Genetics of mineral accumulation in potato tubers. PhD thesis, University of Nottingham.

338 Pages·2017·25.39 MB·English

by  Christine Middleton

The James The University of
Hutton Nottingham
II
lallnstitute
Genetics of mineral accumulation in potato
tubers
Nithya Subramanian
A Thesis Submitted for the Degree of
Doctor of Philosophy
University of Nottingham
September 2011
IMAGING SERVICES NORTH
Boston Spa, Wetherby
West Yorkshire, LS23 7BQ
www.bl.uk
TH ESIS CONTAI NS
.
,
CD
ABSTRACT
As a major food source potato delivers significant levels of minerals to the
human diet. The aim of this study was to understand the control over the
mineral concentrations found in tubers. The three-dimensional patterns of
mineral distribution in tubers give clues to the processes leading to storage in
the tuber. Within the tuber flesh, calcium and phosphorus content decreased
towards the centre of the tuber (on FW basis). The elements iron, magnesium,
zinc, manganese, sulphur and chlorine were higher at the stem end, while
potassium was higher at the bud end. Remobilisation of minerals within the
tuber was evident after six months of cold storage. Mineral variation was
explored in potato germplasm. Three diverse germplasm collections, the
Commonwealth Potato Collection, the Phureja and Tuberosum Core Collection
and the Neotuberosum Population demonstrated wide variation for tuber
mineral concentrations, an interaction with tuber yield and, on multivariate
analysis, consistent parallels between some minerals suggesting unsuspected
shared processes affecting their concentrations. The 12601ab1 x Stirling
tetraploid mapping population was used to identify QTls for tuber mineral
concentration using REML analysis to account for local field variation.
Transgressive segregation for tuber mineral concentrations was detected. The
genetic map for this population was extended using DArT markers and QTLs
were identified on all 12 linkage groups for all minerals studied. Two bulk
segregant analyses were performed to add precision to the QTL analysis. One
approach identified candidate genes on the potato genome sequence and used
nearby SSRs to seek association in the tetraploid mapping population. A second
approach used the variation present in the highly diverse Neotuberosum
Population to identify DArT markers which were associated with the tails of the
distribution of minerals. Using the latter approach, single superscaffolds
containing candidate loci and trait-associated DArT markers could be aligned
with a small part of mapping population QTLs, providing additional resolution.
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ACKNOWLEDGMENTS
I would like to convey my sincere gratitude to my major advisor Dr. Gavin
Ramsay for his advice, guidance and care shown throughout the course of the
project. I am grateful to my co-advisors Prof. Philip White and Dr. Martin
Broadley for their valuable discussions and expert guidance, which made this a
very successful project. I profusely thank Dr. Christine Hackett for her help with
statistical analysis and QTL mapping, without which a comprehensive thesis was
not possible. I extend my gratitude to Dr. linda Cardle for helping with
bioinformatic analysiS. I am very appreciative of my lab manager Gaynor
McKenzie for her assistance with laboratory tools and techniques, which
facilitated the successful completion of various experiments in a timely manner.
I would like to extend my sincere thanks to Drs. Glenn Bryan, Finlay Dale, John
Bradshaw, Sanjeev Kumar, Ankush Prashar and Karen Mclean for their valuable
contributions during different stages of this work. I am thankful to my scientific
assessors Drs. Alison Karley (JHI), Sean Mayes (Nottingham), and liaison officer
Dr. Craig Simpson (JHI) for their guidance and support. My special thanks to Mr.
Ralph Wilson and his associates for help with potato planting and harvesting,
and Mr. Euan Caldwell and his colleagues for field plot maintenance. I am very
grateful to Ms. Jacqueline Thompson and Dr. Alison Karley for their assistance
with acid-digestion and ICP-MS analysis, and Dr. louise Shepherd and her group,
Ms. Jacqueline Thompson and Mrs Gladys Wright for helping with potato sample
preparation. I am also thankful to Dr. John Hammond at Warwick HRI for ICP
mineral analysiS of tuber samples during 2008 and 2009. I am grateful to Mr.
Philip Smith for his help in proofreading my thesis.
My special appreciation to all the staff, student friends and officemates for their
support and for providing an excellent working environment. I particularly thank
Drs. Naeem Sayed and Lea Wiesel for their support throughout my stay at JHI. I
am grateful to Mr. K. V. Subramaniam for providing moral support during critical
times of my thesis. I am very thankful to Ms. Sonoko Mitsui-Angwin at University
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of Nottingham for her invaluable help with my thesis submission. I also thank my
current post-doctoral advisor, Dr. Esten Mason, University of Arkansas, for his
timely support during the process of final thesis submission.
