1/23/20181

Could small-seeded wild relatives of cultivated

peanut be used to increase the size of peanut

seeds?

Fonceka D., Tossim H-A, Nguepjop J.R., Bertioli D.,

Leal-Bertioli S., Jackson S., Rami J.F., Ozias-Akins P.,

PAG– Junuary 2018

Peanut: important food and cash crop



Peanut (Arachis hypogaea L.) is

cultivated in about 120 countries in

the world



Peanut is mainly used to produce

edible oil and for human and animal

consumption.

Tetraploidization

+ domestication

Cultivated peanut: Allotetraploid (AABB)

with low allelic diversity

data from http://www.ars-grin.gov

How about the

allelic diversity

that remains in

wild species?

Genome

duplication

Genetic

improvement

Domestication

Synthetic

tetraploids from

different wild

diploid

species

genomes

Molecular

markers

Exploiting the wide diversity within peanut wild

relatives

A. duranensis

A. ipaensis

A. batizocoi

A. valida

A. hypogaea

Var Fleur11

IS

A

TG

R

2

7

8

-18

F

1

between ISATGR 52B x Fleur11

X

Widening the genepool of cultivated peanut

A. ipaensis

A. correntina

A. villosa

A. hypogaea

Var Fleur11

X

X

A. batizocoi

A. stenosperma

Fleur11(AABB)

AB-QTL

(BC2F3, BC2F4, BC3F2)

x

F

1

BC

4

F

1

A. ipaensis (BB) or A. batizocoi (KK) x A. duranensis (AA)

F

1

sterile

colchicine

AABB or AAKK synthetic

CSSL

(BC

4

F

3

)

Genetic map

Population development using (A. ipaensis x A.

duranensis)

4x

_{and (A. batizocoi x A. duranensis)}

4x



2 years, three locations under rainfed

or off-season environnements



Several traits including

– Biomass

– Plant, pod and seed morphology

– Yield components



Alpha-lattice design

– 3 replication per location

AB-QTLs

AB-QTLs phenotyping in Senegal

a01 b01 a02 b02 a03 b03 a04 b04 a05 b05

a06b06 a07 b07 a08 b08 a09 b09 a10 b10

b11 P n_ w w P w _w w S hw _ w w H I_ w l H I_ w w H w _ w l H w _ w w P b_ w l P b_ w w P c_ w w S TI-Hw G H _ w w P H _w w H w _ w l P n_ w w S n_ w w S TI-Hw S TI-Pn S TI-Pw S TI-Sw S TI-Tb Tb _ w l Tb _ w w G H _ w w H sw _w l H sw _w w P b_ w l P b_ w w P c_ w w P c_ w w P H _ w w P l_ w w P w i_ w l P w i_ w w S l_ w l S l_ w w S s_ w l S s_ w w S T I-H s w S T I-Pn S T I-Sn S w i_ w l S w i_ w l S w i_ w w S w i_ w w P b_ w w P c_ w w P l_ w l P w i_ w w S l_ w w P b _w w P c _w w P l_ w l S l_ w w P c _w w P w i_ w l P w i_ w w H pw _w l H pw _w w H sw _ w l H sw _ w w P b_ w l P w i_ w l P w i_ w w S s_ w l S s_ w w S TI-H p w S TI-H s w S w i_ w l S w i_ w w P m a t_ w w G H _ w w P H _w w G H _ w w H pw _w l H pw _w w P w i_ w l P w i_ w w S TI-H p w S w _w w S w i_ w l S w i_ w w G H _ w w H w _ w l P b _w l P b _w w P m a t_ w l P w i_ w l P w i_ w w S s _w w S T I-Tb S w i_ w l T b _w l D F L P H _ w w G H _ w w P H _ w w P b_ w w P c_ w w P m a t_ w l

Pod number

Pod weight

Pod number

Seed number

Stress tol. indices

Pod width

Seed size

Pod length

Seed length

Pod width

Pod maturity

Yield

components

Fleur11 x AiAd:95 QTLs for 28 traits in 2 env.

Foncéka et al. 2012, BMC Plant Biology

Bambey_ww

Bambey_wl

Nioro-R

Sinthiou-R

Fleur11 x AbAd:232 QTLs for 37 traits in 4 env.

