Progress in Perennial Rice Breeding and Geneticspwheat.anr.msu.edu › wp-content › uploads ›...

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Progress in Perennial Rice Breeding and Genetics Fengyi Hu Food Crops Research Institute,YAAS 22 Sept. WaggaWagga, Australia

Transcript of Progress in Perennial Rice Breeding and Geneticspwheat.anr.msu.edu › wp-content › uploads ›...

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Progress in Perennial Rice Breeding and Genetics

Fengyi Hu

Food Crops Research Institute,YAAS22 Sept. WaggaWagga, Australia

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Introduction • Soil erosion in uplands of southeast Asia has been a serious problem that led to the project of developing perennial upland rice at IRRI (IRRI 1989)

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The idea of developing perennial rice for erosion control

Development of perennial upland rice has been proposed by several authors (IRRI 1989; Wagoner, 1990; Xiu, 1995; Schmit, 1996; Tao et al., 2000, 2001; Sacks, 2001;)

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Cultivars of rice is usual annual food crop after long time domestication by farmer and breeding procedure by breeder or geneticist.

The donor(s) for prerenniality?

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The donor(s) for prerenniality?

All over the world growth of O. sativa is Annual

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The donor(s) for prerenniality?

• O. longistaminata is the logical donor for perenniality from its feature of rhizome as compared to other wild rice species (O. officinalis, O. rhizomatious, O. australiensis)

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Oryza Species, the Species Complex, Chrom.,Genome group and Distribution

Oryza species, the species complexes, chromosome number, genome group and distribution

Section Chromosome Genome Distribution

Complex Number group Species

Oryza O.sativa complex O.sativa L. 24 AA Worldwide O.nivara Sharma et Shastry 24 AA Tropical and Sub.Asia O.rufipogon Griff 24 AA Tropical and Sub.Asia O.meridionalis Ng 24 AmAm Tropical Australia O.glumaepatula Steud. 24 AglAgl South America O.glaberrima Steud. 24 AgAg Africa(mainly West) O.barthii A.Chev. 24 AgAg Africa O.longistaminata Chev.et Roehr 24 AlAl Africa

O.officinalis complex O.officinalis Wall ex Watt 24 CC Tropical and Sub.Asia O.minuta Presl.et Presl. 48 BBCC Philippines O.eichingeri Peter 24 CC Sri Lanka,Africa O.rhizomatis Vaughan 24 CC Sri Lanka O.punctata Kotschy ex Steud. 24,48 BB,BBCC Africa O.latifolia Desv. 48 CCDD Latin America O.alta Swallen 48 CCDD Latin America O.grandiglumis (Doell) Prod. 48 CCDD South America O.australiensis Domin 24 EE Australia

Ridleyanae Tateoka O.brachyantha Chev.et Roehr. 24 FF Africa

O.schlechteri Pilger 48 HHKK Papua New Guinea O.ridleyi complex O.ridleyi Hook.f. 48 HHJJ SE Asia O.longiglumis Jansen 48 HHJJ Irian Jaya,Indonesia

Granulata O.meyeriana Roschev. complex O.meyeriana Baill 24 GG SE Asia

O.granulata Nees et Arn.ex Watt 24 GG S.and SE Asia

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The Diagram of Evolution of Wild Species among AA Genome of Rice

Gondawanaland Common ancestor

South and Southeast Asia Tropical Africa O. rufipogon O . longistaminata

O. nivar O. barthii

Indica ---- Japonica O . glaberrima

Parallel evolution

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Comparing the O. longistaminata and O. rufipogon

O. longistaminata (AA genome)

Photo was cited from Vaughan (1994)

O. rufipogon (AA genome)Photo was cited from Vaughan (1994)Tufted and scrambling herb, stolon

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O. longistaminata• Long anther

• Self-incompatibility

• Allogamy

• Rhizomatous stem

• Bacterial Blight resistance(Xa21)

• Nematode resistance

• …….

The Oryza longistaminata. A: The panicle of the O. longistaminata; B: The performance of O. longistaminata in field; C, D: the strong Rhizome of O. longistaminata.

