SNPs designed for validated in mapping populations and breeding lines, Intertek platform. A set of 20 SNP set useful for screening early generation breeding population will be finalized 800 breeding lines from SA, ESA and WCA breeding programs; 2350 lines from ICAR-IIMR-AICRPS Current season -F2s from RxR nurseries from SA program, on-going discussion with ESA and WCA.

1. Current status and planning for integration of genomics
applications in breeding
Sorghum
RP Genetic Gains meeting with DDG-R
05th January 2021

2. Current status and planning for integration of genomics
applications in Sorghum breeding
Background
Current status
Applications
• Trait-linked SNP panels
• QC panel
• Mid-density panel
• Trait introgression
Integration Strategy
Data management
Resource mobilization – challenges, opportunities

3. Background
• Contents as per current understanding of Product Concept Notes
(PCNs)
• Over all – 8 PCNs; WCA – 2; ESA – 2 and SA – 4 (?)
• Invited to several interactions with EiB Module#2 – breeding
optimization discussions
• Interactions with breeders, RBLs and ESA-Biotechnology
• Genomics tools/technologies – EiB Module#3 – shared services
• CRP-GLDC FP5
Current status and planning for integration of genomics
applications in Sorghum breeding

4. Current Status – genomics tools/technologies
Discovery,
development
Verification/
validation
Routine
breeding
application
Trichome density – SBI10,
Leaf glossiness – SBI05 & 10
(Shoot fly resistance traits)
Transpiration Efficiency–SBI02
Water Use Efficiency – SBI02
(Post-Flow Drought Tol)
Fertility restoration (Rf) genes –
several
(Hybrid breeding trait)
Brown mid-rib genes – bmr6 and
bmr12
(biofuel, biomass and
forage)
ME and IVMOD for fodder
digestibility + NUE
(Fodder Quality traits)
Anthracnose, leaf blight and rust
(Disease resistance)
Aphid resistance and FAW
(Insect resistance)
Develop SNP assays, screen breeding pools, verification in
current breeding population
Screening breeding lines and formulating 10 SNP panels
for routine use
Strategy, planning for wider use
QC panel - for routine use
Mid-density SNP panel – EiB Module#3
shared services

5. SNP panel for routine selection of (Shoot fly resistance component trait) leaf
glossiness, lower leaf trichome density
Sl. No. SNP ID
Chromoso
me
Trait QTL
Favorable
allele
Unfavorable
allele
1 snpSB0106
SBI-05
Leaf
Glossines
s
QTL-J1
C T
2 snpSB0109 C G
3 snpSB110 T G
4 snpSB0143
SBI-10
Leaf
Glossines
s
QTL-G
C G
5 snpSB0144 G A
6 snpSB0146 T C
7 snpSB0148 A C
8 snpSB0158
SBI-10
Trichome
density
(lower
side)
QTL-J2
C G
9 snpSB0164 G A
10 snpSB0169
C T
Rurrent
Parent
F
1
Donor
Parent
Negative
Control
SNPs development … to routine breeding
utilization (shoot fly resistance)
• To confirm efficacy of designed KASP
SNPs, over 5000 breeding lines screened
with 10 SNPs (Intertek platform – HTPG)
• This 10 SNP set useful for screening early
generation breeding population for
selecting individuals with shoot fly
resistance (SFR)
• >800 SA, WCA and ESA breeding lines ;
2350 breeding material from ICAR-IIMR-
AICRPS
Applications – trait linked SNP panels
• Current season - >1800 F2s from SA, 16 plates breeding material from current off-
season nursery in WCA and ESA breeding
Gorthy et. al. (2017)