Pod width

Seed size

Pod width

Seed size

J.R. Nguepjop

(g

)

Cultivated

Wild

B6 chromosome contributed favorable

alleles for seed size

Nguepjop et al., in prep

CSSLs development

Fleur11(AABB)

AB-QTL

(BC2F3, BC3F2)

AiAd (AABB)

x

F

1

BC

4

CSSLs

(

BC

4

F

3

)

Genetic map

BC

1

BC

2

BC

3

BC

4

F

2

CSSLs development: breeding scheme

601792101702502581893216929107961061226173302402241281319377132208552425226126525451200136149509746221190109918319219839220225140244168156901251287113823421566111262152146118183187708112314101851772482492615101126102Chr 1Chr 2Chr 3Chr 4Chr 5Chr 6Chr 7Chr 8Chr 9Chr 10Chr 11Chr 12Chr 13 Chr 14 Chr 15Chr 16Chr 17Chr 18Chr 19Chr 20 Legend:A BGenotype 3Genotype 4HeterozygoteMissing data

22 BC

1

F

1

58 BC

2

F

1

80 BC

3

F

1

100 BC

4

F

1

7

gen

er

at

ion

s

The CSSL Population

Foncéka et al. 2012 Plos ONE

 122 CSSLs

 92% coverage of the map

 39.5 cM on average

 72 lines have an

unique segment

CSSL analysis: phenotyping in Senegal



Subset of 80 CSSLs



4 years in 5 locations under

rainfed and irrigated conditions

totalizing 12 env.

– Alpha-lattice design

– 3 replications/location



Plant architecture



Yield components

Results from 9 environnements: PW, HSW

PC 1 (35% TSS) P C 2 ( 1 8 % T S S )

Pod Weight per plant

method=nipals, center=TRUE, scale=FALSE, missing: 2%

BaE11 BaE12 BaP13 BaS11 BaS12 DaP14 NiE15 NiP14 SiP13 12CS_000 12CS_001 12CS_004 12CS_006 12CS_007 12CS_008 12CS_009 12CS_010 12CS_011 12CS_012 12CS_013 12CS_014 12CS_016 12CS_018 12CS_019 12CS_020 12CS_021 12CS_022 12CS_023 12CS_024 12CS_027 12CS_028 12CS_031 12CS_032 12CS_033 12CS_034 12CS_03612CS_037 12CS_039 12CS_041 12CS_042 12CS_044 12CS_047 12CS_048 12CS_050 12CS_051 12CS_052 12CS_053 12CS_054 12CS_055 12CS_059 12CS_060 12CS_061 12CS_062 12CS_063 12CS_064 12CS_066 12CS_068 12CS_069 12CS_070 12CS_071 12CS_072 12CS_075 12CS_076 12CS_078 12CS_079 12CS_081 12CS_083 12CS_084 12CS_08512CS_086 12CS_090 12CS_091 12CS_092 12CS_09512CS_096 12CS_098 12CS_100 12CS_101 12CS_103 12CS_104 12CS_106 12CS_108 12CS_109 12CS_110 12CS_111 12CS_112 12CS_113 12CS_114 12CS_115 12CS_116 12CS_118 12CS_119 12CS_120 12CS_121 PC 1 (66% TSS) P C 2 ( 8 % T S S )

100-Seed Weight

method=nipals, center=TRUE, scale=FALSE, missing: 2%

BaE11 BaE12 BaP13 BaS11 BaS12 DaP14 NiE15 NiP14 SiP13 12CS_000 12CS_001 12CS_004 12CS_006 12CS_007 12CS_008 12CS_009 12CS_010 12CS_011 12CS_012 12CS_013 12CS_014 12CS_016 12CS_018 12CS_019 12CS_020 12CS_021 12CS_022 12CS_023 12CS_024 12CS_027 12CS_028 12CS_031 12CS_032 12CS_033 12CS_03412CS_03712CS_036 12CS_039 12CS_04112CS_042 12CS_044 12CS_047 12CS_048 12CS_050 12CS_051 12CS_052 12CS_053 12CS_054 12CS_055 12CS_059 12CS_060 12CS_061 12CS_062 12CS_063 12CS_064 12CS_066 12CS_068 12CS_069 12CS_070 12CS_071 12CS_072 12CS_075 12CS_076 12CS_078 12CS_079 12CS_081 12CS_083 12CS_084 12CS_085 12CS_086 12CS_090 12CS_091 12CS_092 12CS_095 12CS_096 12CS_098 12CS_10012CS_101 12CS_103 12CS_104 12CS_106 12CS_108 12CS_109 12CS_110 12CS_111 12CS_112 12CS_113 12CS_114 12CS_115 12CS_116 12CS_118 12CS_119 12CS_120 12CS_121

