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Arachis genomics in South America

Arachis genomics in South America . IBONE - Argentina Guillermo Seijo Antonio Krapovickas. EMBRAPA Patricia Guimar ã es Soraya Leal Bertioli Marcio Moretzsohn Jos é Valls. UCB David Bertioli. Exclusively South American 80 described species (9 taxonomical sections) in diverse habitats.

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Arachis genomics in South America

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  1. Arachis genomics in South America IBONE - Argentina Guillermo Seijo Antonio Krapovickas EMBRAPA Patricia Guimarães Soraya Leal Bertioli Marcio Moretzsohn José Valls UCB David Bertioli

  2. Exclusively South American 80 described species (9 taxonomical sections) in diverse habitats Most wild species are diploid cultivated peanut is tetraploid: Where did it come from ?

  3. Peanut’s origin Diploid species with “BB” genome Diploid species with “AA” genome n = 10 x n = 10 Sterile AB hybrid 2n = 20 Spontaneous duplication (x 2) Arachis hypogaea AABB

  4. Cytogenetics and genomics FISH and GISH Guiding the use of new species for production of synthetics Seijo et al. Am. J. Bot. 91: 1294–1303. 2004 .Seijo et al. Am. J. Bot. in-press

  5. Wild alleles bring many new traits and provide polymorphism for genetics Wild species: Many alleles Diploid A. hypogaea Few alleles Tetraploid

  6. BAC (HindIII) c. 80,000 clones c. 6.5x BAC (HindIII) c. 80,000 clones c. 6.5x Maps for peanut Use wild polymorphism Dissect the tetraploid problem 2 diploid and one tetraploid population A.stenosperma x A.magna x A.duranensis A.ipaensis AB A.hypogaea x (A.duranensis x A.ipaënsis )c

