the genetics of chilling requirement in apricot (prunus armeniaca l.)

224 Pages·2016·4.04 MB·English

Clemson University
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5-2010
THE GENETICS OF CHILLING
REQUIREMENT IN APRICOT (PRUNUS
ARMENIACA L.)
Bode Olukolu
Clemson University, [email protected]
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THE GENETICS OF CHILLING REQUIREMENT IN APRICOT (PRUNUS
ARMENIACA L.)
____________________________________________

A Dissertation
Presented to
The Graduate School of
Clemson University
___________________________________________

In Partial Fulfillment
of the Requirements for the Degree
Doctor of Philosophy
Genetics
____________________________________________

by
Bode Adebowale Olukolu
May 2010
____________________________________________

Accepted by:
Dr. Albert G. Abbott, Committee Chair
Dr. Julia Frugoli
Dr. Chin-Fu Chen
Dr. Amy Lawton-Rauh
ABSTRACT
Commercial production of apricot is severely affected by sensitivity to climatic
conditions, an adaptive feature essential for cycling between vegetative or floral growth
and dormancy. Yield losses are due to either late winter or early spring frosts or inhibited
vegetative or floral growth caused by unfulfilled chilling requirement (CR). Studies in
this dissertation developed the first high-density apricot linkage map; followed by a
comparative mapping strategy to validate conservation of synteny, genome collinearity
and stable quantitative trait loci (QTLs) controlling CR and bud break between apricot
and peach; and ultimately attempt to identify key candidate genes following a linkage
disequilibrium-based association mapping approach to fine map the major CR QTL
genomic regions.
Following a two-way pseudotestcross mapping strategy, two high-density apricot maps
were constructed using a total of 43 SSR (Simple Sequence Repeats) and 994 AFLP
(Amplified Fragment Length Polymorphism) markers that span an average of 502.6 cM
with an average marker interval of 0.81 cM. Twelve putative CR QTLs were detected
using composite interval mapping, a simultaneous multiple regression fit and an additive-
by-additive epistatic interaction model without dominance. An average of 62.3% ± 6.3%
of the total phenotypic variance was explained. We report QTLs corresponding to map
positions of differentially expressed transcripts and suggest candidate genes controlling
CR.
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A majority of the QTLs were shown to be stable between both Prunus species, as well as
similar trends in their QTL effects, with the allele for increasing the trait value mostly
originating from the high chill parents. The denser apricot maps, due to more AFLP
marker polymorphisms, provide a higher resolution to delineate QTLs to smaller genomic
intervals, as well as splitting each of some of the peach QTLs into two. The comparative
QTL mapping strategy presented here reveals the transferability of genetic information
between two Prunus species, the characterization of stable QTLs, the utility of the maps
to consolidate each other and to further validate previously identified CR QTL loci as a
major controlling factor driving floral bud break.
The LD-based association mapping was limited to marker dense genomic regions within
and around previously detected major QTLs on linkage group (LG) 1 and 7. LD decayed
below the centimorgan scale, indicating insufficient marker density averaged at 0.44 and
1.58 cM on LG1 and 7, respectively. Denser marker regions averaged at 0.1 and 0.7 cM
on LG1 and 7, respectively, revealed significant LD estimates above the baseline
threshold. We report significant marker-trait associations and underlying genes the
markers were derived from. Our results demonstrate that an LD-based association
mapping can be used for validating QTLs, fine mapping and detecting CGs in Prunus.
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ACKNOWLEDGEMENTS
I would like to thank my advisor, Dr. Albert Abbott, for giving me the opportunity to
work with him and for always been there as a mentor and guide. I also extend my
gratitude to my committee members: Dr. Julia Frugoli, Dr. Chin-Fu Chen and Dr. Amy
Lawton-Rauh, for all their support and advice throughout the program.
Thanks to Dr. Doron Holland and Taly Trainin for providing, maintaining and scoring the
phentoypes on the apricot mapping population, Dr. William Okie for providing the peach
mapping population, Dr. Gregory L. Reighard and Dr. Douglas G. Bielenberg for
maintaining the peach mapping population an Dr. Valentina Gorina for maintaining and
scoring the phenotypic data on the apricot germplasm used for the association mapping.