A

B D

C

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Additional useful features from O. longistaminata

• A saturated molecular linkage map was constructed (Causse, 1994, Wilson, 1999).• Xa21, resistance to Bacterial Blight has been cloned with map-based (Khush, 1990; Song, 1995).• Resistance to tungro viruses has been verified (Angeles E.R. 1998). • Resistance to root knot nematode M. graminicalawas reported (Imelda R. Soriaano, 1999).• A saturated molecular linkage map based on PCR markers (Hu, 2003)• ……

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Goal

• Exploit the possibility of using perenniality from O. longistaminata for development of cultivars of perennial upland rice (PUR) or perennial rice (PR)

Oryza longistaminataPhoto was cited from Vaughan (1994)

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The Strategy for Perennial Rice Breeding

F1

RD23O. longistaminata

Progeny derived from F1

by Self-intercross, back cross, transgenic and MAS with diversity germplasm of rice

hope to

x

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F1 plant of RD23_Longi

F1

RhizomeF1 plant in greenhouse

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Problems for the PR Breeding and genetics

1, Less F1 progeny from O. longistaminataup to now, there are ~6 cases reported for

obtaining the F1 progeny since it is difficult to obtain the F1 plant in the procedure of interspecific hybrid between O. sativa and O. longistaminata.

among these cases, although F1 plant can get, most of  these  absence  Rhizome.  Including  CIRAD’s  (Ghesquiere, 1991), IRRI’s(Bara,  2000) and Japanese (Maekawa, 1997), and others not so clear.

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2, Lethal geneThe Rhizome present is Linkage to lethal

gene with D1 and D2; (Chu and Oka 1970; Ghesquiere, 1991)

results to obtain the progeny lack with Rhizome, means the Rhizome is usual lost in the progeny lines during the selection for breeding purpose.

Problems for the PR Breeding and genetics

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3, The reproductive barriers (Hybrid Sterility, Sgene)

This is a popular phenomenon between the cultivar and its wild species, even between two sub-species, Indica and Japonica of O. sativa.

It is also a main factor for obtaining the progeny that combine the favorable traits/gene from receiptor and donors. For example, the yield components.

Problems for the PR Breeding and genetics

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4, Photoperiod sensitivity

From Vegetative growth to productive growth, the day-light is important for the short day-light plant, including rice as it derived from tropical zone.

The progeny with strong ability of vegetative growth of O. longistaminata is main factor to lack selection for PR.

Problems for the PR Breeding and genetics

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5, Seed Dormancy

Problems for the PR Breeding and genetics

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6, Shatter grains

Problems for the PR Breeding and genetics

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7, awn

Problems for the PR Breeding and genetics

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How to overcome these problems?

All of these problems are the negative effect for PR improvement.

One of is utilization the traditional methods, such as Self-intercross, Backcross, then select the useful progeny.

Other one is understanding the genetic mechanism of these factor, specially for Rhizome, then using the MAS, Transgenic Strategy for cultivars of PR improvement.

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There are two stages for our results:

Phase I is from 1997-2004;Phase II is from 2005-now.

Progress in PR

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During First stages(1997-2005), there are 6 results has been obtained.

1, Obtaining the F1 plant derived RD23/O. longistaminata. (here, RD23 is an Indica type cultivar of rice)

2, From F2 and the molecular mapping shown that the Two Dominant Complementary Genes (Rhz2 and Rhz3) for Rhizome Expression in O. Longistaminata and mapped on chr3 and chr4, respectively.

3, Rhz2 and Rhz3 have been registered on the International Rice Genetic Committee.

4, The plant of BC2F1 with Rhizome has been obtained.5, The Rhizome related traits has been QTLs analysis.6, The first PCR-based molecular genetic map has been

constructed.

Progress in Phase I

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The F1 plant of the RD23/O. longistaminata cross was obtained by direct hybridization followed by embryo rescue and had 32.5% pollen fertility, indehiscent anthers, rhizomes that were intermediate in size, and abundance between the parents.

This is a important material for development Cultivar of PR or PUR.

