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ESCOLA TÈCNICA SUPERIOR D’ENGINYERIA AGRÀRIA (ETSEA)

3rd UK Cereal Genetics & Genomics Workshop John Innes Centre Norwich UK, 6th & 7th April 2006. Do yield QTLs mean anything? A crop-physiology perspective Gustavo A. Slafer & Ignacio Romagosa. Dr. Gustavo A. Slafer Research Professor of ICREA Department of Crop & Forest Sciences

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ESCOLA TÈCNICA SUPERIOR D’ENGINYERIA AGRÀRIA (ETSEA)

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  1. 3rd UK Cereal Genetics & Genomics Workshop John Innes Centre Norwich UK, 6th & 7th April 2006 Do yield QTLs mean anything? A crop-physiology perspective Gustavo A. Slafer & Ignacio Romagosa Dr. Gustavo A. Slafer Research Professor of ICREA Department of Crop & Forest Sciences University of Lleida - Centre UdL-IRTA ESCOLA TÈCNICA SUPERIOR D’ENGINYERIA AGRÀRIA (ETSEA) www.icrea.es

  2. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida • Yield of cereals has been very strongly increased during the last half century(e.g. Calderini & Slafer, 1998. Field Crops Res., 57:335-347; Slafer & Peltonen-Sainio, 2001. Agric. Food Sci. Finland 10:121-131; Cassman et al., 2003. Annu. Rev. Environ. Resour. 28:315–58) • This was due to genetic improvements in both yield potential and in resistance to diseases as well as to improvements in management (e.g.Slafer & Andrade, 1991. Euphytica, 58, 37-49; Austin, 1999. Crop Science 39:1604-1610) • Improved yield potential has concomitantly improved yield responsiveness to environment (Calderini & Slafer, 1999. Euphytica 107: 51–59)

  3. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida • Further improving yield potential seems not simple: it implies that future genetic improvement should be as efficient as it was in the past, but this time with cereal crops -that have already received an intense breeding effort -that possess a relatively high yield level(which, in turn, is likely the reason why genetic increases in wheat yields are becoming increasingly harder to achieve; Reynolds et al., 1996; In Increasing Yield Potential in Wheat: Breaking the Barriers. Mexico DF: CIMMYT) -that have to be grown with agronomic practices more sustainable than those used in the past(i.e. part of the past yield gains related to the increased use of inputs, largely fertilizers and pesticides, must be replaced by breeding) • In this context, it may be useful to complement traditional breeding with other approaches

  4. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida As molecular biology has the potential to identify and map particular genes or QTLs related to any trait - even quite complex ones such as WUE, NUE or yield… … and its usefulness in the case of traits controlled by major (or few) genes is beyond any questioning It is tempting to believe that the issue will be resolved with molecular biology tools, by simply identifying Yield-QTLs and complement traditional breeding with marker assisted selection

  5. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida However, when dealing with complex traits (such as yield) the effort of finding appropriate QTLs has experienced problems in accuracy, trustworthiness and applicability Most of these problems seem related to the • dependence on the genetic background of the mapping population • strong G x E interaction when the QTL has been identified(e.g. Romagosa et al. 1996. Theoretical & Applied Genetics 93:30-37)

  6. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Although I cannot discuss the issue further here…(but, if you are interested, see details behind this reasoning in “Genetic basis of yield as viewed from a crop physiologist’s perspective” in Ann. Appl. Biol. [2003] 142:117-128; and see also Sinclair et al., 2004. Trends in Plant Science 9:70-75; Slafer et al., 2005. Ann. Appl. Biol. 146:61–70; and Wollenweberet al., 2005. Current Opinion in Plant Biology 8:337-341) …I would like to strongly suggest that these two problems may be behind the scientific curiosity that while the literature .- is plenty of papers with mapped QTLs for yield(that might be “easily” introgressed in the breeding program by marker assisted selection) .- is virtually empty, as far as I am aware, of clear successful ‘case-stories’ in which a QTL for yield may work in different populations and environments to those in which it was mapped

  7. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida It seems clear that we can map virtually any trait but when it comes to yield (or any other complex trait, e.g. WUE, NUE, tolerance to complex abiotic stresses) the direct identification of QTLs in a mapping population doesn’t seem quite useful in practice … … unless the identification of the Yield-QTL is just the first step in a “top-down” approach to identify relatively simple traits related to yield (though in this case, chances are that the GxE interaction for these traits may be similar than that for yield)