Special thanks to members of the Abbott‟s lab. Thanks to Dr. Tatyana N. Zhebentyayeva,
for establishing the collaboration on the association mapping, providing apricot
germplasm DNA samples, designing SSR markers and for her help on several occasions
as a senior colleague and friend. Thanks to Dr. Laura L. Georgi, who made life in the lab
comfortable and who was always available as a resource person. Thanks to Dr. Renate
Horn for all her unrelenting help, Dr. Chittaranjan Kole whose help I can‟t list
exhaustively and to graduate students who showed me the ropes: Renea Hardwick, Fan
Shenghua and Samuel Forrest. I would also like to thank Sherri Hughes-Murphree,
Megan Mosanto and Phullara Kole for their support in the lab and Jeanice Troutman of
CUGI for her help with DNA sequencing.
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TABLE OF CONTENTS
Page
TITLE PAGE ....................................................................................................................... i
ABSTRACT ........................................................................................................................ ii
ACKNOWLEDGMENTS ................................................................................................. iv
LIST OF TABLES ............................................................................................................. ix
LIST OF FIGURES .............................................................................................................x
CHAPTER
I LITERATURE REVIEW ............................................................................1
Introduction .....................................................................................1
Regulation of growth cycles and dormancy
in woody perennials .........................................................................3
Complexity of bud dormancy and its overlap
with related biological processes ...................................................10
Dormancy induction.......................................................................14
Bud dormancy maintenance and release ........................................18
Genetic control of endodormancy-related
traits in woody perennials ..............................................................22
Summary of chapters .....................................................................26
References ......................................................................................30
II GENETIC LINKAGE MAPPING FOR MOLECULAR DISSECTION
OF CHILLING REQUIREMENT AND BUD BREAK IN APRICOT
(PRUNUS ARMENIACA L.) ......................................................................47
Abstract ..........................................................................................48
Introduction ....................................................................................49
Materials and methods ...................................................................50
Results ............................................................................................59
Discussion ......................................................................................70
Conclusion .....................................................................................74
Acknowledgement .........................................................................75
References ......................................................................................76
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III COMPARATIVE ANALYSIS OF QTLS UNDERLYING CHILLING
REQUIREMENT AND BUD BREAK IN PEACH (PRUNUS PERSICA
L.) AND APRICOT (P. ARMENIACA L.) ................................................82
Abstract ..........................................................................................83
Introduction ....................................................................................84
Materials and methods ...................................................................86
Results ............................................................................................90
Discussion ....................................................................................103
Acknowledgement .......................................................................105
References ....................................................................................106
IV ASSOCIATION MAPPING FOR CANDIDATE GENES UNDERLYING
FLORAL BUD BREAK IN APRICOT (PRUNUS ARMENIACA L.) ....109
Abstract ........................................................................................110
Introduction ..................................................................................112
Materials and methods .................................................................115
Results ..........................................................................................122
Discussion ....................................................................................134
Conclusion ...................................................................................142
Acknowledgement .......................................................................143
References ....................................................................................144
V CONCLUSION ........................................................................................152
APPENDICES .................................................................................................................154
A: AFLP E (EcoRI) and M (MseI) primer combinations ......................................155
B1: Comparative analysis of Prunus linkage groups 1 and 4 ..............................156
B2: Comparative analysis of Prunus linkage groups 3 and 4 ..............................157