Progress in Phase I

F1

Rhizome

F1 plant

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Progress in Phase I

Segregation of rhizome trait in the F2 population based on field experiment

absence

0.8011X2(9:7)

106121NumberspresenceRhizome

Result :Two Dominant Complementary, Rhz2, Rhz3, Genes for Rhizome Expression in O. Longistaminata

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PCR-base Molecular Genetic Map

Progress in Phase I

RM4280.0RM32313.1RM28319.0RM2530(6)21.6OSR226.6RM27232.3RM29245.7

RM15866.5

RM30687.8RM23797.5RM297109.5RM302114.7RM212118.1RM319118.3RM265122.4RM315128.5OSR23145.9RM529154.9

RM4850.0OSR179.2OSR1415.1RM27925.5RM42331.8RM55536.8

RM17456.8OSR960.0RM32262.9RM7170.5RM30083.4

RM34196.9

RM327112.7

RM263138.1RM2421148.6RM240157.5

RM166177.7

RM213190.1RM208202.7RM207206.4OSR26214.6

RM600.0

RM23115.2RM5883(10)19.9

OSR1344.0Rhz252.1OSR1653.4RM3657.8RM25166.5RM28275.1RM455184.0RM33889.5

RM156116.2

RM4626133.6RM6097142.7OSR31145.8RM55157.3RM1(1)165.0RM2525167.9RM4612180.9

RM114203.1

RM442224.2

RM5510.0RM51810.6RM26120.6RM18532.4RM14243.9RM11948.4Rhz350.6RM27357.8RM25265.7RM31778.3

RM349104.3OSR15106.1RM348107.2RM127116.4RM280123.5

RM1590.0RM1226.4OSR3511.1

RM1327.3RM40534.9

RM24952.4RM50958.0

RM16479.9

RM29193.9RM163101.7RM161107.3RM421117.0

RM274138.9

RM87151.0RM334163.6RM31167.6

RM1330.0RM4356.2RM17013.7

RM58726.8RM51037.6

RM20455.6RM642067.3RM31474.9RM25377.6RM40283.0RM27686.6RM13698.3RM5818105.4

RM6309128.5RM528132.7RM4509143.4

RM176157.4RM345162.7OSR21174.5

www.gramene.org

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Mapping for Rhz2and Rhz3

The molecular mapping of Rhizome gene Rhz2 and Rhz3 was mapped to the interval between markers OSR16 (1.3 cM) and OSR13 (8.1 cM) on rice chromosome 4 and Rhz2 located between RM119 (2.2 cM) and RM273 (7.4 cM) on chromosome 3.

Progress in Phase I

RM5510.0

RM51810.6

RM26120.6

RM18532.4

RM14243.9RM11948.4Rhz350.6RM27357.8

RM25265.7

RM31778.3

RM349104.3OSR15106.1RM348107.2RM127116.4

RM280123.5

Chromosome 4

RM600.0

RM23115.2RM5883(10)19.9

OSR1344.0Rhz252.1OSR1653.4RM3657.8RM25166.5RM28275.1RM455184.0RM33889.5

RM156116.2

RM4626133.6RM6097142.7OSR31145.8RM55157.3RM1(1)165.0RM2525167.9RM4612180.9

RM114203.1

RM442224.2

Chromosome 3

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Progress in Phase IIThe segregation and recombination of genotype of

two dominant complementary genes, Rhz2 and Rhz3 (9:7 model of Mendelian)

AB Ab aB ab

AB AABB AABb AaBB AaBb

Ab AABb AAbb AaBb Aabb

aB AaBB AaBb aaBB AaBb

ab AaBb Aabb aaBb aabb

AB Ab aB ab

AB AABB AABb AaBB AaBb

Ab AABb AAbb AaBb Aabb

aB AaBB AaBb aaBB AaBb

ab AaBb Aabb aaBb aabb

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The QTLs of Rhizome traits mapping on Chromomsome

Progress in Phase I

RM428RM323RM283RM2530(6)OSR2RM272RM292

RM158

RM306RM237RM297RM302RM212RM319RM265RM315

OSR23RM529

RL

RIL

RM60

RM231RM5883(10)

OSR13Rhz2OSR16RM36RM251RM282RM4551RM338

RM156

RM4626RM6097OSR31RM55RM1(1)RM2525

RM4612

RM114

RBD

RIL

TNR

L

RN

RBN

RIN

RM551

RM518RM261

RM185RM142RM119Rhz3RM273RM252RM317

RM349OSR15RM348RM127RM280

RL

RN

RBD

RBN

RIL

RIN

TN

RD

W

RL RN RBD

RBN RIL RIN

TN RDW

Chr1 Chr3 Chr4

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Progress in Phase IThe QTLs of Rhizome traits mapping on Chromomsome