  8. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida The problem with the “top-down” approach is that any trait that might be putatively associated with yield but whose magnitude of effect may be relatively small would hardly be uncovered. This may be irrelevant for a crop with little selection pressure imposed in the past, but for most important crops we need “fine-tuning” for further rising yield For uncovering these possible traits a bottom-up approach might be rewarding, but avoiding the failures of the past physiological attempts based on traits at a far lower level of organisation to that of crop yield, assuming –perhaps unconsciously- that the interactions among traits at different levels of organisation might be negligible…

  9. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Figures from Structuralism by Jean Piaget Passioura (1979) Accountability, Philosophy and Plant Physiology Search 10:347-350

  10. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Would it be possible to identify traits that being simple (controlled by major -or at least few- genes) would be almost unequivocally related to yield (naturally under in field conditions)? As yield is strongly related to number of grains per m2(grain weight seem to be strongy sink-limited during the effective grain filling period, at least in healthy crops) I will (i) describe very briefly a major physiological attribute (almost) universally related to grain number and (ii) Discuss some approaches to identify genetic bases for this physiological determinant of grain number (and yield)

  11. Anthesis Stem orSpike dry matter BGF Sw At Em FI DR TS Timing when yield is mostly affected Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Number of grains per uinit land area (% unstressed)

  12. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Due to radiation levels Fischer, 1985 (Mexico-Australia); Thorne & Wood, 1987 (United Kingdom); Savin & Slafer, 1991 (Argentina); Abbate et al., 1995 (Argentina, Southern wheat belt); Demontes-Meinard et al., 1999 (France) Fertile florets or grains (m-2) Spike weight at anthesis (g m-2) Slafer et al 2005, Ann Appl Biol 146,61-70

  13. BGF Sw At Em FI DR TS Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Anthesis Stem orSpike dry matter Spike growth rate Spike growth duration

  14. BGF Sw At Em FI DR TS Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida The growth of the spikes in this very short window of time is so relevant that most of the breeding success on improving wheat yields were based on improving this trait (e.g. Slafer et al, 1994; Calderini et al., 1999). Traditional cultivar • G Yield • H Index • G Number • SDW anth (due to smaller stems) • Height! Modern cultivar StemorSpike dry matter

  15. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Due to radiation levels Fischer, 1985; Thorne & Wood, 1987; Savin & Slafer, 1991; Abbate et al., 1995; Demontes- Meinard et al., 1999 Slafer et al., 1994 (modern-old x shading treatments) Due to genetics (semidwarf vs tall cvs.) Brooking & Kirby, 1981; Stockman et al., 1983; Miralles et al., 1998 Due to genetics (old vs modern cvs.) Siddique et al., 1989; Slafer & Andrade, 1993 Fertile florets or grains (m-2) Due to genetics (Introgression of Lr19 from A. elongatum) Reynolds et al., 2001 Spike weight at anthesis (g m-2) Slafer et al 2005, Ann Appl Biol 146,61-70

  16. BGF Sw At Em FI DR TS Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida If further genetic gains in number of grains per m2 are attempted, which would be sound as even modern cultivars are mostly sink-limited during grain filling, future breeding must find alternatives to biomass partitioning between the growing stems and spikes Traditional cultivar Modern cultivar • G Yield • H Index • G Number • SDW anth (due to smaller stems) • Height! Modern cvs already have HI close to maximum (e.g. review by Calderini, Reynolds & Slafer, 1999) StemorSpike dry matter Modern cvs already have “optimum stature” (e.g. Richards 1992; Miralles & Slafer, 1995)

  17. Grain Yield Grain number m-2 Grain # Breeding effects Spike Dry Weight (Anthesis) Grain # Spike DW Partitioning to growing spikes Most management effects Crop growth rate Length of the growth period Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Yield

  18. Anthesis Length of critical phase Number of grains per uinit land area (% unstressed) Spike dry matter Stem dry matter • Growth • Partitioning • SDW anth • GNumber Photoperiod sensitivity? Intrinsic earliness? BGF Sw At Em FI DR TS Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida

