ABSTRACT
The first report of Maize lethal necrosis (MLN) in Kenya was in 2011 in Bomet County. The disease quickly spread to nearby counties causing devastating damage to maize crop yield. The causative agents of MLN are two viruses MCMV and SCMV. The study’s objectives were i) to identify germplasm with resistance to SCMV and ii) to identify the mode of gene action associated with tolerance to the virus. To achieve objective one, 42 parental maize genotypes were planted in a screen house of the Faculty of Agriculture, University of Nairobi, in a completely randomized design to identify the ones with resistance to SCMV using the CIMMYT SCMV disease severity scale. Analysis of variance (ANOVA) tests were conducted on disease severity, disease incidence and Area under disease curve progression (AUDPC) scores using GENSTAT statistical software and showed significant differences among the genotypes for all the parameters. The genotype means were separated using least significant differences (LSD) at 0.05 significance level. Four genotypes had no symptoms of SCMV and 27 genotypes had a score of between 2 to 2.8 and were therefore classified as resistant or tolerant to SCMV, respectively. The rest had a score of 3 and above, and classified as highly susceptible. The resistant/tolerant genotypes are valuable sources of resistance to SCMV and could be employed in development of MLN resistant maize varieties. To achieve objective two, 448 maize genotypes consisting of 60 parents and 388 F1s were planted in the short rains season of 2016 and were self-pollinated and each cob harvested singly to give F2 population. Two populations namely 384 (parents UON-2015-50 × UON-2015-115) and 385 (parents UON- 2015-50 × UON-2015-117) with the common parent 50 previously identified as resistant in MLN screening were selected for further genetic analysis studies. For genetic studies, 150 seeds of each F2 derived families were planted in the screen house in plastic pots and artificially inoculated with SCMV and evaluated for disease symptoms for 6 weeks using the CIMMYT SCMV disease severity scale and then categorized as either resistant or susceptible for based on the F2 generation. Resistant plants had a disease score of 2 and below and susceptible plants had a score of 3 and above. Chi-square goodness-of-fit test was then conducted to find conformity to various genetic ratios. The results of this study showed conformity to the 15:1 ratio which means the resistance to SCMV in these crosses could be controlled by major genes with complementary epistatic effects. These parents could be exploited in developing maize hybrids with resistance to SCMV, and therefore contribute towards management of MLN disease.
TABLE OF CONTENTS
DECLARATION ii
DEDICATION iii
DECLARATION OF ORIGINALITY FORM iv
ACKNOWLEDGEMENTS v
TABLE OF CONTENTS vi
LIST OF TABLES ix
LIST OF ABBREVIATIONS AND ACRONYMS x
ABSTRACT xi
CHAPTER 1
INTRODUCTION
1.1 Maize production and its challenges 1
1.2 Statement of the problem 2
1.3 Justification 4
1.4. Main objective 4
1.4.1 Specific objectives 5
1. 4.2 Hypothesis 5
CHAPTER 2
LITERATURE REVIEW
2.1 Maize production, importance and constraints 6
2.2 Maize lethal necrosis disease 7
2.2.1 History of Maize lethal necrosis and the causative viruses 7
2.2.1.1 Distribution of MLN Disease in East Africa 8
2.3 Maize chlorotic mottle virus 9
2.4 Sugarcane mosaic virus 10
2.5 Plant virus interactions 11
2.5.1 The synergistic interaction between MCMV and SCMV 12
2.6 Alternative hosts of Maize lethal necrosis causative agents 13
2.7 Management of Maize lethal necrosis 14
2.7.1 Host resistance breeding 15
2.7.1.1 Genetics of resistance to MLN and its causal viruses 17
2.7.2 Popular mating designs used in generation of progenies 19
2.8 Significance of SCMV resistance to MLN resistance 22
2.9 Current status of Maize lethal necrosis in Kenya 23
CHAPTER 3
3.1 IDENTIFICATION OF MAIZE GERMPLASM WITH RESISTANCE TO SUGARCANE MOSAIC VIRUS
3.1.1 Location and climatic description of study area 24
3.1.2 Maize germplasm used in the study 24
3.1.3 Experimental design 27
3.1.4 Source of the SCMV inoculum 27
3.1.5 Inoculum preparation and inoculation 27
3.1.6 Data collection 27
3.1.6.1 Assessing for disease incidence and severity 28
3.1.7 Data analysis 28
3.1.7.1 Analysis of Variance 28
3.1.7.2 Area under disease progress curve (AUDPC) 28
3.2 DETERMINING THE NUMBER AND NATURE OF GENES CONTROLLING RESISTANCE TO 30
3.2.1 Development of the F2 maize population used in the genetic studies 30
3.2.2 Assessment of maize genotypes for resistance to SCMV 30
3.2.2.1 Data analysis 31
CHAPTER 4
RESULTS
4.1 ASSESSMENT OF PARENTAL MAIZE GERMPLASM FOR RESPONSE TO SCMV INFECTION 32
CHAPTER 5
DISCUSSION
5.1 Response of the maize genotypes to sugarcane mosaic virus disease 37
5.2 Segregation for the SCMV disease among the F2 derived families for population 384 and 385 40
CHAPTER 6
GENERAL DISCUSSION, CONCLUSION AND RECOMMENDATIONS
6.1 CONCLUSION 43
6.2 RECOMMENDATIONS 44
REFERENCES 45
LIST OF TABLES
Table 3.1 Maize germplasm used in the evaluation for response to SCMV disease 25
