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v Grape ripening and anthocyanin accumulation Phenylalanine - - PowerPoint PPT Presentation

Jan 28, 2024 409 likes •611 views

Carolina Royo , Maite Rodrguez-Lorenzo, Pablo Carbonell-Bejerano, Nuria Mauri, Flix Cibrain, Julin Suberviola, Ana Sags, Javier Ibez, Jos M. Martnez-Zapater v Grape ripening and anthocyanin accumulation Phenylalanine

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SLIDE 1

Carolina Royo, Maite Rodríguez-Lorenzo, Pablo Carbonell-Bejerano, Nuria Mauri,

Félix Cibríain, Julián Suberviola, Ana Sagüés, Javier Ibáñez, José M. Martínez-Zapater

v

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SLIDE 2

Grape ripening and anthocyanin accumulation

Berry growth Anthocyanidins

Anthocyanins

UFGT MybA1 MybA2 Phenylalanine Sugars Anthocyanins

MybA2 MybA1

Chromosome 2

White allele White allele

MybA2 MybA1

White allele Loss of functional allele

MybA2 MybA1

White allele Black allele

MybA2 MybA1

Chromosome 2

Black allele Black allele Carolina Royo - ICVV

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SLIDE 3

Background

Somatic Variation

periclinal chimera (Adapted from Walker et al 2006)

SAM

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SLIDE 4

Carolina Royo - ICVV

Loss Of Heterozygosity around color locus on chr2

(Adapted from Vezzulli et al 2012 , Migliaro et al 2014)

Background Garnacha Tinta Garnacha Roja Garnacha Blanca

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SLIDE 5

Tempranillo Tinto and Blanco Whole Genome Sequence

Background

LG 5 LG 2 LG 9

A

(Mb) SNP CNV

Structural rearrangement graph:

0.5 1 18.8 11 13 1 3 5 7 9 15 17 25 19 21 23 1 3 5 7 9 11 13 15 17 19 21 23 1 3 5 7 9 11 13 15 17 Tail-to-tail inverted Deletion-type Tandem duplication-type Head-to-head inverted Unknown

  • 2

2

Lost fragments Original chromosomes

*

LG 2 LG 5 LG 9

T3 T2 Inv T4 Inv T1 T1 T5 T3 T4 ? T2 ? T5

B

Rearranged chromosomes LG 2 LG 5 LG 9

Inv T3 T5 T4 ? T2 T1

Chromothripsis

Carolina Royo - ICVV

(Adapted from Carbonell-Bejerano et al 2017)

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SLIDE 6

Carolina Royo - ICVV

Tempranillo Blanco Affected Traits

Background

Complex genome rearrangements cause side-effects in yield production

Fruit set

10 20 30 40 50 60 70

Alfaro Rincón R1 Corera Grajera Blanco Cenicero Nalda Albelda Azofra Fonzaleche Grajera Tinto

Fruitset (%)

Rearranged chromosomes are gamete-lethal

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SLIDE 7

Carolina Royo - ICVV

Tempranillo and Garnacha accessions

5 2 60 GB 21 GB 39 GR 2

Plant Materials Garnacha Tinta Garnacha Blanca Garnacha Roja

6 9 1

Tempranillo Tinto Tempranillo Blanco Tempranillo Gris

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SLIDE 8

SNP genotyping along chromosome 2

MybA2 MybA1

18 Mb 17 10 11 12 13 14 15 16 9 8 7 6 5 4 3 2 1

Chromomose 2: Heterozygous in Garnacha Tinta and Tempranillo Tinto Heterozygous in Garnacha Tinta Heterozygous in Tempranillo Tinto

Carolina Royo - ICVV

Loss Of Heterozygosity (LOH) delimits likely deleted fragments Chromosome 2 LOH genotyping: 48 SNP chip: SNP selection from: Lijavetzky et al., 2007, Carbonell-Bejerano et al., 2017, Laucou et al., 2018 Minor Allele Frequency (MAF) ≈ 0.5

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SLIDE 9

Loss Of Heterozygosity in Tempranillo Gris

MybA2 MybA1

18 Mb 17 10 11 12 13 14 15 16 9 8 7 6 5 4 3 2 1

Chromomose 2: Tempranillo Gris type 3 (3 accesion) Tempranillo Gris type 4 (4 accesion) Tempranillo Gris type 2 (1 accesion) Tempranillo Gris type 1 (1 accesion) Tempranillo Blanco WGS

Carolina Royo - ICVV

Results obtained in roots = L2 Heterozygous in Garnacha Tinta and Tempranillo Tinto Heterozygous in Garnacha Tinta Heterozygous in Tempranillo Tinto

