Activities Planned - 2015
Legumes (Odeny)
• Association mapping for drought tolerance in chickpea
• Marker analysis and polymorphism study on parental lines of RIL population for ELS, GRD and drought
tolerance in groundnut
Robut 33-1 ICGV-SM 95714
Origin India Malawi
Botanical class Virginia Valencia
Maturity (days) Early (115) Early (90-100)
Yield (Kgha-1) 1,200 – 1,500 1,700 – 2,000
Dormancy Long None
Disease Reaction Susceptible Resistant
Sex in cross Female Male
Table 1: Characteristics of Parental Lines
3
X
F1
F8 - 113 Recombinant Inbred Lines (RILs)
Robut 33-1 ICGV-SM 95714
QTL Mapping for ELS in groundnut
Funds: USAID (I-FINITE)
Tembo E.1, Charlie H.3, Njoroge S.M.C3, Okori P, Mweetwa A.M.1,
Tembo L.1, Kaimoyo E.1, Monyo E.S.2, Paliwal R.2 and Odeny D.A
4
QTLs Detected - Summary
QTL Category Linkage
group
Position
(cM)
Left Marker Right Marker LOD
score
PVE (%) Additive
Effect
1 Major 2 81 GM1585 GNB284 15.74 37.91 25.65
2 Minor 2 130 GM951 Ah1TC4G02 3.51 7.98 -11.15
3 Minor 9 45 AHGS0798 GNB357 5.52 12.31 12.93
Season of 2014
QTL Category Linkage
group
Position
(cM)
Left Marker Right Marker LOD score PVE (%) Additive
Effect
1 Major 2 81 GM1585 GNB284 22.97 52.4 15.8
2 Minor 2 185 Ah1TC4G02 GM2206 16.3 7.98 -7.9
3 Minor 5 173 pPGPseq2C11 GM2284 5.2 8.1 9.2
4 Minor 8 106 GNB608 GM1996 6.4 13.2 -7.2
Season of 2015_16
Association mapping in chickpea (CRP-funded)
Tesfamichael SM, NVPR Ganga Rao, Githiri SM, Paliwal R and Odeny DA
100 (60 desi & 40 kabuli) diverse chickpea lines
Characterized for agronomic traits (2013 and 2014) at Juja and
kabate locations in Kenya
DNA extracted from 95 (57 desi and 28 kabuli) lines and
generated
Generated >45 Gb of GBS sequencing data from which we identified 923 SNPs markers
After filtering, 358 SNPs used for association studies for 11 agronomic traits
Other Legume activities
• QTL mapping for resistance to rust disease in groundnut
– Funded by USAID-CGIAR linkages (Tuskegee University-
ICRISAT/AWARD)
– Chapwa Kasoma of Zambia
• Assessment of genetic variation for pod borer resistance
among elite pigeonpea accessions in Kenya
– CRP-GL in collaboration with University of Eldoret
– Juliana Cheboi
• Characterization of selected rhizobia isolates from Ethiopia
– In collaboration with Chris Ojiewo and UC-Davis
– Samuel Manthi
Activities Planned - 2015
Cereals
Finger millet
• Molecular characterization of available germplasm and development of genomic tools for genetic
characterization and varietal development of finger millet (Odeny)
• Development of MAS for Striga resistance in finger millet (Odeny)
• Development of early generation mapping population for snapping trait in fingermillet (Paliwal)
• Characterization for different agronomic traits in ESA fingermillet germplasm collection (Paliwal)
• Genetic and nutritional profiling of fingermillet germplasm collection in ESA (Paliwal)
Sorghum
• Molecular characterization for important agronomic traits in ESA sorghum germplasm (Paliwal)
• Characterization of sorghum/maize germplasm for semio-chemical response to stem borer infestation
(Paliwal)
• Genetic characterization for disease resistance in sorghum (Paliwal)
• Genotyping 105 sorghum germplasm across Kenya, Ethiopia and Sudan for their response to Striga
(Odeny)
Molecular characterization of available germplasm and
development of genomic tools for genetic characterization
and varietal development of finger millet
• Funded by Bio-Innovate/ABCF/BecA-ILRI
• Generated NGS data from genotypes KNE796 and KNE755
• Developed SNP markers and converted a representative set into
KASPAR/Sequenom assays
• Tested developed markers across cultivated and wild germplasm
RESULTS Davis Gimode
Wild accessions Cultivated accessions
E.
