Sorghum Mini Core Collection COPY · Presented at the 2018 Global Sorghum Conference at Cape Town,...

Presented at the 2018 Global Sorghum Conference at Cape Town, South Africa, from 9th to 12th April 2018

Hari D UpadhyayaGenebank, ICRISAT

Sorghum Mini Core Collection: a source of multi-trait variation to meet challenge of climate change and for enhanced genetic gains

DO NOT C

OPY

• 5th most important cereal crop grown for food, feed, fodder and bioenergy purposes

• A staple for over 500 million resource-poor people in marginal environments

• Sorghum is cultivated on an area of 44.8 m ha in 110 countries with an annual production of 63.9 m t. during 2016 (http://www.faostat.fao.org; data accessed in March, 2018)

• USA, Mexico, Nigeria, Sudan and India are the top five sorghum producing countries

Introduction – The crop sorghum

DO NOT C

OPY

http://www.faostat.fao.org/

• Sorghum production is constrained by several biotic and abiotic stresses resulting in low productivity of sorghum

• Severe regional imbalances in yield of sorghum which varied from 995 kg ha-1 in Africa, 1299 kg ha-1 in Asia to 3793 kg ha-1 in Americas

• Low use of new variability in crop improvement results in narrow genetic base of cultivars and increased risk of crop vulnerability, i.e., crop failure due to insect pests and disease epidemics or unpredictable climatic effects

Introduction – The crop sorghum

DO NOT C

OPY

Challenges to global agriculture• 9.3 billion people to feed by 2050

• Global warming results in depletion of natural resources biodiversity loss natural calamities change in pest and pathogen dynamics food contamination, etc.

• South Asia and Sub-Saharan Africa are the most affected regions

• Risk absorbing capacity of the people in these regions is low

• Therefore, developing climate-resilient technologies together with judicious management of natural resources is the way forward to address food and nutritional securityDO N

OT COPY

• No such increase was observed in legumes

• Of recent, the yield in many crops either stagnated, declined or showing only marginal increase

Trends in productivity of important cereals and legume crops during 1962-2016.

World productivity of maize, rice, wheat, sorghum, chickpea, pigeonpea and groundnut

DO NOT C

OPY

Genetic gains

∆G = Genetic gainh2 = Heritability of trait

i = Selection intensityσp = Phenotypic standard deviationgi = Generation interval (cycles/year)

DO NOT C

OPY

Genetic gains and yield increase• Sorghum: 0.85% year-1 in sorghum (Woldesemayat et al. 2015)

• Groundnut: 0.43% year-1 to 1.89% year-1 in groundnut (Hagos et al. 2012, Haro et al. 2013)

• Chickpea (Ethiopia): Kabuli- 8.42 kg ha-1 yr-1 (NS zero), Desi18.42 kg ha-1 yr-1 or 1.16% (Belete et al. 2017, Belete 2011)

• Soybean: 22.8 kg ha-1 (Carolyn et al. 2013)

• Maize (Masuka et al. 2016): varied in different conditions

– 109.4 kg ha-1 yr-1 under optimum conditions– 32.5 kg ha-1 yr-1 under managed drought conditions– 22.7 kg ha-1 yr-1 under random drought conditions– 20.9 kg ha-1 yr-1 under low N conditions– 141.3 kg ha-1 yr-1 maize streak virus stress conditions

Need to double the genetic gains for food and nutritional securityDO N

OT COPY

Source: (http://apps3.fao.org/wiews)

Sorghum germplasm collection

Sorghum cultivated germplasm accessions (232,600) Sorghum wild germplasm accessions (4,017)

Global status

DO NOT C

OPY

Largest ex situ sorghum germplasm collections in the world

Country Institution Wild Cultivated Total holding (%)Global International Crop Research Institute

for the Semi-Arid Tropics (ICRISAT), Patancheru, India

461 40562 41023 (17.3)

USA Southern Regional Plant Introduction Station, University of Georgia

197 35,976 36,173 (15.3)

National Center for Genetic Resources Preservation (NCGRP)

