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