6. SBI-02
1
2
3
4
5
1
2
3
4
5
• SNPs development … to routine breeding utilization (post-
flowering drought tolerance – TE = stg3A and WUE = stg3B)
• To confirm efficacy of designed KASP SNPs, over 5000
individuals in MABC project involving 12 genetic backgrounds
(Intertek platform – HTPG)
• A set of 10 SNP set useful for screening early generation
breeding population is identified and being validated in over
1000 breeding lines (from breeding programs across SA, ESA
and WCA); 2350 breeding stocks from ICAR-IIMR-AICRPS
• Currently being used in MBAC projects in Tanzania (through
HTPG); Ghana, Burkina Faso and Senegal (through SMIL)
Applications – trait linked SNP panels cont …
• Current season - >800 F2s from SA, 16 plates breeding material from current off-
season nursery in WCA and ESA breeding

7. SNPs development … to routine breeding utilization (post-
flowering drought tolerance – TE = stg3A and WUE = stg3B)
0
50
100
150
200
250
Grainyield(gm-2)
Staygreen introgessed lines in two genetic backgrounds
(CRS 4 & RSLG 262
B Grain yield
WS
0
200
400
600
800
1000
1200
1400
C5-R
C11
C9
C7-R
C2
C13
C4
R1-W
R7
R3
R10
R8
R5-R
B35
CSV29
Totalbiomas(gm-2)
Staygreen introgessed lines in two genetic backgrounds (CRS
4 & RSLG 262
B Total Biomass
WS
Figure 2: Average biomass accumulation of three
locations in 24 staygreen introgressed lines in two
genetic background (CRS 4- 13 lines; RSLG 262 -11
lines), recipient parents and ckecks grown under
well watered and (WW) and water stressed
conditions at three locations (Hyderabad, Solapur
and Parbhani).
Figure 1: Average grain yield of three locations in 24
staygreen introgressed lines in two genetic
background (CRS 4- 13 lines; RSLG 262 -11 lines),
recipient parents and ckecks grown under well
watered and (WW) and water stressed conditions at
three locations (Hyderabad, Solapur and Parbhani).

8. SNPs development … to routine breeding
utilization (fertility restoration genes -Rf genes)
• We designed 33 SNPs from own studies
and published information
• SNPs designed for – Rf1, Rf2, Rf5, Rf6
• Validated in mapping populations and breeding lines (Intertek platform – HTPG)
• A set of 20 SNP set useful for screening early generation breeding population will be
finalized
• >800 breeding lines from SA, ESA and WCA breeding programs; 2350 lines from
ICAR-IIMR-AICRPS
• Current season - >F2s from RxR nurseries from SA program; on-going discussion
with ESA and WCA
Applications – trait linked SNP
panels cont …

9. QC panel -status
• 72 loci identified from GBS data from a set
of >1900 breeding lines;
• ICRISAT breeding program- Mali, Kenya,
Nigeria, India; ICAR-IIMR; SAUs from India;
national program from Mali; few lines
TAMU
• Verification/first run with 376 breeding
lines completed (235 from SA-breeding
program; 101 from WCA-breeding program
and 40 from ESA)
• A set of 49 SNPs short-listed; and second
run 800 lines from SA, ESA and WCA along
with 2350 breeding lines from ICAR-IIIMR-
AICRPS
SNP Quality No of SNPs
Very Good 30
Good 10
Medium 12
Inconclusive 20
Bad 0
Total 72

10. Status – mid-density panel
• Variant calling using - 1985 Genotypes
and 2.6Million SNPs
• Variant calling criterion
• Pre-defined filtering criteria resulted in
41,844 SNPs
• Functional annotation for each locus
Criteria
• Remove intergenic markers,
Tandem repeats on the flanking
(mono, di)
• Specificity of the flanking
sequences
• GC content on the flanking
sequences
• PIC
• Proportion of Missing
• Markers on upstream and
downstream windows (30bp)
• A/T inversions
• Including the trait linked SNPs
and QC sets
Current season – designing and development in first quarter; first run, validation in second
quarter; short–listing smaller set per breeding program