2 7,535 7,537 (3.2)

China Institute of Crop Science, Chinese Academy of Agricultural Sciences (ICS-CAAS)

18,263 18,263 (7.7)

India National Bureau of Plant Genetic Resources (NBPGR), New Delhi

2,674 14,792 17,466 (7.4)

Ethiopia Institute of Biodiversity Conservation (IBC)

9,772 9,772 (4.1)

Brazil Embrapa Milho e Sorgo (CNPMS) 7,225 7,225 (3.0)World total - 4,017 2,32,970 2,36,987Source: http://apps3.fao.org/wiews.DO N

OT COPY

ICRISAT sorghum germplasm

• > 41,000 accessions from 93 countries– landrace (87%), breeding material (12%), wild (1%)

• > 510,000 samples supplied in 110 countries and within ICRISAT

• > 55,000 accessions restored to Botswana, Cameroon, Ethiopia, India, Kenya, Nigeria, Somalia, Sri Lanka and Sudan

DO NOT C

OPY

• 36,282 accessions at Global Seed Vault at Svalbard, Norway

Safety duplication of sorghum

DO NOT C

OPY

Crop Total collection (countries)

Region/Collection studied

No. of georeferenced landraces (countries represented)

No. of geographical gaps identified

No. of countries with gaps

Reference

Sorghum 39,948 (93) South Asia 5340 (5) 131 4 Upadhyaya et al 2016, PGR 15(6): 527-538

East Africa 7914 (10) 153 10 Upadhyaya et al 2016, (AJCS 11(04): 424-437)

West and Central Africa 3991 (12) 386 11 Upadhyaya et al. 2017, The CropJournal doi:10.1016/j.cj.2017.07.002

Southern Africa 2343 (8) 108 8 -Pearl millet 23,474 (52) West and Central Africa 6434 (8) 145 6 Upadhyaya et al 2009, PGR 8(1):

45-51Asia 5497 (2) 146 3 Upadhyaya et al 2010, PGR 8(3):

267-276.East and Southern Africa

3750 (11) 110 11 Upadhyaya et al 2012, PGR 10(3): 202-213

Pennisetum monodii collection


Pennisetum pedicellatum collection

134 (8) 194 21 Upadhyaya et al 2014, IJPGR 27(2): 93-101

Chickpea 20,764 (59) Collection from Turkey 516 (1) 189 1 -

Pigeonpea 13,778 (74) Cajanus scarabaeoidescollection


East and Southern Africa

916 (7) 138 7 Upadhyaya et al 2015, IJPGR 28(2): 180-188

Groundnut 15,622 (92) South America 1078 (7) 2,913 9 -Small millets11464 (50) - - - - -

Geographical gaps identified in landrace collections of ICRISAT mandate crops

DO NOT C

OPY

Sorghum Germplasm Core and mini core collections

DO NOT C

OPY

Germplasm subsets

No. of acc. used

No. of acc. in subset

Remark Reference

Core 33,100 3,475 Seven morphological traits Prasada Rao and Ramanth Rao, 1995

Core 22,473 2,247 Photoperiod sensitivity grouping and sampling

Grenier et al. 2001b

Mini core 2,246 242 Using 21 morpho-agronomic traits and passport information

Upadhyaya et al. (2009)

Composite collection

- 3,384 This includes accessions from ICRISAT-India, CIRAD-France and CAAS-China

http://www.generationcp.org/issue-59-march-2012/32-research/sorghum/180-sorghum-products

Reference set 3,367 383 Using 41 SSR markers Billot et al. 2013

Sorghum germplasm diversity representative subsets

DO NOT C

OPY

• Core collection evaluated for 11 quantitative and 10 qualitative traits

• The hierarchical cluster analysis of data using phenotypic distances resulted in 21 clusters

• Mini core collection of 242 accessions selected

Sorghum mini core collection

• Developed from core collection of 2,247 accessions

DO NOT C

OPY

Sorghum Mini Core- a sources for multiple trait germplasm and accelerated genetic gains

