escola tÈcnica superior denginyeria agrÀria (etsea) dr. gustavo a. slafer research professor of...

ESCOLA TÈCNICA ESCOLA TÈCNICA SUPERIOR D’ENGINYERIA SUPERIOR D’ENGINYERIA

AGRÀRIA (ETSEA)AGRÀRIA (ETSEA) www.icrea.eswww.icrea.es

Dr. Gustavo A. SlaferDr. Gustavo A. SlaferResearch Professor of Research Professor of ICREAICREA

Department of Crop & Forest SciencesDepartment of Crop & Forest SciencesUniversity of Lleida - University of Lleida - Centre UdL-IRTACentre UdL-IRTA

Do yield QTLs mean anything?Do yield QTLs mean anything?A crop-physiology perspectiveA crop-physiology perspective

Gustavo A. Slafer & Ignacio RomagosaGustavo A. Slafer & Ignacio Romagosa

3rd UK Cereal Genetics & Genomics Workshop3rd UK Cereal Genetics & Genomics WorkshopJohn Innes Centre Norwich UK, John Innes Centre Norwich UK, 6th & 7th April 20066th & 7th April 2006

• Yield of cereals has been very strongly increased Yield of cereals has been very strongly increased during the last half centuryduring the last half century ((e.g. e.g. Calderini & Slafer, 1998. Calderini & Slafer, 1998. Field Crops Res.,Field Crops Res., 57:335-347; Slafer & Peltonen-Sainio 57:335-347; Slafer & Peltonen-Sainio, 2001. , 2001. Agric. Food Sci. FinlandAgric. Food Sci. Finland 10:121-131; 10:121-131; Cassman et al., 2003. Cassman et al., 2003. Annu. Rev. Environ. Resour. 28:315–58Annu. Rev. Environ. Resour. 28:315–58))

• This was due to genetic improvements in both yield This was due to genetic improvements in both yield potential and in resistance to diseases as well as to potential and in resistance to diseases as well as to improvements in management improvements in management ((e.g.e.g. SSlafer & Andrade, lafer & Andrade, 1991. 1991. Euphytica,Euphytica, 58, 37-49; Austin, 1999. 58, 37-49; Austin, 1999. Crop ScienceCrop Science 39:1604- 39:1604-1610)1610)

• Improved yield potential has concomitantly improved Improved yield potential has concomitantly improved yield responsiveness to environment yield responsiveness to environment (Calderini & Slafer, (Calderini & Slafer, 1999. 1999. Euphytica 107: 51–59)Euphytica 107: 51–59)

Gustavo A. SlaferCentre UdL-IRTAUniversitat de LleidaUniversitat de Lleida

http://www.udl.es/

• Further improving yield potential seems not simple: it Further improving yield potential seems not simple: it implies that future genetic improvement should be as implies that future genetic improvement should be as efficient as it was in the past, but this time with cereal efficient as it was in the past, but this time with cereal cropscrops

-that have already received an intense breeding -that have already received an intense breeding efforteffort

-that possess a relatively high yield level-that possess a relatively high yield level (which, in turn, (which, in turn, is is likely the reason why genetic increases in wheat yields are likely the reason why genetic increases in wheat yields are becoming becoming increasingly harder to achieve; Reynolds increasingly harder to achieve; Reynolds et al.et al., 1996; In , 1996; In Increasing Increasing Yield Potential in Wheat: Breaking the BarriersYield Potential in Wheat: Breaking the Barriers. Mexico DF: . Mexico DF: CIMMYTCIMMYT))

-that have to be grown with agronomic practices -that have to be grown with agronomic practices more more sustainable than those used in the pastsustainable than those used in the past ((i.e.i.e. part of the part of the past past yield gains related to the increased use of inputs, largely fertilizers yield gains related to the increased use of inputs, largely fertilizers and and pesticides, must be replaced by breeding)pesticides, must be replaced by breeding)

• In this context, it may be useful to complement In this context, it may be useful to complement traditional breeding with other approachestraditional breeding with other approaches


http://www.udl.es/

As molecular biology has the potential to identify and As molecular biology has the potential to identify and map particular genes or QTLs related to any trait - even map particular genes or QTLs related to any trait - even quite complex ones such as WUE, NUE or yield…quite complex ones such as WUE, NUE or yield…

