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TLI 2012: Physiology and breeding for complex constraints in legumes

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CGIAR Generation Challenge Programme
CGIAR Generation Challenge Programme

This document summarizes research on breeding the crop Sorpea for drought tolerance. It describes analyzing environmental patterns to characterize drought and identifying traits that confer advantage under most frequent drought conditions. It also details mapping yield and water saving quantitative trait loci in the crop Bealet, finding multiple alleles interact to influence transpiration rate depending on environment. Stay green is correlated with extracting more water after anthesis. Candidate genes underlying mapped traits are proposed.

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Physiology and breeding for Complex constraints
Acceleration of breeding for drought tolerance requires deep understanding of GxExM interactions Regardless of crops G YIELD YIELD E M
Scenario analysis – (Case of Sorpea in Inrica) Weather Drought scenario probability Identification of key traits – (Case of Bealet in Amefrica) what trait mapping loci interactions Any resemblance to any crop having existed can only be coincidental Nevertheless, data presented are real !!!
Sorpea growing area in Inrica
2 How to characterize Characterizing drought dynamics - based on S/D ratio simulation and clustering Type 3 intermittent stress Type 4 post-flowering stress Type 1 flowering stress Type 2 pre-flowering stress
2. Environmental patterns major stress patterns 1 0.8 vegetative pre-flowering 0.6 S/D post-flowering post-flowering relieved 0.4 mild 0.2 0 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 o thermal time ( D) 3. Which traits Sorpea growing area in Inrica confer advantage in the most frequent environment?
LG 2 “Tolerant allele” M322 Any difference M394 Terminal M214 Drought in water saving 30 cM tolerance M321 M592 M443 ?? M356 M738 40 cM Tolerant has: Better seed setting Better grain filling Problem? Large interval Bealet Crop GxE
Difference in Transpiration rate (g cm-2 d-1) In Bealet 0.26 LG 2 Tr (g H2O cm day ) 0.24 0.22 -1 M322 M394 0.2 -2 0.18 M214 M321 0.16 M592 M443 M356 0.14 M738 0.12 40cM 0.1 Sensitive Tolerant Tolerant Tolerant Tolerant genotypes
Transpiration response to high VPD 0.045 Transpiration (g cm-2 h-1) 0.04 Terminal drought 0.035 sensitive 0.03 0.025 Terminal drought 0.02 tolerant 0.015 0.01 0.005 0.50 1.00 1.50 2.00 2.50 3.00 3.50 VPD (kPa) 2 mechanisms of water saving: Bealet Crop •Low Tr at low VPD •Further restriction of Tr at high VPD