  19. Variation in stem elongation phase (independent of cycle length) Slafer, 2003. Ann. Appl. Biol., 142:117-128 BONAER. ALAZAN Wheat Long cycle KLEIN ESTRELLA SCHOONER Barley Short cycle WEEAH Kernich et al. (1997) Aust. J. Agric Res PROCTOR 0 500 1000 1500 2000 2500 Barley Long cycle TRIUMPH Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida KLEIN DON ENRIQUE Stem Elongation Sowing-jointing Wheat Short cycle BUCK CHAMBERGO Whitechurch et al. under revision 1600 0 200 400 600 800 1000 1200 1400 Thermal time from seedling emergence (°Cd) Differences may be due to photoperiod or earliness per se

  20. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida • We conducted several studies manipulating photoperiod throughout the season for a single sowing date in which • (i) sensitivity of the length of the stem elongation was clear, and • (ii) changes in number of fertile florets or grains were associated with changes in duration of stem elongation Slafer & Rawson, 1995 J Expt Bot, 46:1877-1886, Slafer & Rawson, 1996. Field Crops Res, 46:1-13, Slafer & Rawson, 1997. Aust J Plant Physiol, 24:151-158, Whitechurch & Slafer, 2001. Euphytica, 118:47-51, Miralles, Ferro & Slafer,2001. Field Crops Res, 71:211-223, Slafer et al.,2001. Euphytica, 119:191-197

  21. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida • Then we determined (in a phytotron) that direct photoperiod effects on this phase were likely and that these effects were correlated to changes in number of fertile florets at anthesis (Miralles & Richards, 2000. Ann Bot, 85:655-663Miralles, Richards & Slafer,2000. Aust J Plant Physiol, 27:931-940) • Gabriela Abeledo (Slafer and Abeledo, unpublished)and more recently Fernanda González (e.g. González, Slafer & Miralles, 2003. Field Crops Res.) studied these effects in field plots

  22. Buck Manantial +6 TSI 0.4 0.3 +0 +6 15 d +0 Dry matter (g/spike) 0.2 0.1 +6 50 d +0 0 0 200 400 600 800 1000 1200 400 600 800 1000 1200 Thermal time (ºCd) Thermal time (ºCd) Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Extended photoperiod only during TSI-Anthesis (+6 h) or natural (+0 h) throughout, under field conditions (González, Slafer & Miralles, FCR, 2003). Study included 15 or 50 d of vernalizaton but BM is insensitive

  23. 25 Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida 600 400 20 Stem elongation (ºCd) 200 15 0 Spikelet position within the spike +6 +0 Photoperiod extension (h) 10 5 0 0 2 4 6 Fertile florets González, Slafer & Miralles, 2003 , Field Crops Res 81:29-38

  24. TS-An Sw Vazquez et al. 2005, 2006 (M Sci. Thesis candidate) TS-An Sw ppd - D1 TR-TS TS-Ant C TS-An Sw ppd - B1 TR-TS TS-Ant C ppd - D1 Ppd - D1 Ppd - B1 ppd - B1 TR-TS TS-Ant C 0 20 40 60 80 100 120 140 Days after transplant

  25. Due to radiation levels Fischer, 1985; Thorne & Wood, 1987; Savin & Slafer, 1991; Abbate et al., 1995; Demontes-Meinard et al., 1999 Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Slafer et al., 1994 Due to genetics Brooking & Kirby, 1981; Stockman et al., 1983; Siddique et al., 1989; Slafer & Andrade, 1993; Miralles et al., 1998; Reynolds et al., 2001 Due to photoperiod effects on the length of stem elongation Miralles et al., 2000 ; Slafer et al., 2001; González et al., 2003; González et al.,2005 Fertile florets or grains (m-2) Spike weight at anthesis (g m-2) Slafer et al 2005, Ann Appl Biol 146,61-70

  26. Due to radiation levels Fischer, 1985; Thorne & Wood, 1987; Savin & Slafer, 1991; Abbate et al., 1995; Demontes-Meinard et al., 1999 Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Slafer et al., 1994 Due to genetics Brooking & Kirby, 1981; Stockman et al., 1983; Siddique et al., 1989; Slafer & Andrade, 1993; Miralles et al., 1998; Reynolds et al., 2001 Due to photoperiod effects on the length of stem elongation Miralles et al., 2000 ; Slafer et al., 2001; González et al., 2003; González et al.,2005 Fertile florets or grains (m-2) Due to photoperiod sensitivity genes??? Spike weight at anthesis (g m-2) Slafer et al 2005, Ann Appl Biol 146,61-70

