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Hybrid pigeonpea purity testing kits
Maintenance of high level of genetic purity of
parental lines and hybrid is crucial to harness
the benefit of high heterosis, which is the key to
bring success in hybrid technology of any
economically important crop.
Rachit K Saxena
Funded through the allocation of ICRISAT
strategic funding and other projects
Hybrid breeding in pigeonpea
 Cytoplasmic genetic
male-sterility (CGMS)
system
 Male sterile or A- line
 Maintainer or B- line
 Fertility restorer or R-
line
Genetic purity
1. Parental lines
2. A- line seed production
3. Hybrid seed production
Genetic purity
 Traditionally Grow-Out Test (GOT):
@ risk due to un-noticed mixtures
and out-crossing
Sensitive to environment and handling
procedure and time consuming
 Molecular markers based testing:
Environment insensitive
Repeatability of the test with 100% accuracy
Cost-effective (land, sowing, cultivation cost etc.)
Time saving
Automation that avoids possibilities of manual
errors
Mitochondrial (nad7a_del) based marker for ICPA 2039 & ICPB 2039
Validation of marker in different A4 derived lines
 Markers for differentiating A and B lines
A B
Genetic purity: markers available
 Markers for differentiating A and B lines:
used by NARS partners
Genetic purity: markers available
Marker assay of 40 lines (A and cognate
B) using nad7a_del.
Restorer lines and non-restorer lines
 Reduce time by at least two years in identification of restorer and maintainer lines
 Markers for identification of fertility restorer lines
Genetic purity: markers available
Hybrid pigeonpea purity testing kits
 Criteria of selecting molecular markers:
(a) markers amplify polymorphic and high quality alleles
between A- and R- lines
(b) markers selected based on criterion (a) do not show
polymorphism between the A- and the B- lines
 Genomic resources used
Hybrid pigeonpea purity testing kits
SNPs have shown 100% efficiency in detecting
heterozygotes
Hybrid pigeonpea purity testing kits
S. No. Hybrid SNPs
1 ICPH 2740 17
2 ICPH 4539 10
3 ICPH 3479 10
4 ICPH 2433 8
5 ICPH 3759 8
6 ICPH 4200 8
7 ICPH 2700 7
8 ICPH 2671 6
9 ICPH 3933 6
10 ICPH 4010 6
11 ICPH 2438 5
12 ICPH 3762 5
13 ICPH 2702 5
14 ICPH 2364 4
15 ICPH 3461 4
16 ICPH 4690 3
17 ICPH 2429 2
18 ICPH 3310 2
19 ICPH 2363 2
20 ICPH 2431 2
21 ICPH 2751 1
22 ICPH 2441 1
23 ICPH 3481 1
24 ICPH 3494 1
25 ICPH 4022 1
SNPs are available for 25 hybrid combinations
S. No. Hybrid No of samples tested
(Hybrids and Parents)
1 ICPH 2438 188
2 ICPH 2671 188
3 ICPH 2433 188
4 ICPH2740 1658
5 ICPH 3933 180
6 ICPH 3762 120
7 ICPH 4690 144
Molecular markers based genetic purity
Unique signature sequences
Mt derived INDEL
Rf associated INDEL
SNPs for 25 hybrids
Unique signature
sequences
Mt derived INDEL
Summary and way forward
SNPs are available for purity testing in 25 hybrid
combinations (available at Intertek for public and private
sector)
Markers are available for CMS and fertility restoration
Unique signature sequences are being developed for
parental lines
Proposed to establish a platform for hybrids/parents seed
production based on markers (will be used by public and
private sector in their breeding programs)
Thank You

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ICRISAT Governing Board 2019 PC meeting: Hybrid pigeonpea purity testing kits - by Dr Rachit K Saxena

  • 1. Hybrid pigeonpea purity testing kits Maintenance of high level of genetic purity of parental lines and hybrid is crucial to harness the benefit of high heterosis, which is the key to bring success in hybrid technology of any economically important crop. Rachit K Saxena Funded through the allocation of ICRISAT strategic funding and other projects
  • 2. Hybrid breeding in pigeonpea  Cytoplasmic genetic male-sterility (CGMS) system  Male sterile or A- line  Maintainer or B- line  Fertility restorer or R- line
  • 3. Genetic purity 1. Parental lines 2. A- line seed production 3. Hybrid seed production
  • 4. Genetic purity  Traditionally Grow-Out Test (GOT): @ risk due to un-noticed mixtures and out-crossing Sensitive to environment and handling procedure and time consuming  Molecular markers based testing: Environment insensitive Repeatability of the test with 100% accuracy Cost-effective (land, sowing, cultivation cost etc.) Time saving Automation that avoids possibilities of manual errors
  • 5. Mitochondrial (nad7a_del) based marker for ICPA 2039 & ICPB 2039 Validation of marker in different A4 derived lines  Markers for differentiating A and B lines A B Genetic purity: markers available
  • 6.  Markers for differentiating A and B lines: used by NARS partners Genetic purity: markers available Marker assay of 40 lines (A and cognate B) using nad7a_del.
  • 7. Restorer lines and non-restorer lines  Reduce time by at least two years in identification of restorer and maintainer lines  Markers for identification of fertility restorer lines Genetic purity: markers available
  • 8. Hybrid pigeonpea purity testing kits  Criteria of selecting molecular markers: (a) markers amplify polymorphic and high quality alleles between A- and R- lines (b) markers selected based on criterion (a) do not show polymorphism between the A- and the B- lines
  • 9.  Genomic resources used Hybrid pigeonpea purity testing kits
  • 10. SNPs have shown 100% efficiency in detecting heterozygotes Hybrid pigeonpea purity testing kits
  • 11. S. No. Hybrid SNPs 1 ICPH 2740 17 2 ICPH 4539 10 3 ICPH 3479 10 4 ICPH 2433 8 5 ICPH 3759 8 6 ICPH 4200 8 7 ICPH 2700 7 8 ICPH 2671 6 9 ICPH 3933 6 10 ICPH 4010 6 11 ICPH 2438 5 12 ICPH 3762 5 13 ICPH 2702 5 14 ICPH 2364 4 15 ICPH 3461 4 16 ICPH 4690 3 17 ICPH 2429 2 18 ICPH 3310 2 19 ICPH 2363 2 20 ICPH 2431 2 21 ICPH 2751 1 22 ICPH 2441 1 23 ICPH 3481 1 24 ICPH 3494 1 25 ICPH 4022 1 SNPs are available for 25 hybrid combinations S. No. Hybrid No of samples tested (Hybrids and Parents) 1 ICPH 2438 188 2 ICPH 2671 188 3 ICPH 2433 188 4 ICPH2740 1658 5 ICPH 3933 180 6 ICPH 3762 120 7 ICPH 4690 144
  • 12. Molecular markers based genetic purity Unique signature sequences Mt derived INDEL Rf associated INDEL SNPs for 25 hybrids Unique signature sequences Mt derived INDEL
  • 13. Summary and way forward SNPs are available for purity testing in 25 hybrid combinations (available at Intertek for public and private sector) Markers are available for CMS and fertility restoration Unique signature sequences are being developed for parental lines Proposed to establish a platform for hybrids/parents seed production based on markers (will be used by public and private sector in their breeding programs)