Apple and peach genetic variability
Maria José Aranzana
Phenotypic diversity
Genetic diversity
Genetic diversity is the heritable variability
Is the basis of selection and crop improvement
An important resource in plant breeding
www.biotechlearn.org.nz
Genetic diversity should be safely conserved
and efficiently used
Reduction of genetic variability: domestication and selection
Wild
Adaptation Domestication
Selection
The extent and distribution
of genetic diversity depends
on its evolution, past
bottlenecks and human
factors
Genetic diversity
Nikolai Vavilov
plants were not domesticated somewhere
in the world at random but there are
regions where the domestication started.
The center of origin is also considered the
center of diversity.
Centres of origin of food and agricultural areas
J. Diamond (2002). Nature 418
Apple genetic variability by geographic origin
FruitBreedomics
Study genetic and phenotypic
diversity in peach and apple
germplasm collections
FruitBreedomics Germplasm collections
UK; 2237
FR; 1054
BE; 1314
CZ; 256
IT; 421 SWE;195
Selection of accessions in germplasm collections
UK310
FR274
BE296
CZ253
IT 232
SWE195
5,477 accessions in
germplasm collections
1,560
accessions with
phenotypic
observations
APPLE
Removing synonyms and triploids
IT-RO; 943
IT-MI; 575FR; 764
ISP; 303CH; 300
2,885 accessions in
germplasm collections
1,296 accessions
with phenotypic
observations
Removing synonyms and selecting
diversity
PEACH
IT-RO178
IT-MI140
FR343
SP353
CH 282
Phenotypic data in the FruitBreedomics database
APPLE
37,818 informative data entries in the
phenotypic database
PEACH
UK FR BE CZ IT FR IT-RO IT-MI SP CH
81,206 informative data entries in the
phenotypic database
Molecular markers
Traditionally, variability has been described visually,
however, over the past few years molecular markers have
been used
Allow a more efficient breeding by the use of genetic
markers that ‘tag’ traits of interest that sometimes are
difficult to select for
Study of peach genetic
variability in FruitBreedomics
germplasm collections
1300 varieties genotyped with the 9K IPSC SNPs chip
PEACH GENETIC VARIABILITY
PEACH GENETIC VARIABILITY
Most representative K is 3:
• Occidental breeding material (352 accessions)
• Chinese / oriental material (58 accessions)
• Occidental old / non breeding material (165 accessions)
• Admixed accessions [Q < 0.8] (665 accessions)
OCCIDENTAL ORIENTAL
CH03g12z4.0
Hi02c0725.0
HB11AG38.0
CHVf156.0
CH05g0877.0
LG01
CH02f061.0
CN49313924.0
CH02c0642.0
CH05e0351.0
CH03d0167.0
LG02
CH03e033.0
CH03g0724.0
Hi03d0643.0
GD1255.0
AU22365776.0
Ms14h0394.0
CH03g12y111.0
LG03
NZ05g080.0CH04e022.0
Hi23g0218.0
CH05d0232.0
Hi07b0255.0
CH02c02b73.0
LG04
Hi09b045.0
Hi04a0820.0
CH03a0934.0
CH05e0645.0
Hi04d0269.0
CH05f0681.0
CH02a0890.0
CH04e03108.0
LG05
HB09TC9.0
CH03d0723.0
CH03d1240.0
CH05a0578.0
LG06
CN4447945.0
Hi03a1026.0
CH04e0535.0
Ms06c0954.0
Hi05b0974.0
LG07
CH01c0618.0
CH01f0933.0
CH01h1052.0
Hi23g1262.0
LG08
NH0029a12.0
CH01f03b24.0
Hi05e0742.0
CH01h0259.0
CN44454269.0CH05d0873.0
LG09
CH03g12z4.0
Hi02c0725.0
HB11AG38.0
CHVf156.0
CH05g0877.0
LG01
CH03g12z4.0
Hi02c0725.0
HB11AG38.0
CHVf156.0
CH05g0877.0
LG01
CH02f061.0
CN49313924.0
CH02c0642.0
CH05e0351.0
CH03d0167.0
LG02
CH02f061.0
CN49313924.0
CH02c0642.0
CH05e0351.0
CH03d0167.0
LG02
CH03e033.0
CH03g0724.0
Hi03d0643.0
GD1255.0
AU22365776.0
Ms14h0394.0
CH03g12y111.0
LG03
CH03e033.0
CH03g0724.0
Hi03d0643.0
GD1255.0
AU22365776.0
Ms14h0394.0
CH03g12y111.0
LG03
NZ05g080.0CH04e022.0
Hi23g0218.0
CH05d0232.0
Hi07b0255.0
CH02c02b73.0
LG04
NZ05g080.0CH04e022.0
Hi23g0218.0
CH05d0232.0
Hi07b0255.0