… … and its usefulness in the case of traits controlled by and its usefulness in the case of traits controlled by major major (or few)(or few) genes is beyond any questioning genes is beyond any questioning

It is tempting to believe that the issue will be resolved It is tempting to believe that the issue will be resolved with molecular biology tools, by simply identifying with molecular biology tools, by simply identifying Yield-QTLs and complement traditional breeding with Yield-QTLs and complement traditional breeding with marker assisted selectionmarker assisted selection


http://www.udl.es/

However, when dealing with complex traits However, when dealing with complex traits (such as (such as

yield) yield) the effort of finding appropriate QTLs has the effort of finding appropriate QTLs has experienced problems in experienced problems in accuracyaccuracy, , trustworthinesstrustworthiness and and applicabilityapplicability

Most of these problems seem related to theMost of these problems seem related to the dependence on the genetic background of the dependence on the genetic background of the

mapping populationmapping population strong G x E interaction when the QTL has been strong G x E interaction when the QTL has been

identifiedidentified ((e.ge.g. . Romagosa et al. 1996. Theoretical & Applied Genetics 93:30-37))


http://www.udl.es/

Although I cannot discuss the issue further here…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] Ann. Appl. Biol. [2003] 142:117-128142:117-128; and see also Sinclair et al., 2004. Trends in Plant Science Trends in Plant Science 9:70-759:70-75; Slafer et al., 2005. Ann. Appl. Biol. 146:61–70Ann. Appl. Biol. 146:61–70; and Wollenweber et al., 2005. Current Opinion in Plant Biology 8:337-341Current Opinion in Plant Biology 8:337-341) …I would like to strongly suggest that these two problems may …I would like to strongly suggest that these two problems may be behind the scientific curiosity that while the literaturebe behind the scientific curiosity that while the literature

.- is plenty of papers with mapped QTLs for yield.- 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.- is virtually empty, as far as I am aware,, as far as I am aware, of clear successful of clear successful ‘case-stories’ in which a QTL for yield may work in different ‘case-stories’ in which a QTL for yield may work in different populations and environments to those in which it was mappedpopulations and environments to those in which it was mapped


http://www.udl.es/

It seems clear that we can map virtually any traitIt seems clear that we can map virtually any trait

but when it comes to yield but when it comes to yield (or any other complex trait, (or any other complex trait, e.g.e.g.

WUE, NUE, tolerance to complex abiotic stresses)WUE, NUE, tolerance to complex abiotic stresses) the direct the direct identification of QTLs in a mapping population doesn’t identification of QTLs in a mapping population doesn’t seem quite useful in practice …seem quite useful in practice …

… … unless the identification of the Yield-QTL is just the unless the identification of the Yield-QTL is just the first step in a “top-down” approach to identify relatively first step in a “top-down” approach to identify relatively simple traits related to yield simple traits related to yield (though in this case, chances (though in this case, chances are that the GxE interaction for these traits may be similar than are that the GxE interaction for these traits may be similar than that for yield)that for yield)


http://www.udl.es/

The problem with the “top-down” approach is that any The problem with the “top-down” approach is that any trait that might be putatively associated with yield but trait that might be putatively associated with yield but whose magnitude of effect may be relatively small whose magnitude of effect may be relatively small would hardly be uncovered.would hardly be uncovered. This may be irrelevant for a crop with little selection This may be irrelevant for a crop with little selection pressure imposed in the past, but for most important pressure imposed in the past, but for most important crops we need “fine-tuning” for further rising yieldcrops we need “fine-tuning” for further rising yield

For uncovering these possible traits a bottom-up For uncovering these possible traits a bottom-up approach might be rewarding, but avoiding the failures approach might be rewarding, but avoiding the failures of the past physiological attempts based on traits at a of the past physiological attempts based on traits at a far lower level of organisation to that of crop yield, far lower level of organisation to that of crop yield, assuming assuming –perhaps unconsciously- that the interactions that the interactions among traits at different levels of organisation might be among traits at different levels of organisation might be negligible…negligible…


http://www.udl.es/

Figures from Figures from Structuralism Structuralism by Jean Piagetby Jean Piaget

Passioura (1979) Accountability, Philosophy and Plant Physiology Passioura (1979) Accountability, Philosophy and Plant Physiology Search 10:347-350Search 10:347-350 Gustavo A. SlaferCentre UdL-IRTAUniversitat de LleidaUniversitat de Lleida

http://www.udl.es/

Would it be possible to identify traits that being simple Would it be possible to identify traits that being simple (controlled by major -or at least few- genes)(controlled by major -or at least few- genes) would be almost would be almost unequivocally related to yield unequivocally related to yield (naturally under in field conditions)(naturally under in field conditions)??

