Sorghum Mini Core Collection COPY · Presented at the 2018 Global Sorghum Conference at Cape Town,...
Transcript of 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
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• 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
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• 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
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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
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• 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
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Genetic gains
∆G = Genetic gainh2 = Heritability of trait
i = Selection intensityσp = Phenotypic standard deviationgi = Generation interval (cycles/year)
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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
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Source: (http://apps3.fao.org/wiews)
Sorghum germplasm collection
Sorghum cultivated germplasm accessions (232,600) Sorghum wild germplasm accessions (4,017)
Global status
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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
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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
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• 36,282 accessions at Global Seed Vault at Svalbard, Norway
Safety duplication of sorghum
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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
335 (13) 354 8 Upadhyaya et al 2014, PGR 12(2): 226-235
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
76 (5) 790 12 Upadhyaya et al 2011, PGR 11(1): 3-14
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
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Sorghum Germplasm Core and mini core collections
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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
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• 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
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Sorghum Mini Core- a sources for multiple trait germplasm and accelerated genetic gains
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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
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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
Sorghum mini core for accelerated genetic gains
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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
Sorghum mini core for accelerated genetic gains
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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
Sorghum mini core for accelerated genetic gains
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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
Sorghum mini core for accelerated genetic gains
Resistance to insect pests
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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
Sorghum mini core for accelerated genetic gains
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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
Sorghum mini core for accelerated genetic gains
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• 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
Sorghum mini core for accelerated genetic gains
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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
Sorghum mini core for accelerated genetic gains
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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
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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
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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 23684 Protein, Brix %, Anthracnose, leaf blight, rust
IS 1212 Fe, Zn, Drought, Low temperature, downy mildew, grain mold
0.460
IS 23684 Protein, Brix %, Anthracnose, leaf blight, rust
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
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Sorghum mini core as an association mapping panel
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• 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
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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
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• 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)
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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
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• 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
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• 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
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Thank You
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