Breeding for durable resistance to angular leaf spot

156 Pages·2014·3.5 MB·English

Breeding for durable resistance to angular leaf spot (Pseudocercospora griseola)
in common bean (Phaseolus vulgaris) in Kenya

By
Ng’ayu-Wanjau Beatrice Njoki

BSc Horticulture and MSc Horticulture
Jomo Kenyatta University of Agriculture and Technology, Kenya

A thesis submitted in partial fulfilment of the requirements for the degree of
Doctor of Philosophy (PhD) in Plant Breeding

African Centre for Crop Improvement (ACCI)
School of Agricultural, Earth and Environmental Sciences
College of Agriculture, Engineering and Science
University of KwaZulu-Natal
Republic of South Africa

November 2013
Thesis abstract
Common bean (Phaseolus vulgaris L.) is an important legume crop in Kenya and is a cheap
source of proteins. The small scale farmers in Kenya produce common bean under low
agricultural input systems and this predisposes the crop to pests and diseases. Among the
diseases, angular leaf spot (ALS) is a major constraint to common bean production and
contributes to yield losses as high as 80%. The causative pathogen Pseudocercospora griseola
(Sacc.) Crous & Braun is highly variable and several races have been reported. There are few
common bean genotypes with resistance to this disease. Therefore breeding for resistance to
ALS is important for the country. This study was carried out to; i) evaluate the common bean
production systems, constraints and farmer varietal preferences in Kenya, ii) evaluate local
landraces and selected introductions of common bean for yield performance and reaction to
ALS, iii) study the genetics of resistance to ALS in common bean and iv) develop a breeding
method for durable resistance to ALS in common bean.
To determine the common bean production systems, farmers’ preferred traits and their
knowledge on common bean constraints including ALS, a survey was conducted in Kiambu
county using a semi-structured questionnaire, interviews, and focus group discussions. The
study revealed that farmers cultivate common beans during the short and long rain seasons.
However, they experience better yields in the short rains due to reduced disease incidence. The
majority of the farmers (71%) intercrop common bean and this ensures maximum utilisation of
space. A high percentage (70%) of the farmers utilise their retained seed for production. The
farmers identified ALS as one of the most important constraints to production. The only
preventative measure they undertake to control the disease is weeding. The farmers reported
that they would prefer improved varieties that were resistant to ALS. Farmers have a preference
for particular common bean traits that include high yield (80%), resistance to insect-pests and
diseases (72%), type I growth habit (52%), early maturity (68%), seed size and colour (21%)
and cooking time (20%). These should be incorporated in breeding programmes.
Two hundred common bean landraces and market class varieties were evaluated for ALS
resistance in a nethouse at University of Nairobi, Kabete Field Station and for ALS resistance
and yield in the field in KARI-Tigoni. The results showed that disease severity scores for the
genotypes were similar in the two locations, with the top three resistant genotypes being
Minoire, GBK 028123 and Murangazi with disease severity scores of 2.9, 2.9 and 3.2 in Kabete
ii
and 2.6, 2.8, and 2.9 in Thika respectively. These resistant genotypes can be used as sources
of resistance in a breeding programme or they can be used as resistant varieties. All the market
class varieties were susceptible to ALS (disease severity score 6.7-8.0). There was a non-
significant correlation between disease and yield most likely because most of the resistant
genotypes were exotic and hence not adapted to the local conditions. There was also a non-
significant correlation between disease and seed size.
The two hundred common bean genotypes were evaluated for yield at University of Nairobi,
Kabete Field Station and KARI-Thika. The results indicated that the 2011 and 2012 seasons
had similar mean yields and that yields at Kabete were higher than at KARI-Thika. The highest
yielding genotypes across the two locations were; GLP 2 (766 kg ha-1), Nyirakanyobure
(660 kg ha-1), GBK 028110 (654 kg ha-1), GLP 585 (630 kg ha-1) and Mukwararaye
(630 kg ha-1). There was a significant genotype x environment interaction and hence it is
important for breeders to carry out stability analysis, so as to recommend varieties for a wide
range of environments.
To study the genetics of ALS resistance in common bean, three inter-gene pool crosses:
Super-rosecoco x Mexico 54, Wairimu x G10909 and Wairimu x Mexico 54 were made. The
resistant genotypes were Mexico 54 and G10909, while Super-rosecoco and Wairimu were
susceptible. The generations F , F , BC P and BC P for each of the crosseswere developed.
1 2 1 1 1 2
The parents P , P and the five generations of each cross were evaluated for resistance to ALS
1 2
in Kabete Field Station. Results showed that both dominance and additive gene action were
important in the expression of resistance to ALS. However, additive gene action was
predominant over dominance gene action. There was a moderately high narrow sense
heritability estimate (52.9-71.7%). The minimum number of genes controlling resistance to ALS
was between 2 and 3. The predominance of additive gene effects and the moderately high
narrow sense heritability estimates recorded imply that progress in resistance to ALS could be
made through selection in the early segregating generations.
A double cross followed by selection against resistant genotypes was used to develop a method
to breed for durable resistance to ALS in common bean. The method was used to accumulate
minor genes of ALS resistance into single genotypes. Four intermediate resistant landraces
were used to develop a double cross population that was screened using a mixture of ALS
races. Selection in F and F population was done on the basis of intermediate resistance
1 2
(disease severity score 4.0-6.0), while selection from F population was based on resistance
3
iii
(disease severity score 1.0-3.0). Ten advanced F lines along with their parents were evaluated
4
for ALS resistance. The F advanced lines had a significantly improved resistance to ALS
4
compared to their parents. Hence the method was successful in accumulating minor genes for
resistance thus showing significant breeding progress in breeding for durable resistance.

