Genome-enabled parental analysis and predictions of breeding values in cassava

polycross mating scheme

Ikeogu Ugochukwu N.1,2*, Uzoechi A. Obioma1, Nwogu Ahamefule1, Ezenwaka

Lydia1, Ogbonna Alex1, Ezenwanyi Uba1, Linda Ezeji1, Ewa Favor1, Joseph Onyeka1, Adeyemi Olojede1, Peter Kulakow3, Egesi Chiedozie1 and Jean-Luc

Jannink2,4

1) National Root Crops Research Institute (NRCRI), Umudike, Nigeria; 2) Section of Plant Breeding, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, USA.; 3) International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria; 4) United States Department of Agriculture,

Agricultural Research Service, NY, USA *uni3@cornell.edu Registrant ID# 3292

World Congress on Root and Tuber Crops Nanning, Guangxi, China, January 18-22, 2016

Conventional mating methods

§ Most widely used §  Relatively precise – we have full control of the pedigree

§  Very simple and easy to implement

§  Expected higher genetic variability

§  Loss of parental control

2. Open pollinated

1. Full-sib

3. Polycross mating – not widely used

Definition: - Open pollination of a group of selected genotypes in isolation from other compatible genotypes

§  Limitations: similar to OP: o  Loss of full pedigree

control- Pollen donor/Father o  Low account of genetic

gain

An Isolated polycross field

Mating constraints- full sib crosses

•  Reduced number of effective parental combinations

•  Constrained genetic variability

•  Variable flower maturation and poor synchronization - same flowers on the same inflorescence can open at different times

•  Loss of potential genetic materials (flowers) in quality control measures : common practice to detach non pollinated flowers from a pollinated stalk

•  Labor intensive and technically demanding – sensitivity: rough handling can effect fruit set

•  Low expected number of progenies compared to other crops – as low as 2 seeds vs average of 300 in maize

Genomics era and implications in crop breeding:

Adopted from Dr. Karin Kassahn

Better marker information is giving rise to new or modified breeding methods

§ We can recover parental control § We can maintain high genetic

variability and increase genetic gain

§ We can save more money

Modified polycross scheme - paternity testing

What if we know the pollen donors?

•  Paternity evaluation to recover parental control •  Assess pollen donor rate and distribution •  Estimate the inbreeding •  Evaluate possible evidence of incompatibility among

pairs of parents •  Possible to estimate genetic effects – GCA, SCA •  Predict breeding values of polycross progenies using

genomic markers

Potentials of Genome-aided polycross scheme

•  438 clones were used to fit a prediction model

•  𝑦 = 𝑋𝛽 + 𝑍𝑢 + 𝑒

•  867 clones were used as selection candidates

•  22731 SNP markers •  31 parents with high GEBVs were selected

for bi-parental full-sib crosses from which 29 were used to design a polycross scheme

Choice of parents – genomic selection

Traits of interest – Selection index

Selection Index = biEBVi

Where i = HI , DMC, Starch, FYLD, Vigor,, CMD,CGM

b = P-1 Gv

p = phenotypic variance – covariance matrix

G = Genotypic variance-covariance matrix

V = economic weights (15,15,15,20,5,-10,-10,-10)

Economic weights were assigned to achieve a desired trait correlation

Field design and Establishment

u Observed maximum isolation – at least 100 m away

from neighboring fields

u Layout was designed to ensured adequate

randomization of clones – GenStat (Neighbor; Complete and quasi-

complete Latin Squares)

u Genotypes had similar flowering period

Schematic field layout of polycross design

Polycross design with 29 clones = 29x29 plots

Columns   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29  Rows        

1   7   18   19   3   12   6   28   20   11   13   21   1   26   4   10   23   9   15   5   16   29   24   22   14   17   25   2   8   27  

2   18   3   7   6   19   20   12   13   28   1   11   4   21   23   26   15   10   16   9   24   5   14   29   25   22   8   17   27   2  

3   19   7   12   18   28   3   11   6   21   20   26   13   10   1   9   4   5   23   29   15   22   16   17   24   2   14   27   25   8  

4   3   6   18   20   7   13   19   1   12   4   28   23   11   15   21   16   26   24   10   14   9   25   5   8   29   27   22   2   17  

5   12   19   28   7   11   18   21   3   26   6   10   20   9   13   5   1   29   4   22   23   17   15   2   16   27   24   8   14   25  

6   6   20   3   13   18   1   7   4   19   23   12   15   28   16   11   24   21   14   26   25   10   8   9   27   5   2   29   17   22  