Last, but not least, I am very thankful for funding from the University of
Nottingham Tuition Fee Scholarship by the International Office and a University
of Nottingham/SCRI studentship, which made my PhD programme possible. Any
omission from this list is only an oversight and does not constitute a lack of
gratitude.
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DEDICATION
This thesis is affectionately dedicated to my family
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DECLARATION
I hereby declare that the following thesis is based on the results of investigations
conducted by myself, and that it is of my own composition. This thesis has not, in
whole or in part, been previously presented for a higher degree or qualification.
Work other than my own is clearly indicated in the text by reference to the
relevant researchers or their publications.
Nithya Subramanian
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TABLE OF CONTENTS
CHAPTER 1 GENERAL INTRODUCTION AND OBJECTIVES ••••••••••••••••••••••••••••••••••• 1
1.1 MINERALS AND HUMAN HEALTH ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 1
1.1.1 Mineral elements required by humans ................................................ 1
1.1.2 Mineral deficiency in humans ............................................................... 1
1.2 PLANT MINERAL NUTRITION •••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 3
1.2.1 Mineral requirements of plants ............................................................ 3
1.2.2 Mineral deficiency in plants .................................................................. 3
1.2.3 Physiological genetics of plant mineral nutrition .................................. 4
1.2.3.1 Iron ................................................................................................. 5
1.2.3.2 Zinc ......................................•.................•......•.......•...•..••..••.....•...•... 8
1.2.3.3 Calcium .....•.............•...•......•.....••...••.••...•..•..•.•.......•.••..••....•.•........... 9
1.2.3.4 Potassium ..................................................................................... 11
1.2.3.5 Copper ........................................•.....................................•........... 12
1.2.3.6 Magnesium ..........................•....•...•.... ,. ............ ,. ...•.............. ,. ....... 14
1.3 ENHANCING MINERAL CONCENTRATIONS IN EDIBLE CROP PARTS FOR
HUMAN NUTRITION ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 14
1.3.1 The need for crop biofortification ....................................................... 14
1.3.2 Agronomic biofortification .................................................................. 15
1.3.3 Genetic biofortification ••...... ,. .........•......•...••..••..•.......•...•..•...•.........•..• 16
1.3.4 Potatoes as a candidate for mineral enhancement ............................ 18
1.4 ABOUT POTATOES ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 19
1.4.1 History of potatoes .•..•.......•.......................•...•......•...••••....•.............•..•• 19
1.4.2 Recent advances in potato genetics .................................................... 20
1.4.3 World potato production and consumption ....................................... 21
1.4.4 Nutritional value of potatoes .............................................................. 22
1.5 PHYSIOLOGY OF MINERAL ACCUMULATION IN POTATO TUBERS .............. 23
1.5.1 Anatomy and morphology of the potato tuber .................................. 23
1.5.2 Potato roots and mineral acquisition .................................................. 25
1.5.3 Mineral composition of tubers during development .......................... 26
1.5.4. The potential to modify/enhance tuber mineral concentrations ...... 27
1.6 LINKAGE MAPPING AND QTL ANALYSIS IN POTATOES .............................. 28
1.7 THESIS OBJECTIVES AND EXPERIMENTAL APPROACH ................................ 33
CHAPTER 2 MATERIALS AND METHODS ......................................................... 35
2.1 PLANT MATERIAL ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 3S
2.1.1 Mineral distribution studies ................................................................ 35
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2.1.1.1 Distribution of minerals within Stirling tubers shortly after harvest
(Experiment 1) ........................................................................................... 35
2.1.1.2 Distribution of minerals within tubers of two genotypes following
long-term cold storage (Experiment 2) ..................................................... 35
2.1.2 Diverse populations ..................•......•..•..••.....•...•...•..•.....•.•.•................• 36
2.1.3 Tetraploid genetic mapping population .............................................. 39
2.2 GROWING CONDITIONS ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 40
2.2.1 Glasshouse and field conditions .......................................................... 40
2.2.2 Meteorological data ............................................................................ 41
2.3 TUBER SAMPLING ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••.••••••• 42
2.3.1 Harvesting ............................................................................................ 42
2.3.2 Sample preparation ............................................................................. 43
2.3.2.1 Mineral distribution studies (Experiments 1 and 2) ..................... 43
2.3.2.2 Diverse (Core Collection and NTB) and mapping populations ..... 46