iv
Declaration
I, Beatrice Njoki Ng’ayu-Wanjau, declare that
1. The research reported in this thesis, except where otherwise indicated, is my original
research.
2. This thesis has not been submitted for any degree or examination at any other university.
3. This thesis does not contain other persons’ data, pictures, graphs or other information, unless
specifically acknowledged as being sourced from other persons.
4. This thesis does not contain other persons' writing, unless specifically acknowledged as
being sourced from other researchers. Where other written sources have been quoted, then:
a) Their words have been re-written but the general information attributed to them has
been referenced
b) Where their exact words have been used, then their writing has been placed in italics
and inside quotation marks, and referenced.
5. This thesis does not contain text, graphics or tables copied and pasted from the Internet,
unless specifically acknowledged, and the source being detailed in the thesis and in the
references sections.

Signed ………………………………………………Date………………………………………..
Beatrice Njoki Ng’ayu-Wanjau

As the candidate’s supervisors, we agree to the submission of this thesis:

Signed ………………………………………………Date………………………………………………

Prof. Rob Melis (Principal supervisor)

Signed ……………………………………………..Date………………………………………………

Prof. Githiri Mwangi (Co-Supervisor)

Signed………………………………………………Date………………………………………………

Dr Julia Sibiya (Co-Supervisor)