As yield is strongly related to number of grains per mAs yield is strongly related to number of grains per m22 (grain (grain weight seem to be strongy sink-limited during the effective grain filling weight seem to be strongy sink-limited during the effective grain filling

period, at least in healthy crops)period, at least in healthy crops) I will I will

((ii) describe very briefly a major physiological attribute ) describe very briefly a major physiological attribute (almost)(almost) universally related to grain numberuniversally related to grain number

and and

((iiii) Discuss some approaches to identify genetic bases for this ) Discuss some approaches to identify genetic bases for this physiological determinant of grain number physiological determinant of grain number (and yield)(and yield)


Sw Em At DR FI BGF TS

Timing when yield is mostly affected

Nu

mb

er o

f gr

ain

s p

er u

init

lan

d

Nu

mb

er o

f gr

ain

s p

er u

init

lan

d

area

ar

ea (%

uns

tres

sed)

(% u

nstr

esse

d)

Anthesis

Ste

mS

tem

or

Sp

ike

Sp

ike

dry

mat

ter


http://www.udl.es/

Spike weight at anthesis (g m-2)

Fer

tile

flo

rets

or

gra

ins

(m-2)

Due to radiation levelsFischer, 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)

Slafer et al 2005, Ann Appl Biol 146,61-70Slafer et al 2005, Ann Appl Biol 146,61-70 Gustavo A. SlaferCentre UdL-IRTAUniversitat de LleidaUniversitat de Lleida

http://www.udl.es/

Anthesis


Ste

mS

tem

or

Sp

ike

Sp

ike

dry

mat

ter

Spike growthSpike growthraterate

Spike growthSpike growthdurationduration


http://www.udl.es/


Ste

m o

ror S

pik

e d

ry m

atte

r

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).

G YieldG Yield H IndexH Index

G NumberG NumberSDW anthSDW anth

(due to smaller stems)(due to smaller stems) Height!Height!

Traditional cultivarModern cultivar


http://www.udl.es/


Fer

tile

flo

rets

or

gra

ins

(m-2)

Due to radiation levelsFischer, 1985; Thorne & Wood, 1987; Savin & Slafer, 1991; Abbate et al., 1995; Demontes-Meinard et al., 1999

Due to genetics (semidwarf vs tall cvs.)Brooking & Kirby, 1981; Stockman et al., 1983; Miralles et al., 1998

Slafer et al 2005, Ann Appl Biol 146,61-70Slafer et al 2005, Ann Appl Biol 146,61-70

Due to genetics (old vs modern cvs.)Siddique et al., 1989;Slafer & Andrade, 1993

Slafer et al., 1994(modern-old x shading treatments)

Due to genetics (Introgression of Lr19 from A. elongatum)Reynolds et al., 2001


http://www.udl.es/


Ste

m o

ror S

pik

e d

ry m

atte

r

Traditional cultivarModern cultivar G YieldG Yield

H IndexH Index G NumberG NumberSDW anthSDW anth

(due to smaller stems)(due to smaller stems) Height!Height!

Modern cvs already have “optimum stature” (e.g. Richards 1992; Miralles & Slafer, 1995)

Modern cvs already have HI close to maximum (e.g. review by Calderini, Reynolds & Slafer, 1999)

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


http://www.udl.es/

YieldYield

Spike Dry Weight (Anthesis)

Spike DW

Gra

in #

Grain number m-2

Grain #

Gra

in Y

ield

Breeding effectsBreeding effects

Most management Most management effectseffects

Length of the growth

period

Crop growth rate

Partitioning to growing

spikes


Anthesis


Sp

ike

dry

mat

ter

Ste

m d

ry m

atte

r

Nu

mb

er o

f gr

ain

s p

er

uin

it la

nd

are

a (%

uns

tres

sed)

GrowthGrowth PartitioningPartitioning SDW anth SDW anth GNumberGNumber

Photoperiod sensitivity?Intrinsic earliness?