RM159RM122OSR35

RM13RM405

RM249RM509

RM164

RM291RM163RM161RM421

RM274

RM87

RM334RM31

RL

RN

RIL

RIN

RBD

Chr5RM133RM435RM170

RM587

RM510

RM204RM6420RM314RM253RM402RM276RM136RM5818

RM6309RM528RM4509

RM176RM345

OSR21

RL

RBD

RIL

TN

RM427RM481

RM125RM180RM214RM320RM11OSR22RM2826RM336RM234RM18RM47RM134RM118

RL

RBD

RIL

RM216

RM467

RM271RM269

RM228

RM333

RM496RM590

RL

RN

RIL

RL RN RBD

RBN RIL RIN

TN RDW

Chr6 Chr7 Chr10

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Progress in Phase I

RM485

OSR17OSR14

RM279

RM423RM555

RM174OSR9RM322

RM71

RM300

RM341

RM327

RM263

RM3421

RM240

RM166

RM213

RM208RM207

OSR26

2Sorghum

LG F

pSB367

pSB107

pSB201

pSB193

pSB341(M4)

pSB637b(M4)

pSB038

pSB512 (M4)

pSB094

RG157

Csu173

CDO686

RG437

RM216

RM467

RM271

RM269

RM228

RM333

RM496RM590

10

SHO68

Csu111a(M1)

CDO98 QRn10

RM428

RM323RM283RM3530OSR2

RM272

RM292

RM158

RM306

RM237

RM297RM302RM212RM319RM265RM315

OSR23

RM529

1

RZ776(M3)

pSB614(M3)

pSB613(M3)

SorghumLG A

QRl1

RM60

RM231RM6883

OSR13

OSR16RM36

RM251

RM282

RM5551RM338

RM156

RM4626

RM7097OSR31

RM55

RM1RM3525

RM5612

RM114

RM442

3

SorghumLG C

pSB088(M5)

pSB300A(M5)

pSB050(M5)

RZ284

R944

Rhz2

QRn3

QRbd2

QRbn2

Comparative mapping (Rice and Sorghum)

PNAS, 2003, 100:4050-4054

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Progress in Phase I

Rhz3

RM427

RM481

RM125

RM180

RM214

RM320RM11OSR22

RM3826

RM336

RM234RM18RM47RM134RM118

7

SorghumLG B

RZ395

pSB077

R1245

RM159

RM122OSR35

RM13

RM405

RM249

RM509

RM164

RM291

RM163

RM161

RM421

RM274

RM87

RM334RM31

5

SorghumLG G

R1436

pSB445

pSB069

RM133

RM435

RM170

RM587

RM510

RM204

RM7420

RM314RM253RM402RM276

RM136

RM5818

RM7309RM528

RM5509

RM176

RM345

OSR21

6

SorghumLG I

pSB355(M6)

CDO17

RZ612

RM551

RM518

RM261

RM185

RM142RM119

RM273

RM252

RM317

RM349OSR15RM348

RM127

RM280

4

SorghumLG D

pSB428a(M2)pSB188(M2)

RZ69

RZ740a

QRl7

QRi6QRn5

QRn7

QRin6

Comparative mapping (Rice and Sorghum)

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Progress in Phase IRhz2 and Rhz3 gene registration

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The BC2F1 Individual

Progress in Phase I

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During in the phase II, the action for PR breeding and genetics are in progress.

The fine mapping of Rhizome genes, Rhz2 and Rhz3, are on the way;

A lots of the breeding lines for PR purpose have been evaluated in field;

The pollen grain fertility loci QTL analysis of F2progeny was detected.