CH02c02b73.0
LG04
Hi09b045.0
Hi04a0820.0
CH03a0934.0
CH05e0645.0
Hi04d0269.0
CH05f0681.0
CH02a0890.0
CH04e03108.0
LG05
Hi09b045.0
Hi04a0820.0
CH03a0934.0
CH05e0645.0
Hi04d0269.0
CH05f0681.0
CH02a0890.0
CH04e03108.0
LG05
HB09TC9.0
CH03d0723.0
CH03d1240.0
CH05a0578.0
LG06
HB09TC9.0
CH03d0723.0
CH03d1240.0
CH05a0578.0
LG06
CN4447945.0
Hi03a1026.0
CH04e0535.0
Ms06c0954.0
Hi05b0974.0
LG07
CN4447945.0
Hi03a1026.0
CH04e0535.0
Ms06c0954.0
Hi05b0974.0
LG07
CH01c0618.0
CH01f0933.0
CH01h1052.0
Hi23g1262.0
LG08
CH01c0618.0
CH01f0933.0
CH01h1052.0
Hi23g1262.0
LG08
NH0029a12.0
CH01f03b24.0
Hi05e0742.0
CH01h0259.0
CN44454269.0CH05d0873.0
LG09
NH0029a12.0
CH01f03b24.0
Hi05e0742.0
CH01h0259.0
CN44454269.0CH05d0873.0
LG09
CH04c06z13.0CH02b0714.0
CH02c1140.0
CH03d1150.0
CH04g09y64.0
CH02b03b81.0
Ms06g03104.0
LG10
CH04h020.0
Hi07d11x10.0
CH02d0831.0
CH04a1246.0
Hi16d0255.0
CH04g0773.0
LG11
CH05d0413.0
NZ28f0429.0
CH01g1245.0
CH04d0251.0
CH01f0255.0
CH03c0261.0
Hi07f0176.0
CH01d03z89.0
LG12
CH05h054.0
Hi04g0518.0
GD14740.0
NH009b70.0
LG13
CH05g07-10.0
CH01g0510.0
CH04c0719.0
U7894842.0
LG14
NZ02b018.0
CH03b0611.0
Hi03g0623.0
CH01d0837.0
Hi04c0555.0
CH02d1177.0
CH02c09110.0
LG15
CH02a038.0
CH05c0614.0
Hi04e0430.0
CH05a0447.0
CH04f1076.0
LG16
CH04c06y0.0
AT00017412.0
CH01h0125.0
Hi03c0535.0
Hi02f1255.0
Hi05c0674.0
CH05d0891.0
Hi07h02100.0
LG17
CH04c06z13.0CH02b0714.0
CH02c1140.0
CH03d1150.0
CH04g09y64.0
CH02b03b81.0
Ms06g03104.0
LG10
CH04c06z13.0CH02b0714.0
CH02c1140.0
CH03d1150.0
CH04g09y64.0
CH02b03b81.0
Ms06g03104.0
LG10
CH04h020.0
Hi07d11x10.0
CH02d0831.0
CH04a1246.0
Hi16d0255.0
CH04g0773.0
LG11
CH04h020.0
Hi07d11x10.0
CH02d0831.0
CH04a1246.0
Hi16d0255.0
CH04g0773.0
LG11
CH05d0413.0
NZ28f0429.0
CH01g1245.0
CH04d0251.0
CH01f0255.0
CH03c0261.0
Hi07f0176.0
CH01d03z89.0
LG12
CH05d0413.0
NZ28f0429.0
CH01g1245.0
CH04d0251.0
CH01f0255.0
CH03c0261.0
Hi07f0176.0
CH01d03z89.0
LG12
CH05h054.0
Hi04g0518.0
GD14740.0
NH009b70.0
LG13
CH05h054.0
Hi04g0518.0
GD14740.0
NH009b70.0
LG13
CH05g07-10.0
CH01g0510.0
CH04c0719.0
U7894842.0
LG14
CH05g07-10.0
CH01g0510.0
CH04c0719.0
U7894842.0
LG14
NZ02b018.0
CH03b0611.0
Hi03g0623.0
CH01d0837.0
Hi04c0555.0
CH02d1177.0
CH02c09110.0
LG15
NZ02b018.0
CH03b0611.0
Hi03g0623.0
CH01d0837.0
Hi04c0555.0
CH02d1177.0
CH02c09110.0
LG15
CH02a038.0
CH05c0614.0
Hi04e0430.0
CH05a0447.0
CH04f1076.0
LG16
CH02a038.0
CH05c0614.0
Hi04e0430.0
CH05a0447.0
CH04f1076.0
LG16
CH04c06y0.0
AT00017412.0
CH01h0125.0
Hi03c0535.0
Hi02f1255.0
Hi05c0674.0
CH05d0891.0
Hi07h02100.0
LG17
APPLE GENETIC VARIABILITY
1,500 apple accessions
Genotyped with 12 SSR
markers
Apple genetic linkage map
Results: apple genetic variability and population structure
Nb of genotypes
Nb of accessions
Belgium 190 209
CZ 120 132
France 225 225
Italy 167 184
Sweden 158 160
UK 271 271
2 countries 78 171
3 countries 20 72
4 countries 12 58
1241 1482
0
1
2
3
4
5
6
7
8
1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70 73 76 79 82 85 88 91 94 97 100 103 106 109
Duplicates - diploids Belgium Czech_Republic France Italy Sweden United_Kingdom
Diploids
Results: apple genetic variability and population structure Diversity –
Partner’s collection
CONCLUSIONS
Is the bases of selection and crop improvement
Evolution, past bottlenecks and human factors have reduced
dramatically the genetic variability in cultivated plants
Genetic diversity should be safely conserved and efficiently used
In FruitBreedomics we have set peach and apple Core
Collections
Phenotypic data into a database
Genetic variability studies on these CC will help to preserve
variability and will allow a more efficient breeding