DO NOT C

OPY

Agronomic traits

• Early flowering (<60d) – 13 accessions

• Large seeded (100-seed weight 3.72- 5.15 g) –10 accessions

• Grain yield (38.39 to 43.32 g plant-1) – 4 accessions

– High grain yielding accessions: IS 4698, IS 23590 and IS 23891 and IS 28141 (38.39 to 43.32 g plant-1) compared to the high grain yielding control, IS 33844 (33.49 to 35.99 g plant-1)

Sorghum mini core for accelerated genetic gains

DO NOT C

OPY

Upadhyaya et al. 2016: Crop Sci. DOI: 10.2135/cropsci2015.05.0308

Grain nutritional traits High Fe - 11 acc. High Zn - 14 acc. High Fe and Zn - 9 acc. High protein - 9 acc.*Lysine - 3 acc.*

* ICRISAT Genebank database http://genebank.icrisat.org/

• Six and four accessions, respectively for Fe and Zn showed 8 to 39% and 8 to 38% greater Fe and Zn than IS 33844, and produced similar grain yields

• Drought stress in relation to irrigated control significantly increased mean seed Fe and Zn concentrations

• Significantly positive correlation between Fe and Zn contents

Grain nutrients


DO NOT C

OPY

Biotic stresses resistance

Diseases No. of acc

References

Grain mold resistant 50 2010, Plant Disease 94: 439-444

Downy mildew resistant

6 2010, Plant Disease 94: 439-444

Anthracnose 13 2012, Plant Disease 96: 1629-1633

Leaf blight 27 Sharma et al. 2012, Plant Disease 96: 1629-1633

Rust 6 2012, Plant Disease 96: 1629-1633


DO NOT C

OPY

Resistance to multiple diseases • Grain mold, anthracnose, leaf blight and rust : IS 473

• Anthracnose, leaf blight and rust : IS 23684 and IS 23521

• Anthracnose and leaf blight : IS 24939

• Grain molds and downy mildew : IS 23992

• Grain mold and leaf blight : IS 12945, IS 26694, IS 29187

• Grain mold and anthracnose : IS 20956

The accessions with multiple disease resistance will be useful in sorghum disease resistance breeding programs

Biotic stresses resistance


DO NOT C

OPY

Insect Mini core accessionsShoot fly IS# 2205, 4515, 4698, 5094 Spotted stem borer IS# 4698, 5094, 1041, 18039, 19445, 23992Sugarcane Aphid IS# 2205, 4515, 4698, 18039, 1004, 3121, 4581,

5386, 12937, 15744, 16528, 20625, 20632, 23514, 23521, 23586, 23684, 24492, 24939, 25089, 25249, 25301, 25548, 27034, 27887, 28614, 29314, 29654, 29772, 31446, 31557, 33023

• Shoot fly - 4 accessions• Spotted stem borer - 6 accessions• Sugarcane aphids - 32 accessions


Resistance to insect pests

DO NOT C

OPY

Abiotic stress tolerance Postflowering drought tolerance - 7 accessions

• DTI as a standard residual after removing the known contributory effects of flowering time and grain yield under optimum irrigation (yield potential) from the grain yield under drought,

• Tolerant accessions belonging to durra, caudatum, or durra-caudatum races

(Upadhyaya et al. 2017, Crop Sci. 57:310-321)

A accession (IS 25836) under irrigated (left) and imposed terminal drought (right) conditions at experimental plotin India


DO NOT C

OPY

Low temperate stress tolerance

The sorghum mini core collection evaluated for seed germination and seedling vigor at 12 °C as a measure of cold tolerance

Seedling vigor under low temperature stress - 6 accIS# 1212, 14779, 15170, 22986, 7305, 7310

Germinability under low temperature - 5 accessions IS# 602, 1233, 7305, 10302, 20956

IS 7305 for both germinability and vigor

Abiotic stress tolerance

Upadhyaya et al. 2016, Genome 59: 137–145


DO NOT C

OPY

• Under drought stress, the mean Brix increased in 169 accessions, decreased in one accession, while the remaining accessions were not affected

Sources for high Brix %Stalk sugar content (Brix: 14.0 to 15.2% %)

IS# 13294, 13549, 23216, 23684, 24139, 24939, 24953

Dual purpose (grain and sweet stalk)

IS# 1004, 4698, 23891, 28141

Bioenergy traits

Upadhyaya et al. 2014: Crop Sci. 54: 2120-2130

Identified • high Brix % - 7 accessions• dual purpose (grain and sweet stalk) -

4 accessions


DO NOT C

OPY

Photo and temperature insensitivity

• Photoperiod and temperature insensitive (PTINS)– 18 acc.