B3: Comparative analysis of Prunus linkage groups 5 and 6 ..............................158
B4: Comparative analysis of Prunus linkage groups 7 and 8 ..............................159
C: Assignment of apricot accessions to subpopulations ......................................160
D: SSR primer sequences used for association mapping .....................................162
E1: SSR markers and predicted genes on linkage group 1 ..................................163
E2: SSR markers and predicted genes on linkage group 7 ..................................164
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F1: Linkage disequilibrium within a 14 cM interval of
linkage group 1 ................................................................................................165
F2: Linkage disequilibrium within a 25 cM interval of
linkage group 7 ................................................................................................166
G: Goldrich apricot BAC clones positive for probes
designed from putative candidate gene sequences ..........................................167
H1: Map-based cloning of CONSTANS from the Goldrich
cultivar apricot BAC library ............................................................................168
H2: Gene phylogeny of CONSTANS ...................................................................172
I1: Map-based cloning of SUCROSE TRANSPORTER
1from the Goldrich cultivar apricot BAC library ............................................173
I2: Gene phylogeny of SUCROSE TRANSPORTER 1 ........................................176
J: Map-based cloning of LEAFY from the Goldrich cultivar
apricot BAC library .........................................................................................177
K: Map-based cloning of APETALA 2 from the Goldrich
cultivar apricot BAC library ............................................................................178
L: Map-based cloning of FLOWERING LOCUS T from the
Goldrich cultivar apricot BAC library .............................................................179
M: Map-based cloning of TERMINAL FLOWER from the
Goldrich cultivar apricot BAC library .............................................................180
N: Map-based cloning of candidate genes for MITOGEN
ACTIVATED PROTEIN KINASE 7 from the Goldrich
cultivar apricot BAC library ............................................................................181
O1: Map-based cloning ABSCISIC ACID–INSENSITIVE 3
from the Goldrich cultivar apricot BAC library ..............................................182
O2: Gene phylogeny of ABSCISIC ACID–INSENSITIVE 3 ................................186
P: Comparative and functional genomics in Rhizobium-
Legume and Frankia-Actinorhizal systems .....................................................187
Q: License for Figure 1.2 .....................................................................................214
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LIST OF TABLES
Table 2.1: SSR markers mapped on parental maps ...........................................................60
Table 2.2: AFLP and SSR marker analysis .......................................................................61
Table 2.3: Results on genetic linkage maps .......................................................................64
Table 2.4: QTLs detected for chilling requirement ...........................................................69
Table 2.5: Digenic interactions of QTL controlling CR ....................................................70
Table 3.1: Stable QTLs between peach and apricot ..........................................................92
Table 3.2: Proportion of phenotypic variance by peach QTLs ..........................................99
Table 3.3: QTLs detected for chilling requirement in apricot .........................................100
Table 3.4: Apricot QTL interactions without dominance a model ..................................101
Table 3.5: Apricot QTL interactions with dominance a model .......................................102
Table 4.1: List of apricot germplasm accessions .............................................................117
Table 4.2: Assignment of subpopulations to geographical regions .................................124
Table 4.3: Allele-frequency divergence between subpopulations ...................................125
Table 4.4: Fst estimates for sub-populations ...................................................................126
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LIST OF FIGURES
Figure 1.1: Timetable of bud development ..........................................................................4
Figure 1.2: Flowering time control in Arabidopsis and cereals ...........................................8
Fig. 2.1: Genetic linkage maps (linkage groups 1, 2, 3, and 4) .........................................63
Fig. 2.2: Genetic linkage maps (linkage groups 5, 6, 7, and 8) .........................................64
Fig. 2.3: Frequency distribution of phenotypes .................................................................68
Figure 3.1: Comparative QTL analysis between peach and apricot ..................................93
Figure 4.1: Bar plots showing population stratification...................................................127
Figure 4.2: Estimating appropriate number of subpopulations ........................................128
Figure 4.3: LD estimates of r2 plotted vs. genetic linkage distance. ................................131
Figure 4.4: Marker-trait association on Linkage groups 1 and 7 .....................................133

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