2.4 ACID DIGESTION AND MINERAL ANALYSIS ................................................ 48
2.5 MOLECULAR METHODS •••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 51
2.5.1 Genomic DNA extraction ..................................................................... 51
2.5.2 Amplified Fragment Length Polymorphism procedure ....................... 51
2.5.3 Simple Sequence Repeats .................................................................... 55
2.5.4 Diversity Arrays Technology ................................................................ 56
2.6 STATISTICAL ANALYSIS ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 57
2.6.1 Statistical analysis for the mineral distribution studies ...................... 57
2.6.2 Statistical analysis for the diverseand mapping populations .............. 57
2.7 CONSTRUCTION OF LINKAGE MAPS AND QTL ANALYSIS ........................... 59
2.7.1 Selection of molecular markers for map construction ........................ 60
2.7.2 Marker ordering ......••..•.....•.•.•....•......•...••......•...•.•.....•...•.......•........•..•. 60
2.7.3 Chromosomal identity ....................................................... , ............•.... 61
2.7.4 Alignment of the parental genetic maps ............................................. 61
2.7.5 QTL analysis using interval mapping ................................................... 61
CHAPTER 3 DISTRIBUTION OF MINERAL ELEMENTS WITHIN POTATO TUBER
FOLLOWING POST-HARVEST STORAGE ....................................................... 64
3.1 INTRODUCTION ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 64
3.2 RESULTS ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 68
3.2.1 Partitioning of minerals between the skin and flesh regions of tuber .... 68
3.2.2 Pattern of OM and mineral distributions within the tuber ..................... 68
3.2.2.1 General patterns of distribution ................................................... 68
3.2.2.2 Effect of genotype ........................................................................ 72
3.3 DISCUSSION ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 77
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3.3.1 Mineral partitioning between the skin and the flesh of potato tubers ... 77
3.3.2 OM and mineral distributions in tubers as influenced by genotype and
post-harvest storage conditions ................................................................... 78
3.3.2.1 Dry matter .................................................................................... 80
3.3.2.2 Magnesium, sulphur, zinc, iron and manganese ......................... 81
3.3.2.3 Phosphorus, calcium and copper ................................................. 83
3.3.2.4 Potassium, caesium and chlorine ................................................. 86
3.4 CONCLUSiONS .....•.....................•..•...•.•...•......••...•..••.•.•....•...•...................• 88
3.4.1 Implications for understanding mineral accumulation in tubers ............ 88
3.4.2 Implications for human nutrition ............................................................. 88
3.4.3 Implications for tuber sampling protocol for mineral analysis ................ 89
CHAPTER 4 TUBER MINERAL CONCENTRATIONS IN DIVERSE POTATO
GERM PLASM ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 90
4.1 INTRODUCTION ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 90
4.2 RESULTS .••...•..••..•••..••...•....••••••.....•••••.•••.••••.•••••••••••••••••••••••.••.••••••.•••...•.•.• 91
4.2.1 Mineral variation in CPC accessions ..................................................... 91
4.2.2 Mineral variation in the Core Collection .............................................. 94
4.2.2.1 Genetic diversity for tuber mineral concentrations ...................... 94
4.2.2.2 Associations among plant maturity, tuber yield, DM and
mineral concentrations ............................................................................. 99
4.2.2.3 Heritabilities ................................................................................ 104
4.2.3 Mineral variation in the NTB population ........................................... 105
4.2.3.1 Genetic diversity for tuber minerals ............................................ 105
4.2.3.2 PCA ordination of the variables .................................................. 107
4.3 DISCUSSION •.............................•....•.......•..............................•......•......... 109
4.3.1 Genetic variation for tuber mineral concentrations .......................... 109
4.3.1.1 CPC accessions ............................................................................ 109
4.3.1.2 Core Collection ............................................................................ 112
4.3.1.3 NTB population ........................................................................... 115
4.3.2 Prospects for mineral enhancements in potatoes ..................................... 118
CHAPTER 5 VARIATION IN TUBER MINERAL COMPOSITION IN A TETRAPLOID
MAPPING POPULATION ...........•...•.......•...••...•..•..................................•...• 122
5.1 INTRODUCTION ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••• 122
5.2 RESULTS ....•.......•.•.•••••.•••...•.....••••...•..................•..•....•••...•.••..................• 123
5.2.1 Phenotypic variation among the clones ................................................ 123
5.2.2 Relationships among plant emergence, maturity, tuber yield, OM, and
mineral concentrations ............................................................................... 127
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