kigeziensis
SP1 SP2
(E. coracana subsp. africana)
E. coracana subsp. coracana
E. coracana subsp. coracana
Cultivated accessions
Whole Genome Sequencing of Finger Millet
• In partnership with…………….Katrien Devos (UGA, USA), F Stomeo (BecA-ILRI),
S de Villiers (PU, Kenya), Allen van Deynze (UC Davis), K Tesfaye (UAA,
Ethiopia), M Dida (UM, Kenya), E Mneney (MARI, Tanzania), E Bongkam-
Rudloff (SLU, Sweden), Mark Wamalwa (BecA-ILRI), Yao Nasser (BecA-ILRI),
Song Bo (BGI, China), Davis Gimode, Erick Owuor
• Funded by Bio-Innovate/African Orphan Crops Consortium (AOCC)/ABCF
Activities
• Generated the whole genome sequence of KNE796
• Undertook whole genome de novo sequence assembly
• Generated comprehensive transcriptome data and genome annotation
• Anchored and refined genome assembly with dense genetic map(s)
Development of early generation mapping population for snapping trait in finger
millet
Paliwal R, Ojulong H, Odeny DA
HOPE2
Two F2 mapping population (U15 x Ex-Alupe-green and KNE-814 x Ex-Alupe-purple)
previously generated by H Ojulong
250 F2 progeny lines per cross were tagged alongside parents for molecular
characterization
Molecular characterization could not be initiated due to lack of funding in year 2015
DNA has been extracted from 230 F2 segregated lines of the cross U15 and KNE-814
and are ready to be sentt for GBS sequencing at Cornell University
Each of the populations will be advanced as RILs
GWAS for Striga Resistance
• In collaboration with KALRO-
Kakamega/University of Eldoret
• 95 breeding lines screened in two
environments
– Locations: Alupe (Busia) and Kibos
(Kisumu)
– Data collected over 2 seasons (long and short rains)
• Genotyping-by-sequencing data generated
– Association mapping going on
Genetic and nutritional profiling of finger millet germplasm collection
in ESA
Paliwal R and Ojulong H
Approximately 500 diverse finger millet accessions previously characterized for
nutritional traits including calcium and iron in two seasons/environments
Molecular characterization could not be initiated due to lack of funding in year
2015
Molecular characterization has been initiated this year and DNA has been
extracted from 400 diverse finger millet accessions
Samples will be sent for GBS sequencing at Cornell University
Subsequent association studies
Results: GWAS Analysis
• The detected
associated SNPs
confirm earlier reports
for locus Dw2-chr6,
Dw3-chr7 and Dw1-
chr9 (Higgins et al.
2014)
• Associated SNPs for
grain color were
identified on chr1,
chr3, chr4, chr6 and
chr10
Characterization and genotyping of maize & sorghum germplasm for semio-
chemical response to stem borer infestation
Funded by BBSRC/BMGF/SCPRID
Paliwal R, Midega C (ICIPE), Khan Z (ICIPE), Odeny DA, Bruce T (Rothamsted Interntational)
1118 maize (representative of 104 diverse accessions) and 204 sorghum (representative of 17
accessions) screened
Presence of volatile induction trait was found to be very rare in improved maize (Fig.2) and
absent in sorghum diverse lines
NS
NS
NS NS NS
0
1
2
3
4
CML442 CKSBL10027 CML395 SCDuma PH4
Meanno.eggs
parasitized/plant
Eggparasitism
GWAS Results
Generated 0.2M SNPs
12K filtered SNPs used for molecular study
In total, 71 SNPs were found significantly associated genome-wide
Fig. 3: Associated SNPs with the semiochemical responses traits in piolt GWAS
using GLM approach
Chromosome Number of
SNPs detected
1 4
2 12
3 16
4 11
5 7
6 5
7 3
8 2
9 4
10 7
Total SNPs 71
Genotyping 105 sorghum germplasm across Kenya, Ethiopia and
Sudan for their response to Striga
Clet Masiga
• In collaboration with HM Abdalla (CRP-DC funded/HOPE)
• Plant material
• Reference sorghum line BTX623
• 10 lines with a sorghum association panel number already
sequenced by Paterson (UGA)
• Various sorghum cultivars from ECA
• Four striga resistant lines released by Abdalla et al 2014
• E-Tian, Ji2731, Keller cultivars
• 44 sorghum genotypes already re-sequenced
• Evaluated for 2 seasons, 2 environments (Uganda, Kenya)
Screened on Striga-free and Striga sick plots
Genotyped-by-sequencing all genotypes at Cornell University
Discovery: GWAS for Striga resistance
Generated >30 Gb of sequencing from which we identified 78.3K SNP
points from 95 sorghum lines;
Retained 27.2K SNPs after filtering, which was used for principal
component (PC) analysis and subsequently for Genome Wide Association
Studies (GLM and MLM)
Genetic characterization for disease resistance (anthracnose & leaf
blight) in sorghum
Paliwal R, Manyasa E, Ojulong H, Otwani DA
100 diverse sorghum accessions were screened for leaf blight (LB), leaf anthracnose
(LA) and overall leaf disease (OLD) under long and short rainy seasons in 2014-15 at
Alupe, in western Kenya
30K SNPs were generated using 14.5 GB raw GBS sequenced zipped (> 40 GB) data of
95 diverse sorghum lines
Out of 30K SNP, 18K SNPS were used for GWAS
Results
• Significant association was observed between 38 SNP markers distributed over 8
chromosomes (chr) with leaf diseases
• SNP_58251473_chr 10 was found to be associated with leaf blight, anthracnose and
overall disease suggesting its potential use for indirect selection for overall disease
response.
Introgression of Striga resistance QTLs
Musyimi S, Odeny DA, Manyasa E
Genotype Response to Striga Female/male plant
N13 R Male
Seredo S Female
Nakhadabo S Female
IESV92041 S Female
IESV92022 S Female
• Used Simple Sequence Repeat markers converted into High Resolution Melting
for rapid screening
• Currently at BC1F1
• 27 lines with <3 Striga resistant QTLs were found
Planned Activities 2016/7
• Finalizing whole genome sequencing (NSF/BREAD)
• Transcriptomic analysis of finger millet in response to Striga (CRP-DC)
• Improving finger millet productivity through exploitation of wild finger
millet (GCDT)
• Genotyping of new F2 populations of groundnut for resistance to diseases
and high oleic acid content (PMIL)
• Characterization and genotyping of maize & sorghum germplasm for
semio-chemical response to stem borer infestation (SCPRID/BBSRC)