11. Status – Genomic prediction
• Utilize the mid-density panel
• Sorghum breeding program – currently running through breeding
optimization exercise with EiB M#2
• After breeding pipelines are finalized; the stages and PCNs for applying
the mid-density panel for genomic prediction
• Plan –
• Use the mid-density panel to genotype current parent pool
• Identify stages and populations within each PCN for implementing
mid-density panel
• A min of two-years 3-4 location each data; e.g. current AYT, PYT
selected

12. Application – Trait introgression
• Working with CMBE and breeding groups for Rapid Generation
Advancement (RGA) optimization
• Sorghum breeding program – currently two generations
• With RGA, at least 3.5 to 4 generations expected
• Plan – develop further this plan for trait x PCN
Trait discovery and validation strategies
• Usually mapping, but focused on using breeding material from PCN;
QTLseq, transcriptomics
• Working with CMBE and breeding groups for trait validation
• Strategy to develop segregating breeding populations

13. Integration with breeding – thought process
• Currently the breeding optimization process going on
• Dealing with breeding process, populations
……selection indices etc.
• Molecular markers and applications –
• Trait linked SNPs – stage, which population and
population size
• Role in each PCN …..
• Capacity of breeding program to adopt ….
Generation Breeding process
PCN-1
Rainy-
Hybrid
A/B-line
PCN-1
Rainy-
Hybrid
R-line
PCN-2
PostRainy
- OPV
PCN-3
Forages
A/B-line
PCN-3
Forages
R-line
PCN-4
Biofuel/
Sweet Sor
PCN-1
Sahel
(dry)
PCN-2
Sudan
(semi-
humid)
PCN-3
Guinea
(humid)
PCN-1
(Semi-
arid)
PCN-2
(Sub-
humid)
Parents
Selection for recycling
and crossing
P1 X P2 Crossing
1, 2, 4
(SFR, Rf)
1, 2, 4
(SFR, Rf)
1, 2, 4
(SFR, TE,
WUE)
1, 2 1, 2 1, 2 1, 2, 4 1, 2, 4 1, 2 1, 2, 4 1, 2, 4
F1 Selfing true-tp-types 3 3 3 3 3 3 3 3 3 3 3
F2 Some selection 2 2 2 2 2 2 2 2 2 2 2
SSD
F3
SSD
F4
SSD
F5
PYT, Stage1-trial; test
cosses
2, 4
(SFR, Rf)
2, 4
(SFR, Rf)
2, 4 (SFR,
TE, WUE)
2, 4 2, 4 2, 4 2, 4 2, 4 2, 4 2, 4 2, 4
F6
AYT, Stage1-trial; test
cosses
2, 4
(SFR, Rf)
2, 4
(SFR, Rf)
2, 4 (SFR,
TE, WUE)
2, 4 2, 4 2, 4 2, 4 2, 4 2, 4 2, 4 2, 4
F7
AYT, Stage 2-trial; test
crosses
F8-desiganted
Product development
process
5 5 5 5 5 5 5 5 5 5 5
Asia WCA ESA
• Genomics Applications -
1. Marker Assisted Quality Assurance/Quality Control; 2. Trait Linked SNPs; 3. Marker Assisted Hybridity Confirmation;
4. Mid-Density SNP panels; and 5. Introgression of target traits

14. Improved – genetically diverse cultivars ADAPTED to target agro-ecology
Germplasm/adapted cultivars
Environment
characterization
Trait variability Trait characterization
and dissection
0.005
0.01
0.015
0.02
0.025
0.03
0.035
0.04
0.045
0.50 1.00 1.50 2.00 2.50 3.00 3.50
Evaporative demand (VPD)
Canopyconductance
Target location testing
Advanced/HTP
phenotyping
Development of BCNAM population(s) along
with Genomics & informatics tools
Advanced breeding strategies
Improved genetics for adaptation
Drought
Insect
Disease
Adaptation based integrated crop improvement scheme by developing BCNAM populations
CMBGE