  7. A1_diploid A2_diploid A3_diploid A6_diploid A4_diploid A5_diploid RN17F12 Leg208 Leg188## AD_15B 0.0 0.0 0.0 0.0 Leg152 gi-620 0.0 0.0 RN2F12 AD_17E 3.0 3.5 S1A37A## A7_diploid A8_diploid A9_diploid 14.0 gi-385 0.5 Ah3 8.1 Leg104 Leg031 5.1 4.0 P21M68_3 15.8 S1A36_C 20.8 AD_13D 17.5 gi-909## Leg176## gi-716 Lec-1# 17.3 0.0 0.0 0.0 TC3H2Ad 19.7 TC7E4### 25.5 22.4 Leg128## Leg033 4.1 RN3E10## 29.1 gi-1170 9.8 TC9F4 5.6 AS_24K# 27.9 Leg066### 29.6 Ap166 33.3 6.3 Ah-558 TC4H2_2As RN13G8### 32.9 36.6 RN0_06Ad 32.2 LegTC987## Ah-649 21.2 RM15C11 8.2 AS_20A# 39.4 TC1A8 TC6G9 37.4 21.3 P21M68_6## 40.8 Leg322 Leg036## 22.2 39.4 AdRGA14A 42.9 TC1E5 11.8 S1A36B## 41.6 TC4G2### PM170# 41.0 24.5 55.2 TC11A4 AS_20F# P25M46_7 46.1 18.5 S1A36D## Leg242 45.0 55.2 RM1A5### TC1D1As 45.5 36.5 ML4D2 25.9 P18M60_1## TC1A2 51.2 55.9 A10_diploid cp4.2_2004 AD_21E Leg33M_Gm 23.8 61.4 60.5 P25M46_4### Leg237### AdRGA26B## Leg24M_Gm 47.3 42.4 33.5 Seq14G3 53.5 Leg092 56.0 AD_25A P21M36_9 28.3 58.1 TC7H11 65.8 Leg076### gi-560### 67.1 RN22G7# 51.2 49.1 RN0_614 57.0 AsRGA14D# 60.7 P21M36_7 29.3 73.5 Leg160 Leg159 TC2C12 Ah-275### LegRAB### 0.0 75.8 TC4G10 60.8 52.1 Seq15D6_2As# 57.1 29.4 P16M48_3 Ah-074 68.3 P19M42_6## 75.3 Ah-614### 65.5 Ah30### 76.3 56.0 TC3G1_2 58.4 PM24 Leg1_Gm Leg044## 54.8 70.4 Leg002 42.3 TC4A2 78.3 Ag99### Leg088### 75.2 77.4 TC9H8# 57.7 TC7C6Ad Leg199 63.8 56.4 73.8 AS_27E# Seq2H11 77.6 P16M48_7 TC11A2 46.0 79.3 PM3### 82.0 P18M45_4### 76.8 PM204 60.3 P25M46_2As# gi-906 P21M36_2 76.2 67.1 60.5 TC9B12Ad# 81.2 gi-7295Ad 51.8 Ah23_2As 81.1 TC0A1Ad## Ah-742### cp6 PM225As 77.1 85.0 65.5 RN0_681 23.7 Leg045## M14# 72.4 82.9 RN1A9 58.9 82.3 AC3C2 P18M45_15# 88.5 TC4E10### Ah4-26### 77.5 PM243## 90.5 66.4 gi-936# 27.3 RGA_H1 AC2C2 80.0 73.6 PM188 60.5 RN0_506 84.6 P22M34_56 93.1 PM45### 78.1 PM42## 90.6 gi-623 28.2 Leg346## 82.5 Ah-636As 75.8 Leg149 77.8 TC6H3 61.0 TC1G4 86.5 Leg4Gm# P26M68_34### Ah20### 80.4 96.8 91.0 P18M45_17 100.8 RN21H1# 88.6 TC9F10 Ah-659Ad 61.6 90.4 TC6E1### Leg181### 91.1 RM15H8## 80.7 40.1 P13M49_9 103.6 AS_11B 93.6 Seq4H6 89.8 RN2H11 67.7 Leg20M_Gm Leg055 100.7 88.9 Leg223## PM36### 81.0 91.2 P18M44_6 109.8 P18M60_3# P25M46_9## 99.6 93.3 P21M68_4 74.9 Leg168## 91.6 RM6E8### 81.5 PM35## Leg186# 104.1 102.7 Leg299 97.2 Leg17M_Gm 91.2 Seq13B7## PM65### 86.1 93.4 AS_26A 116.8 Leg11M_Gm AD_11G# Leg304## 107.1 109.1 120.1 P18M4526 102.4 TC4D9## 58.4 AsRGA15C## TC2B1### 88.3 94.4 TC3H7 110.8 TC1D2## 108.6 RN0_729 126.5 TC7G10## 130.3 TC3A12### 94.8 Leg043## 100.4 Leg228 110.0 AC2H11# 110.8 RM5G08 RM13A12# 109.9 115.7 AS_13C 67.6 Leg930# PM238## 135.4 P20M51_8### 107.1 101.1 TC5A6As# AD_24G# 110.0 117.1 cp3_2005 Ah-594As Leg14M_Gm 139.1 139.2 P18M44_7### TC2C7## 110.7 108.1 AD_11D# 113.2 Leg081 117.5 Leg196 TC9B8As 123.2 AdRGA14 Ah-229 123.5 142.0 Leg225## 144.1 RM9A3### 108.7 120.7 Exportin P18M69_1## 123.0 118.1 Ah-700As Leg156 145.2 148.2 TC1B2_2## 138.0 RM2H10# 113.0 