Genomic prediction in rye Angela Maria Bernal Vasquez

240 Pages·2017·4.62 MB·English

Genomic prediction in rye
A THESIS SUBMITTED TO
THE FACULTY OF AGRICULTURAL SCIENCES
OF UNIVERSITY OF HOHENHEIM
IN FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF
DR.SC.AGR. / PH.D. IN AGRICULTURAL SCIENCES
Angela Maria Bernal Vasquez
FacultyofAgriculturalSciences
UniversityofHohenheim
March2017

FACULTYOFAGRICULTURALSCIENCE
InstituteofCropScience
UniversityofHohenheim
BiostatisticsUnit
Prof. Dr. Hans-PeterPiepho
Genomic prediction in rye
Dissertation
submittedinfulfillmentoftheregulationstoacquirethedegree
“DoktorderAgrarwissenschaften”
(Dr.sc.agr. /Ph.D.inAgriculturalSciences)
tothe
FacultyofAgriculturalSciences
presentedby:
AngelaMariaBernalVasquez
bornin:
Bogota,Colombia
submittedin: March2017
This thesis was accepted as a doctoral thesis (Dissertation) in fulfilment of the regulations
toacquirethedoctoraldegree“DoktorderAgrarwissenschaften”bytheFacultyofAgricultural
SciencesatUniversityofHohenheimonAugust4th,2017
Dateoftheoralexamination: October24th,2017
ExaminationCommittee
Chairpersonoftheoralexamination Prof. Dr. Bennewitz
SupervisorandReviewer Prof. Dr. Hans-PeterPiepho
Co-Reviewer Prof. Dr. Chris-CarolinScho¨n
(TechnischeUniversita¨tMu¨nchen)
Additionalexaminer Prof. Dr. AlbrechtE.Melchinger
iii
To my closest ancestors, my full-sib and my tester
i
ii
Acknowledgments
During this long journey of making my PhD I have met people who have walked with me and
havehelpedmeeitherwithwords,withfactsorwithenergy. ThefirstoneIamindebtedto,and
to whom I will never have enough words to thank is my “Doktorvater” Prof. Dr. Hans-Peter
Piepho. He has guided my research with accurate advice and scientific curiosity. Thank you
for the endless support and patience, for having always time for answers and for your constant
inspiration. Ithasbeenagreathonortoworkwithyou.
Many thanks also to Prof. Dr. Chris-Carolin Scho¨n for her always fine-tuned insights as
project partner, co-author and now as part of the examination committee. Thanks to Prof. Dr.
A. E. Melchinger for his plant breeding lectures building a baseline for this work and also for
agreeingtoserveonmydissertationcommittee.
Massive dues to Dr. Andres Gordillo, who made the bridge for me towards Germany and
had always accurate personal and professional advices. He has contributed with very practical
viewsofthesometimesencryptedresultsandhasalwaysallocatedtimetofollow-upanddiscuss
ourwork.
It was a pleasure for me to be part of the elite group of Rye-Select. I learnt so many things
during the project meetings and profited from the discussions and ideas exchanged. Thanks to
all the group led by Dr. Peer Wilde and Dr. Viktor Korzun, for allowing the use of the data and
the crew support. Big big thanks to my co-authors Malthe Schmidt and Manfred Scho¨nleben
(wherever you are) for such good job cooperation and empathy. To Dr. H. F. Utz, who shared
allhisPlabStatoutliersecretsandwatchedoutthispublication. Doublethankstomycolleague
JensMo¨ringforusefulhintsatthebeginningoftheway,forco-authoringandhisunconditional
supportovertheseyears.
IamverygratefultomycolleaguesintheBiostatisticsgroup,theoldandthenewones,for
iii
the cheerful and positive atmosphere, useful discussions and good laughs. To Zeynep Akyildiz
for taking care of my logistics and her sweet willingness to help. To Joseph O. Ogutu for
his genomic selection input and Waqas Malik for his R guidance, to Vanda Lourenc¸o for her
cheerfuladvice,toTorbenSchulz-StreeckmySASsensei,andtoSteffenHadashforwalk&talk
company while philosophical and statistical musing. Extra thanks to my Hohenheim friends,
the ones that are still there and the ones that have already left, because celebrating success
felt double with your company and sharing sadness felt half: Marcelo (my soul buddy), Oscar,
Joaqu´ın, Hanna & Juan & Isabel, Manuel, Yudith, Valheria & Jose´, Lina, Lucia & Marco. The
thanks also cross the ocean and go to my friends in Colombia (Pipe, Migue, Natali, AngelaP)
and to my former professors Jose´ Miguel Cotes and Luis Ernesto Rodr´ıguez. I could always
countonthemtosolvecontextualizationdoubtsandtokeepconnectedtomyrootsandspirit.
IwanttothankmyGermanfamily,whotookmeintheirheartwithcareandwarmth. Tomy
Colombian family, my mother, my father and my brother to whom I dedicate this work. You
havebeenmyinfinitesunateverymomentfillingmewithlove,passionand“empuje”: Gracias
por su infinito apoyo, a´nimo y energ´ıa!. Thank you to my dearest Gerald, for biking, walking
and swimming with me, no matter what the conditions were, hand in hand all throughout this
GranFondo. Thankyousoooomuchforever!.
Ifinallythankyouunknownreaderforsearchinganswersinmywork.
iv
Table of Contents
Acknowledgments iii
Nomenclature ix
ListofFigures xix
ListofTables xxv
1 Introduction 1
1.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Thehybridryebreedingprogram . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 Residualanalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.4 Phenotypicanalysistowardsgenomicprediction . . . . . . . . . . . . . . . . . 5
1.4.1 Astage-wiseapproachforphenotypicandgenomicpredictionanalyses 5
1.4.2 Genomicpredictionandrelatedfactors . . . . . . . . . . . . . . . . . 6
1.4.3 Genomicpredictionmodels . . . . . . . . . . . . . . . . . . . . . . . 7
1.5 Themodelchoice: linkingphenotypestogenotypes . . . . . . . . . . . . . . . 9
1.5.1 Spatialmodelsasanadd-onofthephenotypicmodel . . . . . . . . . . 9
1.5.2 Genomic prediction - cross validation (GP-CV) as a tool for model
selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.5.3 Accountingforgenotype-by-environment(GE)interactioneffects . . . 11
1.6 Objectivesandhypotheses . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
1.7 Outlineofthethesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
v