http://www.fao.org/agriculture/crops/thematic-sitemap/theme/spi/en/ Presentation by Erik Sacks (University of Illinois) describing the benefits of undomesticated perennial African rice as a source for improving the breeding of domesticated rice. The presentation was delivered in occasion of the “Putting Perennial crops to work in practice” workshop in Bamako, Mali (1-5 September 2015).

1. The Undomesticated Perennial African Rice, Oryza
longistaminata, Is An Outstanding but Overlooked
Source of Genes for Improving Domesticated Rice
Erik Sacks
esacks@illinois.edu
September 2015

2. Talk Outline
• The case for O. longistaminata
• Strategy and recent accomplishments
• Ratoon cropping: a good option for seasonal
(water- or cold-limited) environments

3. The case for O. longistaminata
• Highly diverse
– Broad geographic range
– SI
– ~195 accessions throughout sub-Saharan Africa in gene-bank
• Useful source of genes
– Xa21 for resistance to rice bacterial blight
– Resistance to leaf rollers (insects)—RIL pop of ~300
– Nematode resistance (RKN)
– Heterosis, large anthers/high pollen production, …
– Abiotic stress tolerances: cold, heat, salt, drought, flood
– Super ratooning
• Few O. sativa/O. longistaminata hybrids made so far
=> Big Opportunities to Improve Domesticated Rice

4. http://www.knowledgebank.irri.org/extension/wild-rice-taxonomy.html
Wild, perennial
progenitor
(Diploid, A-genome)
Domesticated
annual or
weakly perennial
O. rufipogon
(stolons)
O. longistaminata
(rhizomes)
O. sativa
O. barthii
Wild, annual
progenitor
O. nivara
O. glaberrima
subsp. indica
subsp. japonica
Origins of Domesticated Rice

5. By Analogy, O. sativa/O. glaberrima (NERICA Project)
Was a Successful Strategy
• O. glaberrima was the primary donor of abiotic stress
tolerances and O. sativa was the primary donor of
yield-potential
• However, genetic and geographic diversity of O.
glaberrima is much less than that of O. longistaminata
• Thus, we expect the opportunities for improving rice
with genes from O. longistaminata to be great

6. Origins of O. longistaminata accessions in the IRRI Genebank

7. Geographical analyses of
environmental stresses at
collection locations for O.
longistaminata accessions
By MS student, Marlee Labroo

18. Strategy & Recent Accomplishments
• Goal: Put useful O. longistaminata genes in hands of farmers
• Strategy:
– Systematic approach to unlocking useful O. longistaminata genes
– ID key accessions & core set
– ID marker-trait associations
– Circumvent breeding barriers
– Put introgressed genes into elite locally-adapted cultivar
backgrounds and confirm benefit via field testing in relevant
environments
• Initial Implementation:
– Survey an O. longistaminata germlasm collection
• ID key accessions and QTL
– Develop interspecific mapping/breeding populations
• Crossable to O. sativa with high fertility
• Key traits tagged with markers
• Types: RILs, BC inbred, Introgression Line (IL)

19. Cold water tank
(Cold water + Warm air)
Growth Chamber
(Cold water + Cold air)
High altitude
(Cold water/air + Warm water/air)
Banaue, Mountain Province, Philippines

20. Survey of an O. longistaminata germlasm collection
• 195 accessions from IRRI genebank
• Genotyping via GBS
• Population structure analysis
– ID core accessions that represent most of the genetic diversity
• Phenotype for abiotic stress tolerances in controlled
environments
• GWAS to identify SNP-trait associations
• Work of MS student, Marlee Labroo

22. GBS (RAD-seq)
• Restriction-site associated DNA sequencing
• A cheap way to both mine and genotype large
numbers of SNPs
• No ascertainment bias
• Reduced representation of the whole genome
– Only sequencing adjacent to restriction cut sites
• Adapted protocol for sorghum, barley and
wheat (Poland et al., 2012)
– We find that it also works for rice