Leg203 119.0 PM119# 130.2 Ah11 Leg136## 151.9 RN10F9## 153.4 Ah-745 120.3 152.6 RN13D4 134.6 Leg074# Leg100# 136.7 120.6 AC3D7## 154.4 155.3 RN10F4## TC1E6# 121.6 Leg356 TC7H2 149.7 121.2 TC5A7## 155.9 121.7 RN9C8## TC1B2Ad Leg12M_Gm 121.5 163.5 173.9 Leg177 Leg4amino gi-832## 148.0 P25M46_8 126.5 160.5 RN9A5 165.2 Ah6-125## 171.5 Ah-671## 122.7 TC4C8As 183.4 PM49## S48RGA2 161.2 Seq3E5 137.8 183.5 160.9 AdRGA9A gi-7295## 138.5 RN0_615 187.8 Leg224## RN5H2## 174.0 AdRGA11F 150.8 163.1 Seq4C1 AS_1A 190.2 163.3 P16M48_1## 154.6 AC2C22As 188.1 Leg083# 169.6 Ah-745_2## 179.0 PM18Ad Seq2D1 173.9 195.1 AD_24C 167.1 cp4 161.5 P13M49_1## Seq2G5 188.4 TC9E8## 179.5 Seq15D6# RN22A12 197.9 171.2 185.2 Leg175# PM181 188.9 203.2 Leg178 Leg070 172.2 193.1 Leg133 AS_21C 174.8 Leg202 191.6 Seq12B2 Leg305 204.2 173.6 RI2D6 197.1 192.0 Ah-573 Seq11C8 198.4 Ah21 Leg30M_Gm 207.6 176.5 AsRGA24A 200.4 RI1F6 193.1 Ah2 208.2 177.0 Leg654 TC4F12Ad 193.8 210.8 TC2A2 Leg050## Ah-193 211.3 TC7A2 209.8 178.8 AdRGA9C 210.6 TC4D2 193.9 Ah-462As# 212.1 209.9 Ap14 RM11H6 185.4 214.8 P25M41_5 RN8C9 218.1 PM8 196.2 PM120## RN11E5 213.1 TC3B5# 210.9 cp2 195.0 RN23F10 222.9 Leg213 199.8 214.6 RN9C2## Leg047 212.2 Leg929 209.5 PM230 202.2 Ah-569## TC2E11Ad 222.6 213.9 Leg924## 212.4 233.9 Seq4F10 203.0 PM32 Ah-408 Leg187 230.5 218.1 TC3E2 237.6 TC4H2# 216.0 TC7H9# 230.1 AD_17B# 224.4 TC1D1 240.7 P18M4556 230.4 H8ARGAAd# 229.6 Leg062## 249.0 250.8 TC2D6 231.4 P18M45_7 AD_19C# 237.2 249.6 TC5C5Ad# TC4G5Ad 251.0 248.9 P22M3411 TC1H4## 253.2 P25M46_11 250.1 RN12E1## 260.0 P18M69_3 251.9 Ah-199 269.0 P22M3415 253.2 AdRGA27B 257.7 P18M60_2 263.5 RM17H9 274.5 281.1 P13M49_5## Leg146 291.7 P19M42_1### 287.2 Ah-330 290.5 P21M3648 292.2 gi-876 298.5 Leg298 303.8 PM22 304.8 314.2 Leg034 318.0 Leg069 RI2A6 321.8 LegTC3145 324.6 cp1 332.7 P25M41_1 P18M45_18 334.8 340.8 P20M37_1 P25M4110 343.8 AD_13B 357.6 gi-919 376.9 TC2E5 383.4 Leg169## 407.9 AA map 186 SSRs (47% poly.) QTLs 81 anchor markers leaf spot 15 RGAs seed weight 47 sequenced AFLPs seed number 10 others > 50% genic 51% distortion Moretzsohn et al. TAG 111, 1060-1071, 2005 and unpublished

  8. Arachis AA vs Medicago

  9. Lj5 Lj6 Lj1 Lj3 Lj4 Lj2 Mt1 Mt2 Mt3 Mt7 Mt4 Mt8 Mt5 Mt6 Models  Reference diploids  Cultivated SSRs Anchors Mt Lj

  10. Outside South America - Partners University of Aarhus, Denmark Jens Stougaard Leif Schauser Birgit Hougaard Jakob Fredslund Lene Madsen Niels Sandal CIRAD France Angelique d'Hont Olivier Garsmeur Jean-Francois Rami Financial Support ICRISAT – India CERAAS/ISRA – Senegal UC Davis – USA UG – USA JIC - UK

  11. Summary Candidate gene Markers. Genome Anchor Markers QTLs BAC libraries Cytogenetic analysis Genetic and Physical maps Synteny SSR Markers Genotyping system Synthetic amphidiploids Evaluation of germplasm. Marker Assisted Selection in breeding programs Improved peanut varieties

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