2.37 Mb 1.44 Mb 1.50 Mb 1.64 Mb 2.87Mb

Chromosome 2 LOH genotyping: 48 SNP chip:

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SLIDE 10

Loss Of Heterozygosity in Tempranillo Gris

MybA2 MybA1

18 Mb 17 10 11 12 13 14 15 16 9 8 7 6 5 4 3 2 1

Chromomose 2: Tempranillo Gris type 3 (3 accesion) Tempranillo Gris type 4 (4 accesion) Tempranillo Gris type 2 (1 accesion) Tempranillo Gris type 1 (1 accesion) Tempranillo Blanco WGS

Carolina Royo - ICVV

Tempranillo Blanco regeneration through somatic embryogenesis from Tempranillo Gris type 1 Heterozygous in Garnacha Tinta and Tempranillo Tinto Heterozygous in Garnacha Tinta Heterozygous in Tempranillo Tinto Chromosome 2 LOH genotyping: 48 SNP chip:

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SLIDE 11

Loss Of Heterozygosity in Tempranillo and Garnacha

MybA2 MybA1

18 Mb 17 10 11 12 13 14 15 16 9 8 7 6 5 4 3 2 1

Chromomose 2: Garnacha Blanca type 1 ( 21 accessions and 2 Garnacha Roja ) Garnacha Blanca type 2 (39 accessions) Tempranillo Gris type 3 Tempranillo Gris type 4 Tempranillo Gris type 2 Tempranillo Gris type 1 Tempranillo Blanco WGS Heterozygous in Garnacha Tinta and Tempranillo Tinto Heterozygous in Garnacha Tinta Heterozygous in Tempranillo Tinto

2.37 Mb 1.44 Mb 1.50 Mb 1.64 Mb 2.87Mb 0.68 Mb 1Mb

Chromosome 2 LOH genotyping: 48 SNP chip:

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SLIDE 12

Loss Of Heterozygosity in Garnacha Blanca

Carolina Royo - ICVV

MybA2 MybA1

18 Mb 17 10 11 12 13 14 15 16 9 8 7 6 5 4 3 2 1

Chromomose 2: Garnacha Blanca type 1: WGS  GT 77 and GB 77 Garnacha Blanca type 2: WGS  GT 1608 and GB 1662 14123701 15130499 14661047 14983912 14123701 15130499 Selection of two pairs of Garnacha for Whole Gemone Sequencing (WGS) Heterozygous in Garnacha Tinta and Tempranillo Tinto Heterozygous in Garnacha Tinta Heterozygous in Tempranillo Tinto Chromosome 2 LOH genotyping chip: 48 SNP

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SLIDE 13

Garnacha Whole Genome Sequence analysis in progress

Loss Of Heterozygosity (LOH) Copy Number Variation (CNV): Structural variation as deletions, insertions, and duplications.

Carolina Royo - ICVV

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SLIDE 14

Carolina Royo - ICVV

Garnacha WGS: Heterozygosity on chromosome 2

LOH Garnacha Blanca type 2 LOH Garnacha Blanca type 1 SNP number

10 Mb 15 Mb 5 Mb chr2 position 10 Mb 15 Mb 5 Mb MybA MybA

GT77 / GB77 GT1608 / GB1662 chr2:14123701-14661047 chr2:14983912-15130499 chr2:14123701 -15130499 SNP genotyping:

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SLIDE 15

Garnacha WGS: LOH and Copy Number Variation on chromosome 2

LOH Garnacha Blanca type 2 LOH Garnacha Blanca type 1 GT77 / GB77 GT1608 / GB1662 SNP number

10 Mb 15 Mb 5 Mb chr2 position 10 Mb 15 Mb 5 Mb

Log2 Ratio

10 Mb 15 Mb 5 Mb chr2 position 10 Mb 15 Mb 5 Mb

GT77 / GB77 GT1608 / GB1662

MybA MybA

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SLIDE 16

Carolina Royo - ICVV

1. The genotyping tool that we design proved useful to delimit deletions on chromosome 2. 2. The loss of color is related to hemizygous deletions at the color locus in all the variants studied by whole-genome sequencing. 3. In Tempranillo, multiple independent SV types were detected, including minimal deletion lines suited for the development of improved clones of Tempranillo Blanco. 4. In Garnacha Blanca, the results indicate the likely presence of recurrent SV fragile sites.

Conclusions

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SLIDE 17

Maite Rodríguez-Lorenzo Pablo Carbonell-Bejerano Nuria Mauri Javier Ibáñez José M. Martínez-Zapater Félix Cibríain Julián Suberviola Ana Sagüés

Carolina Royo

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SLIDE 18

Carolina Royo