Length of critical Length of critical phasephase


http://www.udl.es/

Variation in stem elongation phase (independent of cycle length) Slafer, 2003. Ann. Appl. Biol.,

142:117-128

0 200 400 600 800 1000 1200 1400

BUCK CHAMBERGO

KLEIN DON ENRIQUE

Whe

atW

heat

Sho

rt c

ycle

Sho

rt c

ycle

1600

BONAER. ALAZAN

KLEIN ESTRELLA

Whe

at

Whe

at

Lon

g cy

cle

Lon

g cy

cle

Thermal time from seedling emergence (°C d)0 500 1000 1500 2000 2500

Ker

nic

h

Ker

nic

h e

t al.

et a

l. (

1997

) (

1997

)A

ust.

J. A

gric

Res

Aus

t. J.

Agr

ic R

es

PROCTOR

WEEAH

SCHOONER

TRIUMPH

Bar

ley

Bar

ley

Sho

rt c

ycle

Sho

rt c

ycle

Bar

ley

Bar

ley

Lon

g cy

cle

Lon

g cy

cle

Wh

itec

hu

rch

W

hit

ech

urc

h e

t al.

et a

l.un

der

revi

sion

unde

r re

visi

on

Differences may be due to photoperiod or earliness Differences may be due to photoperiod or earliness per seper se

Sowing-jointing Stem Elongation


http://www.udl.es/

• We conducted several studies manipulating We conducted several studies manipulating photoperiod throughout the season for a single photoperiod throughout the season for a single sowing date in which sowing date in which

• (i) sensitivity of the length of the stem elongation (i) sensitivity of the length of the stem elongation was clear, and was clear, and

• (ii) changes in number of fertile florets or grains (ii) changes in number of fertile florets or grains were associated with changes in duration of were associated with changes in duration of stem elongation 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


http://www.udl.es/

• Then we determined (in a phytotron) that direct Then we determined (in a phytotron) that direct photoperiod effects on this phase were likely and that photoperiod effects on this phase were likely and that these effects were correlated to changes in number of these effects were correlated to changes in number of fertile florets at anthesis fertile florets at anthesis ((Miralles & Richards, 2000. Ann Bot, 85:655-663 Miralles, Richards & Slafer, 2000. Aust J Plant Physiol, 27:931-940)

• Gabriela Abeledo Gabriela Abeledo (Slafer and Abeledo, unpublished) and and more recently Fernanda González more recently Fernanda González (e.g. González, Slafer &

Miralles, 2003. Field Crops Res.) studied these effects in studied these effects in field plotsfield plots


http://www.udl.es/

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

0

0.1

0.2

0.3

0.4

400 600 800 1000 1200

+6

+0

Thermal time (ºCd)D

ry m

atte

r (g

/sp

ike)

Buck ManantialBuck Manantial

0 200 400 600 800 1000 1200

50 d

+0

+6

Thermal time (ºCd)

15 d

+0+6

TSITSI


http://www.udl.es/

0

5

10

15

20

25

0 2 4 6Fertile florets

Sp

ikel

et p

osi

tio

n w

ith

in t

he

spik

e

González, Slafer & Miralles, 2003 , Field Crops Res 81:29-38

0

200

400

600

+0+6

Ste

m e

lon

gat

ion

(ºC

d)

Photoperiod extension (h)


http://www.udl.es/

0 20 40 60 80 100 120 140

TR-TS TS-Ant C

TR-TS

TR-TS

TS-Ant C

TS-Ant C

TS-An Sw

TS-An Sw

TS-An Sw

Days after transplant

Vazquez et al. 2005, 2006(M Sci. Thesis candidate)

ppd-D1

ppd-B1

ppd-D1

Ppd-B1

Ppd-D1

ppd-B1


Fer

tile

flo

rets

or

gra

ins

(m-2)

Due to photoperiod effects on the length of stem elongationMiralles et al., 2000 ; Slafer et al., 2001; González et al., 2003; González et al., 2005


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


Slafer et al., 1994



Fer

tile

flo

rets

or

gra

ins

(m-2)


Due to photoperiod sensitivity genes???Due to photoperiod sensitivity genes???