Seed size QTL validation using the CSSL

Decreasing Increasing



16 CSSL selected based on

yield component traits. 2

years, three locations under

rainfed conditions totalizing 6

environnements



Traits

– Total Biomass

– Yield t/ha

– Hundred pod and seed weight



Alpha-lattice design

– 3 replication per location

CSSL

1 2C S _ 00 0 1 2C S _ 00 6 1 2C S _ 02 8 1 2C S _ 03 1 1 2C S _ 03 4 1 2C S _ 03 7 1 2C S _ 03 9 1 2C S _ 04 8 1 2C S _ 05 0 1 2C S _ 05 2 1 2C S _ 06 8 1 2C S _ 06 9 1 2C S _ 07 5 1 2C S _ 09 1 1 2C S _ 09 8 1 2C S _ 11 5 1 2C S _ 12 0 2.2 2.4 2.6 2.8 3.0 Lines lin ea r pre d ic to r a b a b a b a b a b b a a b a a b a a b b a a b a b a b a b

Nioro-2014

1 2C S _0 00 1 2C S _0 06 1 2C S _0 28 1 2C S _0 31 1 2C S _0 34 1 2C S _0 37 1 2C S _0 39 1 2C S _0 48 1 2C S _0 50 1 2C S _0 52 1 2C S _0 68 1 2C S _0 69 1 2C S _0 75 1 2C S _0 91 1 2C S _0 98 1 2C S _1 15 1 2C S _1 20 1.5 2.0 2.5 3.0 Lines lin e ar pre dic to r c a c a c a c a a c a c b c c a c a c a c a c a c a b a c c

Sinthiou-2014

1 2C S _ 00 0 1 2C S _ 00 6 1 2C S _ 02 8 1 2C S _ 03 1 1 2C S _ 03 4 1 2C S _ 03 7 1 2C S _ 03 9 1 2C S _ 04 8 1 2C S _ 05 0 1 2C S _ 05 2 1 2C S _ 06 8 1 2C S _ 06 9 1 2C S _ 07 5 1 2C S _ 09 1 1 2C S _ 09 8 1 2C S _ 11 5 1 2C S _ 12 0 2.0 2.5 3.0 Lines lin ea r p re d ic to r b c a c b c b c a c b c a c a c a a c b c a b a c a c a b a c c

Nioro-2015

1 2C S _ 00 0 1 2C S _ 00 6 1 2C S _ 02 8 1 2C S _ 03 1 1 2C S _ 03 4 1 2C S _ 03 7 1 2C S _ 03 9 1 2C S _ 04 8 1 2C S _ 05 0 1 2C S _ 05 2 1 2C S _ 06 8 1 2C S _ 06 9 1 2C S _ 07 5 1 2C S _ 09 1 1 2C S _ 09 8 1 2C S _ 11 5 1 2C S _ 12 0 1.5 2.0 2.5 3.0 3.5 Lines lin ea r p re d ic to r c a c c a c b c a c a c b c a c a c a c b c b c a b a c b c

Sinthiou-2015

CSSL analysis: Pod Yield per environment

1 2 C S _ 00 0 1 2 C S _ 00 6 1 2 C S _ 02 8 1 2 C S _ 03 1 1 2 C S _ 03 4 1 2 C S _ 03 7 1 2 C S _ 03 9 1 2 C S _ 04 8 1 2 C S _ 05 0 1 2 C S _ 05 2 1 2 C S _ 06 8 1 2 C S _ 06 9 1 2 C S _ 07 5 1 2 C S _ 09 1 1 2 C S _ 09 8 1 2 C S _ 11 5 1 2 C S _ 12 0 35 40 45 50 55 60 65 70 Lines lin e ar p re d ic to r b d b c e f g g h f h b f b d f g d f g c d f d f g h b f a b f d f g b d e 1 2 C S _ 0 0 0 1 2 C S _ 0 0 6 1 2 C S _ 0 2 8 1 2 C S _ 0 3 1 1 2 C S _ 0 3 4 1 2 C S _ 0 3 7 1 2 C S _ 0 3 9 1 2 C S _ 0 4 8 1 2 C S _ 0 5 0 1 2 C S _ 0 5 2 1 2 C S _ 0 6 8 1 2 C S _ 0 6 9 1 2 C S _ 0 7 5 1 2 C S _ 0 9 1 1 2 C S _ 0 9 8 1 2 C S _ 1 1 5 1 2 C S _ 1 2 0 24 25 26 27 28 29 30 Lines lin e a r p re d ic to r b b e f d e f c d d e f f d e f c e c e b c c e b a b c c e c e

CSSL analysis: 100-seed weight and pod length

CSSL : Some lines registered as variety in Senegal

Pyramiding of seed size QTLs

Decreasing Increasing

Hodo-Abalo Tossim

12CS_069

12CS_031

43 double homozygous lines selected over about 1000 F2

X

Pyramiding of seed size QTLs

A09

B06

Pyramiding of seed size QTLs



42 pyramiding lines plus the 2

CSSL parental lines (12CS_031

and 12CS_069 and Fleur 11.

