  9  6.4  snpOS0040  Submergence  T  C
 Panel 3  RTSV1  7  22.11  snpOS0050  Rice tungro spherical virus   GTGCT  ATGTT
 Panel 3  Chalk5  5  3.34  snpOS0024  Grain chalkiness  G  A



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 - Wx(g1) - Wx(g2)   Grain quality - Amylose Content   3
 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.

For inquiries, please contact us at gsl@irri.org.