Mapping of water saving traits in Bealet Crop Weighing: 7-11am = low VPD 11am-15pm = high VPD RH & T hourly recording 4 replications 8” pots re-saturated every day soil evaporation minimized with plastic beads
0.0 PgPb8984 13.8 PgPb10594 29.8 PgPb8607 45.5 PgPb9081 Tr 63.9 PgPb11433 Quantitative traits usually influenced by multiple alleles 65.5 PgPb9681 100.8 PgPb9143 113.3 PgPb11732 whose effects can vary depending on environment 132.1 PgPb10852 142.0 PgPb9167 155.6 PgPb10902 167.7 Xctm03 178.4 PgPb7431 Yield and water saving trait QTLs 188.5 PgPb12731 191.8 PgPb7979 193.1 Xpsmp2237 196.3 PgPb8512 198.8 PgPb10563 QTL for Yield under terminal drought 200.7 PgPb11193 201.2 PgPb6613 PgPb6558 204.5 PgPb6013 205.8 PgPb8369 Bealet chromosome 2 206.6 PgPb8177 207.0 PgPb6628 PgPb7120 211.7 PgPb7413 218.4 Xipes0007 219.5 PgPb6184 221.1 PgPb11036 222.1 PgPb10525 222.6 PgPb6471 223.1 Xicmp3056 224.5 PgPb10361 225.0 Xipes0117 226.0 PgPb8259 231.8 PgPb8902 240.3 PgPb12641 242.2 PgPb6880 248.8 PgPb8268 255.2 PgPb9046 256.1 PgPb9970 258.7 PgPb8464 PgPb10086 260.7 PgPb8139 Tr 263.8 PgPb11702 266.5 PgPb8214 271.1 PgPb8035 274.9 PgPb9474 277.9 PgPb13146 287.0 PgPb8457 295.6 PgPb8244 299.1 PgPb9338 Tr 303.5 Xipes0003 304.9 PgPb11641 305.4 PgPb6117 307.5 PgPb9306 309.6 PgPb7336 315.3 PgPb11469 318.7 Xctm21 Tr 320.5 PgPb10526 322.3 PgPb8443 322.7 PgPb6665 324.4 PgPb13198 327.1 PgPb11611 327.5 Xpsmp2059 328.5 PgPb12897 331.9 PgPb8694 335.9 PgPb7330 341.5 Xipes0210 Xipes0218 344.6 PgPb6669 349.3 PgPb8856 351.6 PgPb12598 355.3 PgPb7028 355.7 PgPb7861 363.1 PgPb7019 PgPb13134 365.4 PgPb10206 370.3 Xipes0118
Example of loci interaction explaining Tr in Bealet Allele from parent A Allele from parent B High Tr in low VPD High Tr in high VPD Alleles interaction Multiple alleles depends interact on environment
Relation of water extracted at 3 weeks after anthesis and staygreen score 3 weeks stress 5 weeks stress R2 = 0.52 6 Stay-Green score 5 R2 = 0.70 4 3 2 1 0 0 500 1000 1500 2000 2500 Water extraction Bealet stays green because it extract more water
Allele effect Tolerant Sensitive Flowering time Increased decreased Xpsmp2237 Grain Yld decreased Increased 17.1 cM Tr rate Increased decreased Xpsmp2072 12.0 cM Xpsmp2066 decreased Increased Stay green decreased Increased Tr rate 19.1 cM Xibmsp23 Xpsmp3056 Xibmsp62 Xibmsp27 14.2 cM Xibmsp9 Xibmsp12 Stay green Xibmsp60 Xibmsp34 Increased decreased Xibmsp15 Xibmsp14 Xibmsp24 Xpsmp2206 decreased Increased Xibmsp31 Xibmsp11 2.5 cM Xibmsp44 Xpsmp2059 Xibmsp4 Grain Yld Flowering time Increased decreased Xibmsp7 Stay green Candidate genes Zn finger CCCH-type, serine/threonine protein kinase, MADS-box, acetyl CoA carboxylase Seghal et al (under review)