7   28   12   11   19   21   7   26   18   10   3   9   6   5   20   29   13   22   1   17   4   2   23   27   15   8   16   25   24   14  

8   20   13   6   1   3   4   18   23   7   15   19   16   12   24   28   14   11   25   21   8   26   27   10   2   9   17   5   22   29  

9   11   28   21   12   26   19   10   7   9   18   5   3   29   6   22   20   17   13   2   1   27   4   8   23   25   15   14   16   24  

10   13   1   20   4   6   23   3   15   18   16   7   24   19   14   12   25   28   8   11   27   21   2   26   17   10   22   9   29   5  

11   21   11   26   28   10   12   9   19   5   7   29   18   22   3   17   6   2   20   27   13   8   1   25   4   14   23   24   15   16  

12   1   4   13   23   20   15   6   16   3   24   18   14   7   25   19   8   12   27   28   2   11   17   21   22   26   29   10   5   9  

13   26   21   10   11   9   28   5   12   29   19   22   7   17   18   2   3   27   6   8   20   25   13   14   1   24   4   16   23   15  

14   4   23   1   15   13   16   20   24   6   14   3   25   18   8   7   27   19   2   12   17   28   22   11   29   21   5   26   9   10  

15   10   26   9   21   5   11   29   28   22   12   17   19   2   7   27   18   8   3   25   6   14   20   24   13   16   1   15   4   23  

16   23   15   4   16   1   24   13   14   20   25   6   8   3   27   18   2   7   17   19   22   12   29   28   5   11   9   21   10   26  

17   9   10   5   26   29   21   22   11   17   28   2   12   27   19   8   7   25   18   14   3   24   6   16   20   15   13   23   1   4  

18   15   16   23   24   4   14   1   25   13   8   20   27   6   2   3   17   18   22   7   29   19   5   12   9   28   10   11   26   21  

19   5   9   29   10   22   26   17   21   2   11   27   28   8   12   25   19   14   7   24   18   16   3   15   6   23   20   4   13   1  

20   16   24   15   14   23   25   4   8   1   27   13   2   20   17   6   22   3   29   18   5   7   9   19   10   12   26   28   21   11  

21   29   5   22   9   17   10   2   26   27   21   8   11   25   28   14   12   24   19   16   7   15   18   23   3   4   6   1   20   13  

22   24   14   16   25   15   8   23   27   4   2   1   17   13   22   20   29   6   5   3   9   18   10   7   26   19   21   12   11   28  

23   22   29   17   5   2   9   27   10   8   26   25   21   14   11   24   28   16   12   15   19   23   7   4   18   1   3   13   6   20  

24   14   25   24   8   16   27   15   2   23   17   4   22   1   29   13   5   20   9   6   10   3   26   18   21   7   11   19   28   12  

25   17   22   2   29   27   5   8   9   25   10   14   26   24   21   16   11   15   28   23   12   4   19   1   7   13   18   20   3   6  

26   25   8   14   27   24   2   16   17   15   22   23   29   4   5   1   9   13   10   20   26   6   21   3   11   18   28   7   12   19  

27   2   17   27   22   8   29   25   5   14   9   24   10   16   26   15   21   23   11   4   28   1   12   13   19   20   7   6   18   3  

28   8   27   25   2   14   17   24   22   16   29   15   5   23   9   4   10   1   26   13   21   20   11   6   28   3   12   18   19   7  

29   27   2   8   17   25   22   14   29   24   5   16   9   15   10   23   26   4   21   1   11   13   28   20   12   6   19   3   7   18  

Results

u Over 16,000 seeds generated from

29 families

u  Sampled 950 individuals for

genotyping using GBS

u Average of 7 seeds from 4

individuals per family Differential seed yield

Expected analyses

u Paternity evaluation using genotype data •  Non-exclusion probability

•  Likelihood ratio

u  Determine pollen donor rate, rate of outcrossing/ inbreeding

u Estimate genetic effects - GCA and SCA

u Compare predictions and response to selection from full-sib mating: •  GBLUP

•  Pedigree-BLUP

Added benefits of modified polycross scheme

u Reduced chances of family contaminations

u Revelation of unexpected technical errors – transplanting and genotyping errors

u Reduced cost of generating seeds especially in small breeding programs

Important note: Efforts should be made to ensure that the clones do not have very wide flowering periods

Acknowledgements

Committee members q  Jean-Luc Jannink q  Susan McCouch q  Donald Viands

Jean-Luc & M. Sorrel’s Lab:

Thank you for Listening

Thank you