23. GBS (RAD-seq)
A
B
C
D
E
F
G
H
1 2 3 4 5 6 7 8 9 10 11 12
DNA from
96
individuals
Digest with rare-cutter (PstI, 6 bp)
and common-cutter (MspI, 4 bp)
Add barcoded adapters that will pair
to PstI site.
ACGT GC
TGCA
Add MspI adapter and ligate.
CG
Illumina
primer
site
Illumina
primer
site
Barcode
sequence
Genomic DNA
Pool into one
tube
PstI site MspI site

24. Pool into one
tube
Size select on gel
(200-500 bp)
PCR with Illumina primers
(Just amplify PstI-MspI,
not MspI-MspI)
• Quantify with Picogreen
• Size range on Bioanalyzer
• Dilute to 10 nM
• Quantify with qPCR
• Run on Illumina HiSeq
GBS (RAD-seq)

25. Development of a High Density Genetic Map for an O.
sativa/O. longistaminata RIL Population
• Collaboration with Dr. Fengyi Hu at YAAS
– Visiting scholar, Shilai Zhang, currently at UI
• Co-funded with UI ACES International Matching Grant
• O. sativa ‘RD23’ x O. longistaminata population
– >300 RILs developed
– Cross made by Drs. Tao and Sripichitt in 1990’s
• Goal: develop this genetic resource to facilitate
identification and marker-assisted introgression of QTL
via a high-density genetic map
• Genotyping via GBS
• Provide an example using leafroller resistance

26. Segregation for resistance to leafroller (Cnaphalocrocis medinalis) in RIL
population derived from the cross O. sativa ‘RD23’ x O. longistaminata

28. Final map will
be based on
7209 filtered
SNPs

29. Ratoon cropping: a good option for seasonal
(water or cold-limited) environments
• Traditional SE Asian practice, now being promoted again in
some areas
• Common practice in southern U.S. and southern China
• Good cv’s for ratooning in Asia ID’ed in 1970’s and 1980’s
• Advantages:
– Plant once, harvest twice (less labor, soil erosion and risk)
– Less inputs needed than new planting (less, water, fertilizer, time)
– Obtain 2nd harvest in less time than with new planting (important
if growing days restricted by dry season or cold)
– Greater overall yields
– Reduced risks from tropical storms

30. Ratooning
• Research gaps:
– Ratoon yield is usually lower than new planting (30-40% of
main crop yield)
– Usually restricted to 1 ratoon because low yields of 2nd ratoon
• Research opportunities:
– Develop improved cultivars selected for:
• Greater ratoon yields and overall yield/time
• Improved ratooning ability  What about 3+ harvests?
• Drought tolerance, esp. during reproductive stage to increase yield of
ratoon crop in locations with strong wet/dry seasons
– Improve cultural practices and provide info to farmers
• Low-hanging fruit
– Low risk, moderate gains

31. Breeding for Greater Ratoon Yields
• Fengyi’s PR23 has shown us a good path forward
• Introgression from PR23 (or other selected progeny
derived from O. longistaminata) can boost ratoon
stand and yields
– Shorter duration needed for season-limited
environments
– Local adaptation needed
• Thus, backcrossing to elite germplasm would be key

32. Rice Ratooning in the US
• Started in 1940’s-50’s
• Nathan Evatt (agronomist) and Hank
Beachell (breeder) promoted ratooning
• In southern US, the season is too short
(cold/frost) for 2 consecutive crops from seed
• Short-duration cv’s allow a main crop and a
ratoon crop
– => greater overall yields
– => reduced risk from tropical storms

33. Rice Ratooning in the US: Current Status
• In TX, ~50-55% of the crop is ratooned
• In LA, ~30-35% of the crop is ratooned
• Ratoon yields are typically 30-40% of
main crop yields

34. http://www.trekearth.com/works
hops/444929/photo70841.htm
Ratooning
Harvest more rice with ratooning
by Junelyn S.de la Rosa
January-March 2004
Bar Digest
Farmers can harvest more rice and gain more
income by ratooning or double harvest- an
indigenous practice in rice farming that induces the
formation of shoots or ratoons from the mother
crop after the previous growth has been cut back.
http://philippinetambayan.com/2008/10/24/harvest-more-rice-with-
ratooning/
TX

35. THANKS!
esacks@illinois.edu