Progress in Phase II

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F2 Individual in Field for Rhizome Evaluation and Mapping

Progress in Phase II

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F2 plant in field for Rhizome genes fine mapping and breeding lines selection

Progress in Phase II

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Experiment: determination of Rhizome expression with 3 replications with random plot design for by cutting method

Progress in Phase II

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Result of fine mapping renewed

Progress in Phase II

RM5510.0

RM51810.6

RM26120.6

RM18532.4

RM14243.9RM11948.4 Rhz350.6RM27357.8RM25265.7

RM31778.3

RM349104.3OSR15106.1RM348107.2RM127116.4RM280123.5

Chromosome 4

RM600.0RM23115.2RM5883(10)19.9

OSR1344.0Rhz252.1OSR1653.4RM3657.8RM25166.5RM28275.1RM455184.0RM33889.5

RM156116.2RM4626133.6RM6097142.7OSR31145.8RM55157.3RM1(1)165.0RM2525167.9RM4612180.9

RM114203.1

RM442224.2

Chromosome 3

RM14603Rhz2OSR16

1.12.1

RM119Rhz3RM17000

0.30.4

9.528kb~35kb

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Progress in Phase II Microarray

In this study, the specific gene expression patterns across five tissues in O. longistaminata, especially in the rhizome were characterized by using the Affymetrix microarray platform. Results showed that the different gene sets were determined exclusively expressed in five tissues, 58 and 61 genes were identified as prevalent sets in rhizome tip and internode respectively. Cis-element analysis and co-localization of rhizome related QTLs for the rhizome prevalent gene set were further performed

1a 1b 1c 2a 2b 2c 3a 3b 3c 4a 4b 4c 5a 5b 5c

The results will be accepted by Plant biology of BMC

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Progress in Phase II Microarray

0

10

20

30

40

50

60

70

80Up-regulated GenesDown-regulated Genes

Functional classification of the differentially expressed genes in the rhizome tip in comparison with shoot tip.

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Progress in Phase II Fosmid library

• The library consists of 110,000 clones, which has insertion with an average size of about 43kb and represents 10 genome equivalents and is no bias (10X). The results indicate that the fosmid library has high quality and deep coverage that is sufficient for target gene isolation, physical mapping,gene functional analysis and so on. The Fosmid library of O. longistaminatais first report.

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Breeding lines

Progress in Phase II

BC1 RLR504

• Two rhizome gene locus are heterozygote in O. Longi (AaBb);

• 5% grain filling;

• Normal pollen fertility

• Strong Rhizome

• Less cultivar-like plant type

• Short awn

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Breeding lines

Progress in Phase II

BC1 RLR540

• Two rhizome gene locus are heterozygote in O. Longi (AaBb);

• 5% grain filling;

• Normal pollen fertility

• Strong Rhizome

• Less cultivar-like plant type

• Short awn

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Breeding lines

Progress in Phase II

200808_11 BC1 plant

• Two rhizome gene locus are homozygote in O. Longi (AABB);

• 75% grain filling;

• Normal pollen fertility

• Strong Rhizome

• Self-compatibility

• Less cultivar-like plant type

• Short awn

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Breeding lines (F2) AaBb AaBB AABb AABB

Progress in Phase II

36-1 F2 plant AaBb

Two rhizome gene locus are heterozygote;

Normal grain filling;

Strong rhizome presence

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Breeding lines

Progress in Phase II

• One rhizome gene locus is heterozygote, other one is homozygote

• Normal grain filling;

• Normal pollen fertility

• Strong rhizome presence

• Self-compatibility

22-93 F2 plant AaBB

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Progress in Phase II

34-31 AABb • One rhizome gene locus is heterozygote, other one is homozygote

• Normal grain filling;

• Normal pollen fertility

• Strong rhizome presence

• Self-compatibility

Breeding lines

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Progress in Phase II

14-2 AABB

• Two rhizome gene locus are homozygote

•• Normal grain filling;

• Normal pollen fertility

• Strong rhizome presence

• Self-compatibility

Breeding lines

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Breeding lines

Progress in Phase II

• Two rhizome gene locus are homozygote in O. longi;

• 75% grain filling;

• Normal pollen fertility

• Rhizome absence

• Self-compatibility

• Awn less

6-28 F2 pant

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Breeding lines

Progress in Phase II

• Two rhizome gene locus are homozygote;

• 75% grain filling;

• Normal pollen fertility

• Rhizome absence

• Self-compatibility

10-25 F2 plant

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Breeding lines

Progress in Phase II

• Rhz2 is heterozygote, Rhz3 is homozygote;

• 70% grain filling;