  27. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Mercia isogenic lines (recessive, Ppd-D1 and Ppd-B1) 18 R2 = 0.80 p < 0.001 16 14 Number of fertile florets (10-3 m-2) 12 10 8 6 20 40 60 80 100 120 140 Main shoot spike dry weight (g m-2) González, Slafer & Miralles, 2006 , Euphytica

  28. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Ppd-D1→ Yes→Scarth et al., 1985 - (Ann. Bot.) →Gonzalez et al., 2006 (Euphytica) → No→Foulkes et al., 2004 - (Euphytica) Ppd-B1→ Yes→Whitechurch & Slafer, 2001 (Euphytica) → Yes→Whitechurch & Slafer, 2002 (Field C. Res) → No→Gonzalez et al., 2006 (Euphytica) → No→Scarth et al., 1985 - (Ann. Bot.) Ppd-A1→ No studies that I am aware

  29. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Lack of consistency may be due to • interactions with genetic background • interactionswith environmental background (in which treatments were imposed) • Different types of lines (with more or less contributions from other genes to the different phenotype) • Lack of knowledge on the effects of Ppd alleles that have not been discovered yet but must be located in chromosomes 1 and 6, from evidences available on photoperiod sensitive genes in barley (Snape et al., 2001; Euphytica 119)

  30. 1000 Sowing to the onset of stem elongation (ºC d) 750 Thermal time (ºC d) 500 250 Lines 1000 Stem elongation (ºC d) 750 Thermal time (ºC d) 500 250 Lines Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Genetic control of duration of stem elongation • Population Oregon Wolfe Barley, 94 di-haploid lines, extreme morphological variation • Glasshouse study under natural photoperiod Martí, Romagosa & Slafer, unpublished

  31. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida 1(7H) 2(2H) 3(3H) 4(4H) 5(1H) 6(6H) 7(5H) Chromosome 9 Sowing-onset stem elongation 8 6 LOD 5 3 2 0 9 Stem elongation 8 6 5 LOD 3 2 0 Martí, Romagosa & Slafer, unpublished

  32. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Genetic control of duration of stem elongation • Population from Wageningen University, 120 di-haploid lines, parents differing in yield potential and yield stability (Meltan x Hennie) • Field study in two contrasting conditions (Gimenells = irrigated and Foradada = rainfed) • It was found, in both experiments, that the duration of phases occurring before or after the onset of stem elongation were controlled, in part, by independent QTLs, • For the stem elongation phase we found a QTL located in chromosome 2 (LOD=4.5) that did not affect development before jointing…. But this is in conflict with results from the OWB population (chromosome 1), indicating that the genetic control may be more complex than I expected beforehand Borras, Slafer, Romagosa & van Eeuwijk, unpublished

  33. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Conclusions • Identifying QTLs for yield or any complex trait may be only useful as an initial step for uncovering bases (genetic and physiological) useful for further rise productivity • This top-down approach to uncover useful bases might not identify traits that being putatively related to tield may still have a relatively small impact compared with that of large differences in biomass or partitioning • A bottom-up approach should only be followed with traits putatively related to the complex trait we are interested in, and only under realistic (field) conditions

  34. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida Conclusions • One alternative might be increasing sensitivity to photoperiod in the late reproductive phase so that stem elongation becomes longer (combined with a shorter vegetative+early reproductive phases)then increasing growth when the inflorescences grow and reducing rate of degeneration of floret primordia • The alternative seemed likely from experiments manipulating either photoperiod or photoperiod-sensitivity genes • Although with only incipient results so far, it seemed that genetic control of duration of different pre-anthesis phases may be at least partially independent, though the genetic bases seems not simple

  35. Gustavo A. Slafer Centre UdL-IRTA Universitat de Lleida ACKNOWLEDGEMENTS Daniel J. MIRALLES Eileen M. WHITECHURCH Fernanda G. GONZALEZ Ignacio ROMAGOSA Gisela BORRAS L. Gabriela ABELEDO Jordi MARTI

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