Breeding Progress for Increasing
Soybean Yield:
P
Past,Present,PanddF
FutureRandall Nelson
USDA-Agricultural Research Service
University of Illinois

Eras of U.S. Soybean Breeding
 Soybean introduction (to 1943)
 Varieties introduced from Asia
 Within and among variety selection
Scientific plant breeding (1944-1965) 15 soybean breeders in North America
 Fewer than 2 varieties/year Hand planting and harvesting

Eras of U.S. Soybean Breeding
3500
3000
2500
2000
1500
1000
500
022 kg/ha/year

24
1930
1936
1942
1948
1954
1960
1966
1972
1978
1984
1990
19962002

 Transgenics (1996 to present) Equipment advances Off season nurseries Marker assisted selection
 Increase in genetic research

Changes in US yield (kg/ha)

19Expansion and mechanization (1966 to 1995)
 Tractor planting and combines
 Computers for data management
 More private and public breeders
 Transition to proprietary varieties

1What determines average yield?
• Environment• Rainfall• Soil type• Diseases and pests• Genetic base of the crop
• Genetic potential of each variety

How do we increase yield?

Where are we?
We are still makingg progressp gGains per unit input are decreasing
There is potential for increase

What can plant breeders do?

• Improve physiological efficiencies• Provide protection from diseases and pests• Change breeding efficiency• Tolerance to abiotic stresses• Expand the genetic base
• Incorporate
It transgenes
t2Increasing breeding efficiency

Expanding the Genetic Base

Variety development time

• Current U.S. g
genetic base

Improved selection techniques

35 ancestors account for 96% of genes
6 ancestors provide 60% of the genes
7 crosses contributed 70% of the genes
Pool ~85%
85% complete by 1954
Pool ~95% complete by 1970

Marker assisted selection• Disease and insect resistance• Yield• Parent selection• Within population selection
Improved field testing

Conventional View of Genetic Diversity

Japanese Soybean Gene Pool
53 ancestors account for 80% of genes
18 ancestors account for 50% of genes
91% of ancestral lines from Japan
Regionally distinct gene pools
L coefficientLow
ffi i t off parentagetamong cultivars
lti++Glycine soja
Zhou et al. 2000. Crop Sci. 40:1794–1802

DOM
ESTICAT
I AsianO primitive
N varietiesINTRODUCTIONPL
A
NTNorthAmericanancestors

BRE
E Modern
D Cultivars
ING3

Sequence Analysis of Cultivatedand Wild Soybean


26 G. soja accessions from China, Korea,
Japan and Russia
Russia.



52 Asian G. max primitive varieties fromChina, Korea and Japanj ancestors of N. American
17 majorcultivars



25 modern U.S. cultivars
Hyten et al. 2006. PNAS 103: 16666

Sequence Analysis of 120 Cultivatedand Wild Soybean Genotypes
111 Sequence Tagged Sites derived from102 complete GenBank genes and cDNAs

21.9 kbp coding
17.9 kbp intron
11.2 kbp '3 & 5' UTR
2.2 intergenic sequence

Wild soybean

Primitive varieties

U.S. ancestors

Modern cultivars

Nucleotide Diversity
Terminology
Watterson’s θ = Mean SNPs
per site adjusted for population
size (θw = 0.001 = 1 SNP/kbp)

Total = 53.1 kbp

4Revised View of Genetic Diversity

Nucleotide Diversity, θw (x 103) in Coding and Noncoding Regions in Four Soybean Populations
Population
Wild soybean

Total coding Total non-coding

Total

1.63 a3.06 a2.35 aAsian primitive varieties 0.81 b

1.36 b

1.15 bN A
N.
Americani
ancestorst

0 73 b0.73

1 16 b
1.16bc1.00 bc

Modern cultivars

0.59 b

0.92 c0.83 c++Glycine soja

DO
M
ES
T
I
C
A
T
I
O
N

Asian
primitivevarieties

I
N
T
R
O
DU
C
T
I
O
N

P
L
A
N
T

North
Americanancestors

B
R
E
E
ModernD
cultivars
I
N
G

Allele frequency changes in 102 genes

Expanding the Genetic Base

Domestication bottleneck• Current g
genetic baseG. soja/Prim. varieties:

61 genes

Introduction bottleneck• Understanding genomic control• Sequencing of the soybean genome

Prim. varieties/N. Am. Ancestors: 28 genes• Many germplasm lines not used

Improvement bottleneck
N. Am. ancestors/Elite cultivars:7 genes

5Uniform IV Test 2007-08

PI 90566-1 x Williams 82 (4)EntryKg/haWilliams 82
LG05c-1341
IA3023

3272
3910
4078

Mat
9-27
9-27
9-20

Ldg
1.7
1.9
1.4

109
109
91

PI 90566-1 came from Jilin, China in 1930
LG05c-1341 has 93% of Williams 82 genes
And 7% of the genes from PI 90566-1

2008 Uniform IV Test at 11 locations
Entry%exotic Pedigree

LG04-5190
LG045190 (50)LG04-5372 (37)LG04-4866 (25)LD00-3309

LG97-9384
LG979384 x LG97
LG97-9301
9301
Rend x LG97-9301
LG97-9015 x HS93-4118
Check22 locations

Hgt

Kg/ha Mat3944
3937
3863
3837

2.5
25-2.2
3.9
0.0

Entry

PedigreeKg/haMat

LG04-6000
LD00-3309

HS93-4118 x LG97-9912
Check3964
3669

3.9
0.0

Jilin 15 is derived from 3 primitive Chinese
varieties and was released in 1978.
Jilin 15 is 13% of the parentage of LG04LG04-6000.

Origin of “Exotic” parents
PI number Cultivar

Origin

YearPI 90566-1
PI 253665D
PI 283331
PI 391594
Jilin No. 8
PI 436682
Jilin NoNo. 15
PI 437851A

China
China
Morocco
China
China
China

19301958
1962
1974
1979
1980

6

Yield QTL in Exotic by Elite Populations
A1 A2 B1 B2 C1 C2 D1a D1b D2 EF

G

H

I

1240

1

180

3E7 1

160K

11N

3

120 meters

O

3Wind, O3 and CO2sensors

211212

12

1

13120

M

11100

L

1202JE3

1E1WindGas release
1140160

43 yield QTL mapped to 29 genomic positions.

180

Evidence of yield increasing allele in elite (17 QTL).

Soybean Free Air Concentration Enrichment

No evidence of yield increasing allele in elite (12 QTL).
Currently confirming with near isogenic lines (13 QTL)

CO2 Concentration (ppm)
600

400
300

553

552500

552

54254
5553

54
63
73

3
763
78

3
80

382

3
8
4

384

2002

2003

2004

2005

2006

2007

2008

200

ambient
treatment

Differential CO2 Responders
5 year average increase from elevated CO2Kg/haKg/ha

EntryAmbientElevated%Δ

Loda

3621

4488

24%

HS93-4118

3541

3661

4%

10007

Differential O3 Responders
5 year average decrease from elevated O3Transgenics• Mostlyy pproprietary
py research

K /hKg/ha

K /hKg/ha

Entry

Ambient

Elevated%Δ

Dwight

3742

3225

-14%

LN97-15076

3191

2997

-6%

• Broad spectrum disease resistance?
• Yield is genetically complex• Second generation genes?

How to Increase Soybean Yield• Shorter variety development time
• Selection for disease/pest resistance

Questions?
Questions?

• Understanding the genetics of yield• Selection for parents and lines• Use of exotic germplasm for yield• Use of transgenes

8