• Normal pollen fertility

• Rhizome absence

• Self-compatibility

• Cultivar-like plant type

• Short awn12-38 F2 plant

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Spikelet fertility improvement

Progress in Phase II

Rang:

0%-90% above

0% ~2% ~10% ~30% >50% >90%

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• NILs with Rhizome constructionProgress in Phase II

0% ~2% ~10% ~30% >50% >90%

F2

F3

F4F5

Fn

NILs with Rhziome

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Reproductive Ability after three times for cutting of F2 population

Progress in Phase II

Aug., 2007

Feb., 2008

Aug., 2008

Sep., 2007

Apr., 2008

After Aug., What happen? Dec. 2009?? 2010???

Oct., 2007

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Progress in Phase II

F3 population from 34-31(F2) used to reproduced ability test from 2008 to now

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Progress in Phase II Reproductive Ability after three times for cutting

2008 2009 2010

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• Genetic study on perenniality of rice• Perennial rice breeding• Other perennial crops screening in Kunming

Progress in Phase II(2010)

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Two rhizome gene cloning1, Whole genome de novo sequence of O.

longistaminata (finished and data analysis on going)

2, Fine mapping3, Candidate gene of Rhz2 and Rhz34, Transformation for candidate genes

Progress in Phase II(2010)

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Whole genome sequence of O. longistaminata

70X coverage the physical map of O. longistaminata

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Transgenic results

RI CE_13428 3 Os03t 0216000- 01 Si mi l ar t o Zi nc- f i nger pr ot ei nKNUCKLES, Zi nc f i nger , C2H2- t ype

RNAi

and

Overpress

AABB as receiptor

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Perennial Rice Breeding1, NILs2, Obtained the materials with Rhizome in F3,

F6, F7 with different genotype3, Problem?

Progress in Phase II (2010)

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NILs of RD23/O. longistaminata

• F7 population with 336 family lines

• Rhizome with normal pollen fertility

• Larger varieties of agronomic traits: plant high, tiller,

• Favorable genes mining, stem borer-resistance

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Breeding materials for PR

F3 lines from 22-93(AaBB)

Two plants, AaBB, aaBB

22-93(18), aaBB

22-93(36), AaBB

MAS

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F3 lines from 34-31 (AABb)Two plants, AABb, AAbb

Breeding materials for PR

34-31(6-12), AABb

34-31(4-29), AAbb

MAS

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• F6 and F7 lines from NILs (AABB)Breeding materials for PR

F6

F7F6

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• Problems and prospect

Progress in Phase II (2010)

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Rhizome gene Rhz2, Rhz3 cloning

Hope to understand the genetics of Rhizome and using transgenic method for perennial rice breeding.

Next step

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Next step

Large population (F3, F4, F5 ) in MAS with 4 different genotypes: AaBB, AABb, AaBb and AABB.

Hope to select the plant with rhizome and good fertility panicle.

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Next step

The individuals with Rhizome and Fertility after selected screening both Upland and Aerobic land.

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Next stepInternational Cooperation

2009, in field at experimental station in Sanya, China

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Next stepWashington State University: perennial wheat

The Land Institute: perennial sorghum, sunflower, wheat, +.

University of Manitoba: (potentially) perennial rye, wheat

Yunnan Academy of Agricultural Sciences: perennial rice

FFI-CRC: perennial wheat

云南农科院,多年生水陆稻

澳大利亚美国土地研究所

Washington State University: perennial wheat

The Land Institute: perennial sorghum, sunflower, wheat, +.

University of Manitoba: (potentially) perennial rye, wheat

Yunnan Academy of Agricultural Sciences: perennial rice

FFI-CRC: perennial wheat

International Network of Perennial Crops

云南农科院,多年生水陆稻

澳大利亚美国土地研究所

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NATURE|Vol 456|4 December 2008

可能改变世界的5个作物科学家

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Acknowledgment

Financial support from

• National Natural Science Foundation of China

• The Land Institute

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Dr. E. Sacks

Prof. Dayun Tao

Thanks  to….The UR GroupPeng Xu

Xiangneng Deng

Jiawu Zhou

Jin Li

Wei Deng

Qiong Li

Lijuan Li

Yang Yu

Wenting Wan

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Thank you for your attention!