v
Acknowledgements
I would like to express my sincere gratitude to my supervisors, Professor Rob Melis, Professor
Githiri Mwangi and Dr Julia Sibiya for their assistance and support throughout the study and
final completion of the thesis. I am also grateful to my in-country supervisor, Professor Paul
Kimani for his valuable assistance. I acknowledge the National Gene Bank of Kenya and the
East and Central Africa Bean Research Network for providing germplasm for the study.
My sincere appreciation goes to the Alliance for a Green Revolution in Africa (AGRA) for the
financial support that made this study possible. I thank the ACCI Director, Professor Mark Laing
and the entire staff for their diligent facilitation throughout the study.
I am very grateful to the Horticultural Crops Development Authority (HCDA) Director, Dr Alfred
Serem for granting me study leave and for the institutional support and facilitation that was
accorded. I acknowledge the support of the University of Nairobi, College of Agriculture and
Veterinary Sciences for providing the Kabete Field Station and the laboratory to carry out the
research. Special mention goes to Mr Gathuma, for his assistance in the laboratory, Mr Mwaura
and Ms Wanjiku for their tireless effort during the field research. I sincerely appreciate the KARI-
Tigoni Director, Dr Kabira, and the KARI-Thika Director, Dr Waituru for allowing me to carry out
the field trials at the research stations.
To the ACCI 2009 cohort; Benjamin, Lawrence, Lilian, Murenga, Nathan, Netsanet, Rebeka,
Robooni, and Wende, you are good friends and colleagues.
I am deeply indebted to my dearest husband Dr Kenneth Wanjau, for his love, support and
patience throughout the study period. I most sincerely thank my parents John and Alice Ng’ayu,
my brothers and sisters James, Isaiah, Fred, Elizabeth and Rosemary for their love and prayers.
Shawn and Samara, you have been a blessing. God bless you all abundantly.
Above all, I thank God for His steadfast love, His mercies and blessings were abundant, He
renewed my strength every morning, Great is His faithfulness!

vi
Dedication
I dedicate this thesis to my dearest and beloved husband Dr Kenneth Lawrence Wanjau and to
the Ng’ayu’s family; my parents John Ng’ayu and Alice Nyawira, my brothers and sisters, James
Wang’ombe, Isaiah Mukundi, Fred Alan Muya, Elizabeth Wangechi and Rosemary Wanjiku, and
to my nephew Shawn Alan Mukiri and my niece Samara Wairimu.

