genome-wide association analysis for terminal drought tolerance … · 2017. 11. 20. · stanley...

Feed the Future Innovation Lab for Collaborative

Research on Grain Legumes

Genome-Wide Association Analysis for Terminal

Drought Tolerance in Andean Common Beans

Dramadri Isaac Onziga,

Stanley T.Nkalubo , James D. Kelly

Feed the Future Innovation Lab for Collaborative Research on Grain Legumes

Drought stress and common bean productivity in Uganda

Common bean provides essential dietary protein and is a source of income in Uganda.

Production is done by smallholder farmers under rain fed conditions.

In Uganda, rainfall patterns have drastically changed becoming unpredictable or insufficient.

Drought effects are variable depending on duration, time of the stress, and growth stage.

The reproductive stage is the most critical stage -affecting the productivity of common bean.

Drought stress at reproductive stage


Identify genomic regions associated with drought tolerance at pod filling stage of common bean.

Research Questions Which phenotypic traits contribute to differences in drought tolerance at pod

filling stage.

What genomic regions and/or genes cause variability in drought tolerance at pod filling stage.

Research objective


Field Phenotyping for drought stress 2 drought nurseries were established in Uganda at

Namulonge and Kasese to evaluate the ADP panel

under water stressed conditions after flowering

(terminal drought) and irrigated (non-stressed

conditions).

Drought stress was applied by withholding watering after flowering to all genotypes grown under non irrigated conditions in the field.

Phenotypic data collected on agronomic traits;• Days to 50 % flowering,• Plant height, • Days to harvest maturity• Yield component traits.

ADP Panel consisting of 247 lines


Photosynthetic traits measured at pod

filling stage;

Relative chlorophyll content (SPAD)

Photosystem II efficiency (Phi2)

Non-photochemical quenching(PhiNPQ)

Phenotyping with MultispeQ(PhotosynQ.org)


Traits Mean Variance

Drought Irrigated Drought Irrigated

Shoot biomass (g) 83.9±37.1 129.7±28.8 2427*** 1221.9**

Pod biomass (g) 33.7±16.1 48.79±17.6 510.3*** 395.6*

Seed Weight (g) 11.7±8.8 11.4±5.5 146.2** 16.36*

Harvest Index (HI) 13±10.6 17.1±12.5 138.3* 188.9*

Pod Harvest Index 28.6±12.0 39.0±14.6 327.2** 616.2ns

Pod Partitioning Index 40.4±14.9 39.5± 17.5 195.3** 408.7*

Mean and Variance for agronomic traits under irrigated and non irrigated conditions

in 2016 at Kasese (247 ADP Lines)


Photosynthetic traitsMean (60DAP) Variance (60DAP)

Drought Irrigated Drought Irrigated

SPAD 35.57±6.37 34.70±6.8 32.9*** 90.50***

Phi2 0.25±0.05 0.33±0.08 0.004*** 0.015***

PhiNPQ 0.47±0.15 0.41±0.16 0.010*** 0.040**

NPQt 1.14±0.44 1.45±0.79 0.21ns 0.89***

PhiNO 0.30±0.05 0.26±0.10 0.004** 0.012*

Mean and Variance for Photosynthetic traits under irrigated and non irrigated conditions in

2016 at Kasese (247 ADP Lines)


SNP markers from the BARCBean6K_3 Beadchip containing 5398 SNPs filtered to remove low quality and monomorphic.

3568 SNPs used in association analyses after filtering and MAF>0.01

PCA for population structure and Kinship matrix (K) using Scaled Identity by Descent method in TASSEL 5.0

The Mixed Linear Model (MLM) for SNP-trait associations for SPAD in TASSEL.

Y=Xα +Pβ+Kμ+e

Bonferonni correction p=1.4x 10-5 (for α = 0.05 and 3568 SNPs) Significance threshold for SNPs

GWAS_ Analysis


Pod Partitioning Index under drought

R2

Pv03=0.11

Pv07=0.12

Pv09=0.12


SNPs Chr BP R2 Candidate gene(s)

ss715647195

ss715646071 Pv09

34,026,183

to

34,556,171

(530kb)

0.12

43 genes

Oligosaccharyltransferase complex/magnesium transporter family

protein (Abiotic stress protein)

ss715646352

ss715640392

Pv07 3,466,123

to

5,032,818

(1.5Mb)

0.13

166 genes Late embryogenesis abundant (LEA) proteins Seed maturation protein Chaperone DnaJ-domain superfamily protein (hsp40) Oligosaccharyltransferase complex/magnesium transporter family

protein

ss715645580

ss715645578

Pv03

50,004,386

to

50,018,510

(14kb)

0.11

--


R2

Pv11=0.13

Pv04=0.12

Pv10=0.12

Pv08=0.12

Photosynthetic trait PhiNO under drought


SNPs Chr Position R2 Candidate gene(s)

ss715650748 Pv011 48,779,978 0.131 gene within 70kb region

Glutaredoxin family protein (cell redox homeostasis and electron carrier activity)

ss715645808 Pv04 44,404,426 0.124 genes 104kb region

Late embryogenesis abundant (LEA) proteinsheat shock transcription factor C1multiprotein bridging factor 1Caldehyde dehydrogenase 2C4

ss715647383 Pv010 43,057,231 0.12 2 genes 62.6Kb region downstream mainly for cell repair

Chaperone DnaJ-domain superfamily protein(hsp40)Rad23 UV excision repair protein family and YGGT family protein

(radiation tolerance)

ss715644456 Pv08 28,865,385 0.12 --


Genomic regions associated with partitioning of assimilates under terminal drought stress were identified.

Genomic regions associated regulation of photosynthesis under drought stress were also Identified.

This study provides insights into the genetic architecture of biomass partitioning and regulation of photosynthesis under drought stress at pod

filling stage in common bean.

Conclusions


Acknowledgements

Dr. James Kelly Dr. David Kramer Dr. Stanley Nkalubo and staff of beans program

Genome-Wide Association Analysis for Terminal Drought Tolerance in Andean Common Beans�Drought stress and common bean productivity in UgandaResearch objectiveSlide Number 4Slide Number 5Slide Number 6Slide Number 7Slide Number 8Slide Number 9Slide Number 10Slide Number 11Slide Number 12ConclusionsSlide Number 14

genome-wide association analysis for terminal drought tolerance … · 2017. 11. 20. · stanley...

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