One year, two locations under

rainfed conditions



Traits

– Total Biomass

– Yield t/ha

– Hundred pod and seed weight

– Pod length and width



Alpha-lattice design

Pyramiding of seed size QTLs: 100-seed weight

F le u r 1 1 P yr1 -1 0 0 P yr1 -5 9 2 P yr1 -1 2 6 P yr1 -4 0 3 1 2 C S _ 0 3 1 P yr1 -7 2 9 P y r1 -3 P yr1 -7 2 3 P yr1 -3 6 5 P yr1 -2 5 0 P yr1 -2 0 2 P yr1 -7 3 5 P yr1 -6 5 3 P yr1 -7 9 7 P yr1 -4 9 6 P yr1 -5 5 7 P y r1 -5 9 P yr1 -9 9 5 P yr1 -6 7 2 P yr1 -7 4 4 P yr1 -4 0 1 P y r1 -8 2 P yr1 -2 9 0 P yr1 -6 9 6 P yr1 -1 3 1 P yr1 -1 8 5 1 2 C S _ 0 6 9 P yr1 -3 3 6 P yr1 -4 4 7 P yr1 -3 4 5 P y r1 -5 8 P yr1 -1 8 6 P yr1 -9 5 0 P yr1 -8 0 1 P yr1 -6 1 4 P yr1 -5 4 4 P y r1 -9 6 P yr1 -3 3 9 P yr1 -2 5 1 P yr1 -6 8 5 P yr1 -4 2 6 P yr1 -3 1 7 P yr1 -3 7 0 P yr1 -6 3 8 5 5 60 6 5 7 0 75 8 0 i h i fg h i c d e fg h g h i e fg h i c d e fg h cdefgh c d e fg h cd e fg h i c d e fg h i c d e fg h cdefgh d e fg h i b cd e fg h c d e fg h c d e fg h a b c d e fg h a b c d e fg h a b c d e fg h a b c d e fg h a b c d e fg h a b c d e fg h a b c d e fg h a b c d e fg h a b c d e fg h a b c d e fg h a b c d e fg h ab c d e fg h a b c d e fg h a b c d e fg h a b c d e fg h a b c d e fg a b c d e fg h a b c d e fg abcde a b c d e a b c a b c d ab c d a b c d e f a b cd a b c a a b

10.%

32%

Pyramiding of seed size QTLs: Pod length and width

Fle ur 11 P yr1-4 03 P yr1-4 01 P yr1-7 29 Pyr1 -3 P yr1-4 96 12C S_069 P yr1-7 97 P yr1-2 50 P yr1-9 95 P yr1-1 00 P yr1 -59 P yr1-6 53 P yr1-6 96 P yr1-5 57 P yr1 -82 P yr1-9 50 P yr1-7 44 P yr1-6 85 P yr1-5 92 P yr1-3 39 P yr1-4 26 P yr1-3 65 P yr1-2 02 P yr1-3 45 P yr1 -58 P yr1-7 35 P yr1-6 72 P yr1-6 14 P yr1-1 26 P yr1-3 17 P yr1-6 38 P yr1-7 23 P yr1-8 01 P yr1-2 90 P yr1-1 86 P yr1-1 31 P yr1-2 51 P yr1-3 36 12C S_031 P yr1 -96 P yr1-1 85 P yr1-3 70 P yr1-4 47 P yr1-5 44 28 29 30 31 32 33 l k jk hijkijk gh ijk ghij k fg hijkfgh ijk efg h ijk cde fg hijk de fg hijkb cde fg hijk b cd efg hij k d efg h ijk bcd efg h ijkbcd efg h ijk bcd efg h ijk ab cde fg h b cde fg hijk ab cde fg hijk b cd efg hij k b cde fg hijk a bcd efg h ijk bc defg h ijkabc defg hi a bcd efg hija bcd efg h i abc def a bcd efg h i a bc defg a bcd e ab cde f ab cde ab cde f abc def ab cde f abc de a bc defa bcdabc ab cdab aa