vii
Table of contents
Thesis abstract ......................................................................................................................... ii
Declaration ............................................................................................................................... v
Acknowledgements .................................................................................................................vi
Dedication ...............................................................................................................................vii
Table of contents ................................................................................................................... viii
Introduction to Thesis ............................................................................................................. 1
1. Importance of the common bean ................................................................................................1
2. Common bean production ..........................................................................................................1
3. Angular leaf spot and its control .................................................................................................2
4. Breeding for angular leaf spot resistance .....................................................................................3
5. Durable resistance ......................................................................................................................4
6. Importance of landraces in breeding ...........................................................................................4
7. Farmer participation in breeding .................................................................................................5
8. Problem Statement ....................................................................................................................5
9. Goal and objectives of the study .................................................................................................6
10. Outline of Thesis .......................................................................................................................6
References .....................................................................................................................................8
CHAPTER 1 .............................................................................................................................12
Literature Review ....................................................................................................................12
1.1 Introduction ........................................................................................................................... 12
1.2 Origin and distribution of common bean ................................................................................. 12
1.3 Taxonomy and morphology of common bean .......................................................................... 13
1.4 The inflorescence and pod formation of common bean ........................................................... 13
1.5 Growth habit of common bean ............................................................................................... 14
1.6 Genetic diversity of common bean .......................................................................................... 15
1.7 Common bean production constraints ..................................................................................... 15
1.8 Angular leaf spot of common bean .......................................................................................... 16
1.9 Taxonomy and epidemiology of angular leaf spot .................................................................... 17
viii
1.10 Symptoms of angular leaf spot in common bean .................................................................... 19
1.11 Variability of the angular leaf spot pathogen Pseudocercospora griseola ................................ 21
1.12 Sources of resistance to angular leaf spot .............................................................................. 22
1.13 Breeding common beans for resistance to angular leaf spot ................................................... 23
1.13.1 Types of disease resistance ................................................................................................................. 23
1.13.2 Breeding for minor gene resistance .................................................................................................... 25
1.13.3 Gamete selection ................................................................................................................................. 26
1.14 Importance of landraces in breeding ..................................................................................... 27
1.15 Participatory plant breeding .................................................................................................. 28
1.16 Summary .............................................................................................................................. 29
References ................................................................................................................................... 31
CHAPTER 2 .............................................................................................................................41
Evaluation of common bean production systems, constraints, and farmer varietal
preferences in Kenya ..............................................................................................................41
Abstract ....................................................................................................................................... 41
2.1 Introduction ........................................................................................................................... 42
2.2 Materials and Methods ........................................................................................................... 44
2.2.1 Study area .............................................................................................................................................. 44
2.2.2 Farmer surveys and focus group discussions ........................................................................................ 44
2.2.3 Data analysis .......................................................................................................................................... 45
2.3 Results ................................................................................................................................... 46
2.3.1 Common bean production and cropping systems ................................................................................. 46
2.3.2 Sources of seed and varietal preferences by farmers ........................................................................... 49
2.3.3 Common bean production constraints experienced by the farmers .................................................... 51
2.3.4 Farmer preferred common bean traits for improvement during breeding .......................................... 54
2.4 Discussion and conclusion ....................................................................................................... 55
References ................................................................................................................................... 58
CHAPTER 3 .............................................................................................................................67
Evaluation of local landraces and selected introductions of common bean for yield
performance and resistance to angular leaf spot .................................................................67
Abstract ....................................................................................................................................... 67
3.1 Introduction ........................................................................................................................... 68
3.2 Materials and Methods ........................................................................................................... 69
3.2.1 Study sites .............................................................................................................................................. 69
3.2.2 Plant materials ....................................................................................................................................... 69
ix
3.2.3. Pathogen isolation and inoculum preparation ..................................................................................... 70
3.2.4 Experimental procedures ...................................................................................................................... 71
3.2.5 Data analysis .......................................................................................................................................... 74
3.3 Results ................................................................................................................................... 75
3.3.1 Rainfall and mean temperatures ........................................................................................................... 75
3.3.2 Angular leaf spot evaluation at Kabete nethouse ................................................................................. 76
3.3.3 Angular leaf spot and yield evaluation at KARI-Tigoni ........................................................................... 78
3.3.4 Yield evaluation at Kabete Field Station and KARI-Thika ....................................................................... 82
3.4 Discussion and conclusion ....................................................................................................... 84
References ................................................................................................................................... 87
CHAPTER 4 .............................................................................................................................95
Genetic analysis of resistance to angular leaf spot in common bean ................................95
Abstract ....................................................................................................................................... 95
4.1 Introduction ........................................................................................................................... 96
4.2 Materials and Methods ........................................................................................................... 98
4.2.1 Study site ............................................................................................................................................... 98
4.2.2 Isolation and identification of Pseudocercospora griseola races .......................................................... 98
4.2.3 Generation means analysis .................................................................................................................. 100
4.2.4 Data analysis ........................................................................................................................................ 102
4.3 Results ................................................................................................................................. 105
4.3.1 Identification of Pseudocercospora griseola races .............................................................................. 105
4.3.2 Comparison of means among generations .......................................................................................... 106
4.3.3 Gene effects for disease resistance ..................................................................................................... 112
4.3.4 Heritability estimates and minimum number of genes controlling disease resistance ...................... 113
4.4 Discussion and conclusion ..................................................................................................... 115
References ................................................................................................................................. 118
CHAPTER 5 ........................................................................................................................... 122
Development of a breeding method for durable resistance to angular leaf spot in
common bean ........................................................................................................................ 122
Abstract ..................................................................................................................................... 122
5.1 Introduction ......................................................................................................................... 123
5.2 Materials and Methods ......................................................................................................... 124
5.2.1 Study site and parental selection ........................................................................................................ 124
5.2.2 Parental selection ................................................................................................................................ 124
5.2.3 Development of the inter-gene pool double cross population and advancement to F ..................... 125
3
5.2.4 Experimental design and evaluation of F lines ................................................................................... 127
4
5.2.5 Data analysis ........................................................................................................................................ 127
x