A number of advances in genetics and genomics research of pigeonpea. These advances have enhanced our understanding of structural and functional aspects of genome and also provided us opportunities to deal with constraints impeding production of pigeonpea in precise and faster manner. Availability of the draft genome sequence and large-scale molecular markers has made it possible to map traits of interest in speedy manner. Although germplasm re-sequencing has already been started in pigeonpea, large-scale germplasm including elite breeding line, landraces and wild species is expected to be fully sequenced very soon.

1. Pigeonpea Genomics: Trait discovery & deployment
by
Rachit K Saxena
Senior Scientist- Applied Genomics

2. Focus areas
 Trait discovery:  Development of genomic resources
 Molecular markers
 Sequencing data
 Transcriptome
 Genome assembly
 Development of genotyping platforms
 Mapping of target traits
 Identification of markers traits association
 High-resolution mapping for candidate genes
 Validation of traits associated markers/ candidate genes
 Trait deployment:
 Markers assisted selection (MAS & EGS: early generation selection)
 Markers assisted back-crossing (MABC)
 Optimizing novel genomics approaches
 Genomic prediction
 Haplotypes for candidate genes

3. Genomic resources
Draft genome
(Nature Biotechnology 2012)
Mt genome
(DNA research 2013)
HapMap
(Plant Biotechnology Journal 2016)
WGRS 292 lines
(Nature Genetics 2017)
Gene expression atlas
(J of Exp Botany 2017)
SSRs 3,200
SNPs ~16 million
GoldenGate 768 SNPs
KASPar assays 1,616 SNPs
SNP Array 56 K
454 /FLX reads 496,705
TUSs 21,432
Sequencing data ~1,000 linesPangenome
(Plant Biotechnology Journal 2020)

4. 103 pigeonpea lines:
63 released varieties (1960 to 2014)
40 founder lines
 Almost similar nucleotide diversity in
varieties released in
RP1 (θπ = 0.43)
RP2 (θπ = 0.48)
RP3 (θπ = 0.49)
RP4 (θπ = 0.48)
 The top six founders contributed 50.8% to the genetic base of the released varieties
 Founders T1, T190 and Bahar appeared in 28.6% varieties
Limited genetic base of released cultivars
 51,201 polymorphic SNPs/Indels
Genotyping platforms
 High-Density Axiom Cajanus SNP Array (56K SNPs)

5. Genotyping platforms
 Mid-Density Cajanus SNP
Array (2 to 3K SNPs)
 10 SNPs panel for traits
associated markers

6. High density genetic maps and novel
approaches for MTAs
 6,818 SNPs mapped in 974cM
Genome-wide
association
analysis

7. High resolution mapping of
restoration of fertility (Rf)
 4867 SNP markers on the genetic map derived from ICPA 2039 × ICPL 87119 (F2) population
Population size Mapped markers Average inter marker distance LOD PVE % References
Genetic map (cM) Genome QTL size (Mb)
188 78-140 SSRs
7.3-3.1 5598311 to 7664779 2 8.9 13.98-24.17 Bohra et al. 2012
186 306 SNPs
3.2 6474381 to 7664779 1.2 8.7 28.5 Saxena et al. 2018
369 4867 SNPs
0.3 7295478 to 7706211 0.41 51.58 45.06 Present study

8. Traits
mapped
Hybrid related traits
Restoration of fertility
Cytoplasmic male sterility
Hybrid seed purity
Abiotic stress
Drought
Biotic stress
Fusarium wilt
Sterility mosaic disease
Yield related traits
Days to 50% flowering
Days to 75% maturity
Pods per plant
Seed size
Plant height
Seeds per pod
Seed yield per plant
Number of primary branches
Number of secondary branches
Quality trait
Seed protein content
Other traits
Cleistogamy
Growth habit
Must have traits (3-5 years)
Nice to have traits (>5 years)
Product Concept Notes (PCN)
PCN in pigeonpea
PCN1: Medium duration climate resilient varieties,
parental lines and hybrids with resistance to
diseases and pests
PCN2: Mid-early duration climate resilient
varieties, parental lines and hybrids with resistance
to diseases and pests
PCN3: Early duration climate resilient varieties,
parental lines and hybrids with resistance to
diseases and pests
PCN4: Super-early climate resilient varieties, with
resistance to diseases and pests
PCN1 PCN2 PCN3 PCN4
PCN1 PCN2 PCN3 PCN4
PCN1 PCN2 PCN3 PCN4
PCN1 PCN2 PCN3 PCN4
PCN1 PCN2 PCN3 PCN4
PCN1 PCN2 PCN3 PCN4
PCN1 PCN2 PCN3
PCN1 PCN2 PCN3
PCN1 PCN2 PCN3
PCN1 PCN2 PCN3 PCN4
PCN1 PCN2