Due to photoperiod effects on the length of stem elongationMiralles et al., 2000 ; Slafer et al., 2001; González et al., 2003; González et al., 2005


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

Slafer et al., 1994


6

8

10

12

14

16

18 Mercia isogenic lines (recessive, Ppd-D1 and Ppd-B1)

R2 = 0.80p < 0.001

20 40 60 80 100 120 140Main shoot spike dry weight (g m-2)N

um

ber

of

fert

ile f

lore

ts (

10-3 m

-2)

González, Slafer & Miralles, 2006 , EuphyticaGustavo A. Slafer

Centre UdL-IRTAUniversitat de LleidaUniversitat 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


Lack of consistency may be due to

•interactions with genetic background

• interactions with 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)


Genetic control of duration of stem elongation• Population Oregon Wolfe Barley, 94 di-haploid lines, extreme

morphological variation• Glasshouse study under natural photoperiod

250

500

750

1000Stem elongation (ºC d)

Lines

Th

erm

al t

ime

(ºC

d)

250

500

750

1000Sowing to the onset of stem elongation (ºC d)

Th

erm

al t

ime

(ºC

d)

Lines

Martí, Romagosa & Slafer, unpublishedGustavo A. Slafer


Sowing-onset stem elongationSowing-onset stem elongation

Stem elongationStem elongation

02 3 5 6 8 9

LO

DL

OD

0235689

LO

DL

OD

Martí, Romagosa & Slafer, unpublished

1(7H) 2(2H) 3(3H) 4(4H) 5(1H) 6(6H) 7(5H) Chromosome


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 Gustavo A. Slafer


Identifying QTLs for yield or any complex trait may be Identifying QTLs for yield or any complex trait may be only useful as an initial step for uncovering bases only useful as an initial step for uncovering bases (genetic and (genetic and physiological)physiological) useful for further rise productivity useful for further rise productivity

This top-down approach to uncover useful bases might not This top-down approach to uncover useful bases might not identify traits that being putatively related to tield may still identify traits that being putatively related to tield may still have a relatively small impact compared with that of large have a relatively small impact compared with that of large differences in biomass or partitioningdifferences in biomass or partitioning

A bottom-up approach should only be followed with traits A bottom-up approach should only be followed with traits putatively related to the complex trait we are interested in, putatively related to the complex trait we are interested in, and only under realistic (field) conditionsand only under realistic (field) conditions

ConclusionsConclusions


One alternative might be increasing sensitivity to One alternative might be increasing sensitivity to photoperiod in the late reproductive phase so that stem photoperiod in the late reproductive phase so that stem elongation becomes longer elongation becomes longer (combined with a shorter vegetative+early (combined with a shorter vegetative+early

reproductive phases)reproductive phases) then increasing growth when the then increasing growth when the inflorescences grow and reducing rate of degeneration of inflorescences grow and reducing rate of degeneration of floret primordiafloret primordia

The alternative seemed likely from experiments The alternative seemed likely from experiments manipulating either photoperiod or photoperiod-sensitivity manipulating either photoperiod or photoperiod-sensitivity genesgenes

Although with only incipient results so far, it seemed that Although with only incipient results so far, it seemed that genetic control of duration of different pre-anthesis phases genetic control of duration of different pre-anthesis phases may be at least partially independent, though the genetic may be at least partially independent, though the genetic bases seems not simplebases seems not simple

ConclusionsConclusions


ACKNOWLEDGEMENTSACKNOWLEDGEMENTS

L. Gabriela L. Gabriela ABELEDOABELEDO

Eileen M. Eileen M. WHITECHURCHWHITECHURCH

Fernanda G. Fernanda G. GONZALEZGONZALEZ

Daniel J. Daniel J. MIRALLESMIRALLES

IgnacioIgnacioROMAGOSAROMAGOSA

Jordi Jordi MARTIMARTI

Gisela Gisela BORRASBORRAS


escola tÈcnica superior denginyeria agrÀria (etsea) dr. gustavo a. slafer research professor of...

Documents

yield of cereals

improved yield potential

increasing yield potential

improved yield responsiveness

slafer andrade

past yield gains

high yield level

environment calderini