Genome-enabled parental analysis and predictions of breeding values in cassava polycross mating scheme Ikeogu Ugochukwu N. 1,2 * , Uzoechi A. Obioma 1 , Nwogu Ahamefule 1 , Ezenwaka Lydia 1 , Ogbonna Alex 1 , Ezenwanyi Uba 1 , Linda Ezeji 1 , Ewa Favor 1 , Joseph Onyeka 1 , Adeyemi Olojede 1 , Peter Kulakow 3 , Egesi Chiedozie 1 and Jean-Luc Jannink 2,4 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 *[email protected]Registrant ID# 3292 World Congress on Root and Tuber Crops Nanning, Guangxi, China, January 18-22, 2016
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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 *[email protected] 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-