Pod Length

F leu r 11 Py r1 -3 12C S _031 Pyr1 -8 2 P yr1 -1 26 P yr1 -7 29 P yr1 -7 97 P yr1 -1 00 P yr1 -9 95 P yr1 -4 26 P yr1 -4 96 P yr1 -1 85 12C S _069 P yr1 -6 72 P yr1 -5 57 P yr1 -4 03 P yr1 -1 31 P yr1 -3 36 P yr1 -7 23 P yr1 -6 96 P yr1 -2 02 P yr1 -6 85 P yr1 -5 44 P yr1 -4 47 P yr1 -4 01 P yr1 -1 86 P yr1 -6 53 Pyr1 -5 9 P yr1 -7 35 P yr1 -7 44 P yr1 -9 50 P yr1 -5 92 P yr1 -3 45 P yr1 -2 50 P yr1 -6 38 P yr1 -2 51 Pyr1 -5 8 P yr1 -6 14 P yr1 -3 17 Pyr1 -9 6 P yr1 -3 39 P yr1 -3 65 P yr1 -3 70 P yr1 -8 01 P yr1 -2 90 12.0 12.5 13.0 13.5 14.0 14.5 f d ef ef cd eb cd e c de f b cd e c de bc de bc de b cd e b cd e c de ab cd e b cd e b cd e b cd e b cde bc debc de ab cd eab cd e a bc deab cd e ab cd e ab cd ab cd e a bc de ab cd e a b cdea bc de a b ab cd eab cd a bc dabca bc a bc d a bc d a bc d ab c ab cabc a ab

Pod width

Graphical genotypes of F2

Precising the Pod Length QTL(s) position(s) on A09

Pyr35

Pyr369

Pyr734

Pyr351

B

A

A

B

A

A

B

A

A

B

B

A

A

B

A

A

B

B

B

B

B

Pod Length

Markers

Seq17E03 Seq9B04 Seq4G02 RN25B01 PM170 Seq8D09

Seq18G01

Chromosome

A09

A09

A09

A09

A09

A09

B06

Pos. (cM)

0

11.1

23.6

47.4

65.2

83.4

104.4

12CS_069

A

A

A

A

A

A

B

12CS_031

B

B

B

B

B

B

A

Pyr29

B

B

A

A

A

A

B

Pyr424

B

B

A

A

A

A

B

Pyr204

B

B

B

A

A

A

B

Pyr35

B

B

B

B

A

A

B

Pyr369

B

B

B

B

A

A

B

Pyr734

A

A

A

B

B

B

B

Pyr351

A

A

A

A

A

B

B

Po

d

len

gt

h

x

(

)

A. duranensis A. ipaensis

1

x

x

(

)

A. hypogaea

A. duranensis A. ipaensis

2

Hybridization

601792101702502581893216929107961061226173302402241281319377132208552425226126525451200136149509746221190109918319219839220225140244168156901251287113823421566111262152146118183187708112314101851772482492615101126102 Chr 1Chr 2Chr 3Chr 4Chr 5Chr 6Chr 7Chr 8Chr 9Chr 10Chr 11Chr 12Chr 13 Chr 14 Chr 15Chr 16Chr 17Chr 18Chr 19Chr 20 Legend:ABGenotype 3Genotype 4HeterozygoteMissing data

3

4

The beautiful story of the partnership

Summary



We crossed (A. ipaensis x A. duranensis)

4x

_{and (A. batizocoi x A.}

duranensis)

4x

_{to Fleur11 for developping AB-QTL and CSSL}

populations



We phenotyped extensively the AB-QTLs and CSSL populations

and found that wild alleles can contribute positive variation to

seed size and other agronomic traits



AB-QTL and CSSL populations are accurate for QTL mapping



We used the CSSL lines for QTL validation, for pyramiding of seed

size QTLs and for refining the QTL position.



The CSSL population has been distributed to many partners and

are being evaluated for various traits

J-C Glaszmann

Brigitte Courtois

Jean-Francois Rami

Joel Romaric Nguepjop

Hodo-Abalo Tossim

Aissatou Sambou

Maguette Sèye

Issa Faye

Shivali Sharma

Nalini Mallikarjuna

Rajeev Varshney

David Bertioli

Soraya Leal-Bertioli

Marcio Moretzsohn

J.M Valls

Acknowledgments

Peggy Ozias-Akins

Scott Jackson

Tom Stalker