Quality approach in oil palm selection and seed productivity by using ID Cecking test with 12 SSR markers

(1)

Quality approach in oil palm selection

and seed production by using ID Checking test

with 12 SSR markers

Virginie Pomiès1_{,Virginie Riou}1

Aurore Manez1_{, Albert Flori}1

Florence Jacob2 _{, Benoît Cochard}2

1 _{CIRAD, UMR AGAP (Genetic Improvement and}

Adaptation of Mediterranean and Tropical Plant Research Unit), Montpellier, France

2 _{PalmElit SAS, Montferrier sur Lez, France}

Correspondence:

virginie.pomies@cirad.fr

Errors during breeding process have already been evidenced (Corley, 2005). Since 2009, CIRAD and PalmElit, as part of a quality approach, are routinely using a fingerprinting method to detect illegitimate individuals within the plant material in selection and seed production processes.

Control and data cleaning

Relationship between number of inconsistent markers and status according to the LScore

Implementation

Relationship between number of inconsistent markers and status according to the LScore

Applications

Materials and methods

• « Sample ID » follows all the processes

• Automates used to minimize errors

• Amplification of 12 SSR in 2 multiplexe PCR

• Quality controls of data to eliminate false illegitimates • Missing data management

• 4 600 palms analyzed/year

• Illegitimate palm = more than 3 inconsistent markers

• 13 palms to test a progeny

• % of illegitimate + doubtful palms serve as indicator to ban a cross

• Seed production: parentage of palms, quality approach of

planting material (60% of analysis) • Field trials: quality data for

breeding (40% of analysis) Genoty pi ng da ta av ail abil ity

Illegitimate Doubtfull Legitimate

LScore = Q1 – 1.5 x (Q3-Q1)

Genitor X Genitor Y

Progenies

M1_All1 M1_All2 M2_All1 M2_All2 M3_All1 M3_All2 … M11_All1 M11_All2 M12_All1 M12_All2 M1_All1 M1_All2 M2_All1 M2_All2 M3_All1 M3_All2 … M11_All1 M11_All2 M12_All1 M12_All2

No more 2 markers missing data

Parental data

Analy

sis

Generating Legitimacy Score (Lscore)

R esul t in terpr et ation Cl eanin g da

ta Data Base / new GeneMapper data product

Homozygote result plate1 Heterozygote result plate2

Inconsistency of result on the same sample

Distribution of logarithms of probabilities

-40 -30 -20 -10 0 Automated DNA extraction SSR Amplification and Genotyping DNA Cell organelles and proteins

DNA Lysis Binding

NucleoMag® C-Beads, Macherey-Nagel

Washes DNA elution

Biomek FX

(Beckman) ABI 3500xL, Applied, _{(Life Technology)}

M3 M5 M7 _M12 Leaf sampling and grinding

Analysis

• Probabilistic approach to

calculate « legitimacy score » • A defined threshold

determines the level of sample legitimacy M8 M1 M2 M4 M6 M10 M9 M11 www .cirad.fr