• Photoperiod sensitive and temperature insensitive (PSTINS) – 205 acc.

• Photoperiod and temperature sensitive (PTS)– 19 acc.

Identified several accessions with desirable agronomic traits for use in breeding program to develop cultivars with wider adaptation

• PTINS - 3 accessions• PSTINS - 15 rainy adaptation and 15 postrainy adaptation• PTS - 2 accessions


DO NOT C

OPY

Identity Genetic distance Abiotic stress tolerant

IS 9108 and IS 5094 0.427IS 9108 and IS 1212 0.419

Biotic stress resistantIS 30466 and IS 21512 0.499 IS 29654 and IS 21512 0.498

High grain nutrientIS 30460 and IS 25989 0.526 IS 25989 and IS 5386 0.521

Agronomic traitsIS 28141 and IS 16382 0.455IS 16382 and IS 4698 0.452

Bioenergy traitsIS 27887 and IS 4698 0.457IS 28141 and IS 24139 0.456

Genetically diverse trait specific accessions from sorghum mini core

DO NOT C

OPY

Sorghum mini core as a source of multiple traits germplasm in superior agronomic background

IS# Traits Grain yield(g plant-1)

4698 Brix (%), spotted stem borer, shoot fly, aphids 43.3223891 Large seeds, high Brix (%), post-flowering drought,

charcoal rot40.91

28141 High grain yield, Brix (%), large seeds 40.201004 Brix (%), Aphid 38.7123590 Grain mold, charcoal rot 38.3915466 Large seeds, post-flowering drought 37.7215744 Large seeds, aphids 36.964515 Post-flowering drought, charcoal rot, shoot fly,

aphids34.28

5094 Post-flowering drought, downy mildew, charcoal rot, spotted stem borer, shoot fly

31.27

31714 Large seeds, post-flowering drought, downy mildew 30.80DO NOT C

OPY

Pair of accessions and traits Genetic Distance

IS 23684 Protein, Brix %, Anthracnose, leaf blight, rust

IS 5094 Drought, downy mildew, Charcoal rot, stem borer, shoot fly

0.478

IS 28141 Grain yield, large seeds, Brix % IS 23684 Protein, Brix %, Anthracnose, leaf blight, rust

0.465

IS 24139 Zn, Brix % IS 5094 Drought, downy mildew, Charcoal rot, stem borer, shoot fly

0.462


IS 1212 Fe, Zn, Drought, Low temperature, downy mildew, grain mold

0.460


IS 4698 Brix %, Grain yield, stem borer, shoot fly and aphids

0.458

IS 31714 Large seeds, drought, downy mildew IS 24139 Zn, Brix % 0.457IS 24139 Zn, Brix % IS 1212 Fe, Zn, Drought, Low temperature, downy

mildew, grain mold0.456

IS 16382 Early flowering, Fe IS 5094 Drought, downy mildew, Charcoal rot, stem borer, shoot fly

0.456

IS 28141 Grain yield, large seeds, Brix % IS 24139 Zn, Brix % 0.456IS 28141 Grain yield, large seeds, Brix % IS 16382 Early flowering, Fe 0.455

Multi-trait specific sources

Genetically diverse trait specific accessions from sorghum mini core

DO NOT C

OPY

Sorghum mini core as an association mapping panel

DO NOT C

OPY

• Sorghum mini core collection is being used as an association mapping panel for genetic dissection of complex traits mainly because of

- Manageable size (242 accessions)