9. Validated markers
Mitochondrial gene specific marker in
different A4 derived lines
Restorer lines and non-restorer lines
Growth habit

10. Diagnostic markers
 Successfully converted in to Intertek platform
 13 SNPs for Fusarium wilt resistance
 12 SNPs for Sterility mosaic disease resistance
 One SNP for Days to 50% flowering
 Two SNPs for 100 Seed weight
 Six SNPs for Restoration of fertility
Early generation screening
Hybrid purity testing
 43 SNPs for 25 hybrids
combinations
https://excellenceinbreeding.org/module3/kasp
SNP based QC panel
Dataset used: 8.6million SNPs from elite breeding lines
Validation of KASP assays: 40 SNPs from selected
48 SNPs
Minimum number of markers for QC: 10 SNPs

11. Deployment of molecular markers for
pigeonpea improvement at NARS and ICRISAT
 ~ 104,000 data points (~84K until Q3 2020 + 20K estimated in Q4) have
been generated with diagnostic markers
 > 8,000 (~6K until Q3 2020 + 2K estimated in Q4) samples tested
 Institutes availing facility:
 ICRISAT
 ICAR- Indian Institute of Pulses Research (IIPR), Kanpur
 Agricultural Research Station (ARS) - Tandur, PJTSAU
 Institute of Biotechnology, Hyderabad, PJTSAU
 Zonal Agricultural Research Station, Kalaburagi, UAS-R
 Regional Agricultural Research Station, LAM Farm, Guntur, ANGRAU
 Mahatma Phule Krishi Vidyapeeth (MPKV) Rahuri

12. Modernization of Pigeonpea improvement

13. Deployment of genomics activities in breeding
scheme

14. Introgression of Fusarium wilt and Sterility mosaic
disease resistant QTL in elite pigeonpea cultivars
@ ICRISAT and NARS
FW SMD
Maharashtra BDN711 X
Karnataka X ICP 8863, TS3R
Madhya Pradesh TJT501, JKM189 X
Uttar Pradesh BAHAR X
Telangana PRG176 PRG176
Andhra Pradesh LRG41, LRG52 LRG41, LRG52
ICRISAT ICPL88039, UPAS120
 ICPL 20096 used as a common source/ donor parent for FW and SMD resistance
 ICRISAT has also supplied seeds of ICPL 20096 to partner institutes from a common source

15. Novel approaches
 Family based mapping approach using MAGIC and NAM populations
 Early maturity
 Protein content
 Yield & Yield
related traits
 New breeding material
 Establishment of haplotypes for target traits

16. Genomic prediction for next generation
hybrids and heterotic groups
 WGRS of 104 hybrid parental lines
 ~70R X 10 A = 700 crosses (F1)
 F1s + 104 parents + 14 checks:
phenotyped @ two locations
 WGRS of 292 lines
 2 years phenotyping @ two locations
 >10 years historical data
78,210 potential single-cross hybrids
 65% higher than the average yield of all hybrids
 191% higher than average yield of all inbred lines
 Combinations are being tested by ICAR-IIPR

17. The IMPROVED pigeonpea genome
 The contact matrices depict the correction of the draft assembly (left) and the improved
assembly (right) using the Hi-C approach
Unpublished

18. Data management
 Submitted genomics datasets from the year 2010 to 2020 @ ICRISAT Dataverse
 Available at https://cegsb.icrisat.org/openaccess/
 Available at http://bms.icrisat.org/ibpworkbench/main
 Published sequencing datasets are also available at NCBI

19. Constraints & possible solutions
 Limited collaboration in themes and research programs
 Lack of visibility for crop Scientists
 Respective Scientist not included in institute’s initiatives (CtEH; USAID-AVISA)
 Disproportionate funds for research activities (ICAR-ICRISAT; CRP)
 Crop specific Scientists in ONE research program
 Less hierarchical organizational structure
 Promote interdisciplinary teams across the region
 Appropriate funds distribution according to research activities