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TLI 2012: Physiology and breeding for complex constraints in legumes

  • 1. Physiology and breeding for Complex constraints
  • 2. Acceleration of breeding for drought tolerance requires deep understanding of GxExM interactions Regardless of crops G YIELD YIELD E M
  • 3. Scenario analysis – (Case of Sorpea in Inrica) Weather Drought scenario probability Identification of key traits – (Case of Bealet in Amefrica) what trait mapping loci interactions Any resemblance to any crop having existed can only be coincidental Nevertheless, data presented are real !!!
  • 5. 2 How to characterize Characterizing drought dynamics - based on S/D ratio simulation and clustering Type 3 intermittent stress Type 4 post-flowering stress Type 1 flowering stress Type 2 pre-flowering stress
  • 6. 2. Environmental patterns major stress patterns 1 0.8 vegetative pre-flowering 0.6 S/D post-flowering post-flowering relieved 0.4 mild 0.2 0 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 o thermal time ( D) 3. Which traits Sorpea growing area in Inrica confer advantage in the most frequent environment?
  • 7. LG 2 “Tolerant allele” M322 Any difference M394 Terminal M214 Drought in water saving 30 cM tolerance M321 M592 M443 ?? M356 M738 40 cM Tolerant has: Better seed setting Better grain filling Problem? Large interval Bealet Crop GxE
  • 8. Difference in Transpiration rate (g cm-2 d-1) In Bealet 0.26 LG 2 Tr (g H2O cm day ) 0.24 0.22 -1 M322 M394 0.2 -2 0.18 M214 M321 0.16 M592 M443 M356 0.14 M738 0.12 40cM 0.1 Sensitive Tolerant Tolerant Tolerant Tolerant genotypes
  • 9. Transpiration response to high VPD 0.045 Transpiration (g cm-2 h-1) 0.04 Terminal drought 0.035 sensitive 0.03 0.025 Terminal drought 0.02 tolerant 0.015 0.01 0.005 0.50 1.00 1.50 2.00 2.50 3.00 3.50 VPD (kPa) 2 mechanisms of water saving: Bealet Crop •Low Tr at low VPD •Further restriction of Tr at high VPD
  • 10. Mapping of water saving traits in Bealet Crop Weighing: 7-11am = low VPD 11am-15pm = high VPD RH & T hourly recording 4 replications 8” pots re-saturated every day soil evaporation minimized with plastic beads
  • 11. 0.0 PgPb8984 13.8 PgPb10594 29.8 PgPb8607 45.5 PgPb9081 Tr 63.9 PgPb11433 Quantitative traits usually influenced by multiple alleles 65.5 PgPb9681 100.8 PgPb9143 113.3 PgPb11732 whose effects can vary depending on environment 132.1 PgPb10852 142.0 PgPb9167 155.6 PgPb10902 167.7 Xctm03 178.4 PgPb7431 Yield and water saving trait QTLs 188.5 PgPb12731 191.8 PgPb7979 193.1 Xpsmp2237 196.3 PgPb8512 198.8 PgPb10563 QTL for Yield under terminal drought 200.7 PgPb11193 201.2 PgPb6613 PgPb6558 204.5 PgPb6013 205.8 PgPb8369 Bealet chromosome 2 206.6 PgPb8177 207.0 PgPb6628 PgPb7120 211.7 PgPb7413 218.4 Xipes0007 219.5 PgPb6184 221.1 PgPb11036 222.1 PgPb10525 222.6 PgPb6471 223.1 Xicmp3056 224.5 PgPb10361 225.0 Xipes0117 226.0 PgPb8259 231.8 PgPb8902 240.3 PgPb12641 242.2 PgPb6880 248.8 PgPb8268 255.2 PgPb9046 256.1 PgPb9970 258.7 PgPb8464 PgPb10086 260.7 PgPb8139 Tr 263.8 PgPb11702 266.5 PgPb8214 271.1 PgPb8035 274.9 PgPb9474 277.9 PgPb13146 287.0 PgPb8457 295.6 PgPb8244 299.1 PgPb9338 Tr 303.5 Xipes0003 304.9 PgPb11641 305.4 PgPb6117 307.5 PgPb9306 309.6 PgPb7336 315.3 PgPb11469 318.7 Xctm21 Tr 320.5 PgPb10526 322.3 PgPb8443 322.7 PgPb6665 324.4 PgPb13198 327.1 PgPb11611 327.5 Xpsmp2059 328.5 PgPb12897 331.9 PgPb8694 335.9 PgPb7330 341.5 Xipes0210 Xipes0218 344.6 PgPb6669 349.3 PgPb8856 351.6 PgPb12598 355.3 PgPb7028 355.7 PgPb7861 363.1 PgPb7019 PgPb13134 365.4 PgPb10206 370.3 Xipes0118
  • 12. Example of loci interaction explaining Tr in Bealet Allele from parent A Allele from parent B High Tr in low VPD High Tr in high VPD Alleles interaction Multiple alleles depends interact on environment
  • 13. Relation of water extracted at 3 weeks after anthesis and staygreen score 3 weeks stress 5 weeks stress R2 = 0.52 6 Stay-Green score 5 R2 = 0.70 4 3 2 1 0 0 500 1000 1500 2000 2500 Water extraction Bealet stays green because it extract more water
  • 14. Allele effect Tolerant Sensitive Flowering time Increased decreased Xpsmp2237 Grain Yld decreased Increased 17.1 cM Tr rate Increased decreased Xpsmp2072 12.0 cM Xpsmp2066 decreased Increased Stay green decreased Increased Tr rate 19.1 cM Xibmsp23 Xpsmp3056 Xibmsp62 Xibmsp27 14.2 cM Xibmsp9 Xibmsp12 Stay green Xibmsp60 Xibmsp34 Increased decreased Xibmsp15 Xibmsp14 Xibmsp24 Xpsmp2206 decreased Increased Xibmsp31 Xibmsp11 2.5 cM Xibmsp44 Xpsmp2059 Xibmsp4 Grain Yld Flowering time Increased decreased Xibmsp7 Stay green Candidate genes Zn finger CCCH-type, serine/threonine protein kinase, MADS-box, acetyl CoA carboxylase Seghal et al (under review)