- Representing diversity of entire collection

- Included all races and intermediate races

- Diverse origin (57 countries from Africa, the Americas, Asia, Mediterranean, Oceania)

Sorghum mini core collection as an association mapping panel

DO NOT C

OPY

Trait Marker type No. of significant associations

Reference

Plant height 703 SSRs 4 SSRs for plant height Wang et al. 2012; Mol. Breed. 30:281-292

Plant height and maturity 14739 SNPs 6 SNPs for plant height and 10 for maturity

Upadhyaya et al. 2013; TAG 126: 2003-2015

Plant height and maturity 703 SSRs 5 SSRs each for plant height and maturity

Upadhyaya et al. 2012; Genome 55:471-479

Kernel weight and tiller number

43 SSRs 1 SSR for kernel weight and 2 for tiller numbers

Upadhyaya et al. 2012; Euphytica 187: 401-410

Plant height and inflorescence architecture

~2,65,000 Several SNP loci for plant height and inflorescence architectural traits

Morris et al. 2013; PNAS 110: 453-458

Grain mold and rust resistance

14,739 SNPs 2 SNPs for grain mold and 5 for rust resistance

Upadhyaya et al. 2013; Mol. Breed. 32: 451-462

Anthracnose resistance 14,739 SNPs 8 SNP loci Upadhyaya et al. 2013; TAG 126: 1649-1657

Germination under low temperature

162,177 SNPs 1 SNP Upadhyaya et al. 2016; Genome 59: 137-145

Saccharification yield 703 SSRs 2 SSRs Wang et al. 2011; Genome 54: 883-889

Saccharification yield 14,739 SNPs 7 SNPs Wang et al. 2013; Genome 56: 659-665

Mini core collection as an association mapping panel – sorghum as an example

DO NOT C

OPY

• Normal x High oil and High oil x High oil crosses

• >80 lines with exceptionally high oil (up to 63%) identified

• Multi-location evaluation is in progress

• Correlation between pod yield-oil content (-0.233*) and oil-protein (0.072)

New exceptionally high oil lines developed

Used high oil parents from mini core collection (Upadhyaya et al 2012)

DO NOT C

OPY

Algeria, Argentina, Australia, Bangladesh, Burkina Faso, Canada, China, Egypt, Ethiopia, France, Germany, Guyana, India, Iran, Italy, Japan, Kenya, Korea, Malawi, Mali, Mexico, Niger, Nigeria, Pakistan, Senegal, Sweden, Syrian, Tanzania, Thailand, Turkey, Uganda, UAE, UK, USA, Viet Nam, Zimbabwe

NARS and mini core collections• Total 338 sets (36 countries) and 127 sets ICRISAT

• 59 sets of sorghum core/mini core supplied to 15 countries and in ICRISAT

DO NOT C

OPY

• Germplasm is basic to sorghum improvement programs for enhanced and sustainable productivity

• Using sorghum mini-core collection, several new diverse sources for grain nutritional (Fe and Zn), biotic (drought, low temperature stress) and for abiotic stress (downy mildew, grain mold, leaf blight, rust, anthracnose) and multiple traits were identified

• Molecular characterization of mini-core collection revealed large diversity

• GWAS using sorghum mini core collection have identified significant SNP loci and candidate genes for important traits

• Using diverse multiple trait sources in the breeding would enhance yield, broaden genetic base and accelerate genetic gains

Conclusions

DO NOT C

OPY

• Genebank team, M Vetriventhan and others involved in germplasm work

• National partners in 36 countries working and using mini core collections to identify diverse trait-specific germplasm

• Physiologists (V Vadez, J Kholova), Pathologist (R Thakur, R Sharma), Entologists (HC Sharma, J Jaba) and Genomics (S. Deshpande)

Acknowledgements

DO NOT C

OPY

Thank You

DO NOT C

OPY

Sorghum Mini Core Collection COPY · Presented at the 2018 Global Sorghum Conference at Cape Town,...

Documents

Transcript of Sorghum Mini Core Collection COPY · Presented at the 2018 Global Sorghum Conference at Cape Town,...