Table 3.2: List of maize populations used for the genetic study to identify the genes and their number for resistance to Sugarcane mosaic virus 31
Table 4.1 Weekly disease severity progression, AUDPC scores and disease incidence of the different maize genotypes in the study 33
Table 4.2 Segregation data among the F2 derived families in population 384 (UON-2015- 50 × UON-2015-115) 35
Table 4.3 Segregation data among F2 derived families in population 385 (UON-2015-50
× UON-2015-117) 36
LIST OF FIGURE
Figure 5.0: Image showing maize plant with Sugarcane mosaic virus symptoms. 38
LIST OF ABBREVIATIONS AND ACRONYMS
F1 First filial generation
F2 Second filial generation
GCA General combining ability
MCMV Maize chlorotic mottle virus
MLN Maize lethal necrosis
QTL Quantitative trait loci
SSR Single sequence repeats
siRNA Small interfering ribonucleic acid
SCMV Sugarcane mosaic virus
CHAPTER 1 INTRODUCTION
1.1 Maize production and its challenges
Maize is an important cereal crop globally (Ekpa et al., 2018). About 85% of the populace in Eastern and Southern Africa relies on maize for food (Boddupalli et al., 2020). It is cultivated by mostly smallholder farmers for human consumption, animal feed and processed to produce vegetable oils (Nyaligwa et al., 2017).
The sub Saharan Africa (SSA) population is estimated to increase threefold by 2050 (Ekpa et al., 2018), thus increasing demand for maize. However, the maize yield in SSA is below the global average at 1.8 t/ha (Semagn et al., 2014). The major reasons for the low production are use of landraces and obsolete hybrids (Ekpa et al., 2018), low use of fertilizer, poor agronomic practices and abiotic factors such as poor soils and erratic rainfall. Biotic factors such as pests like the fall army worm, stalk borers and Striga weed (Keno et al., 2018) and diseases such as Grey Leaf Spot, Maize streak virus (MSV) and the Northern Leaf Blight (Sibiya et al., 2013) are prevalent with Maize lethal necrosis being the latest scourge in the eastern Africa region (Beyene et al., 2017).
Maize lethal necrosis occurs when maize plants are infected by Maize chlorotic mottle virus (MCMV) and Sugarcane mosaic virus (SCMV) simultaneously (Hilker et al., 2017). The disease can occur by double infestation of MCMV and other potyviruses (Gowda et al., 2018). The earliest report of MLN was in Peru in 1976, then later in USA and China (Wu et al., 2013). SCMV was reported in Kenya in 1973 (Kulkarni, 1973; Louie, 1980) and MCMV in 2011 (Wangai et al., 2012; Mahuku et al., 2015). MLN was initially recorded in Kenya in September 2011 (Mahuku et al., 2015; Wangai et al., 2012) in Bomet County and quickly spread to nearby counties and by 2012, other counties in the Rift valley, Nyanza, Western and Eastern regions had reported the disease (Wangai et al., 2012). MLN also spread to nearby countries namely Uganda in 2013 (Kagoda et al., 2016) and Tanzania, Rwanda (Adams et al., 2014), Congo, Ethiopia and South Sudan (Mahuku et al., 2015). Several management practices have been attempted such as rouging and use of pesticides to target vectors such as aphids and thrips but there’s a danger of causing ecological damage and is not affordable for majority of smallholder farmers. Use of germplasm that is tolerant to MLN, MCMV and SCMV is the most durable, cost-effective way to manage the disease and has least environmental impact.
1.2 Statement of the problem
About 77,000 hectares under maize production in Kenya was affected by MLN in 2012, translating to 52 million US dollars in losses (Mahuku et al., 2015). In 2014/2015 season, 10% yield losses were reported which amounted to US$ 50 million (Beyene et al., 2017). The disease was reported to affect most of the commercial varieties with losses in yield ranging from 30% to 100% subject to variety and phase of infection (Mahuku et al., 2015). When a field is diseased early in the season, 100% yield loss can occur (Beyene et al., 2017). CIMMYT screened about 95,000 maize germplasms including elite commercial hybrids like H614D from Eastern and Southern Africa and reported high susceptibility to MLN (Beyene et al., 2017).
The prevalence to MLN has been aggravated by a number of factors such as favourable weather which promotes survival and spread of the viruses’ vectors; maize monoculture which leads to build-up of the viruses and occurrence of new and more virulent strains of MCMV and SCMV (Manje, 2015) and recycling of infected seed (Beyene et al., 2017). The presence of a potyviruses increases the concentration of MCMV particles up to five times in a co-infected plant. The increase in MCMV concentration is due to synergism which results in increased severity of symptoms than in a single virus infection. The potyvirus has the ability to suppress the host plant’s mechanisms that limit MCMV multiplication in cells consequently permitting easier spread of MCMV and subsequently heightened symptoms.
Since maize is a staple food to 98% of the Kenya’s population with a consumption rate of 125 kg per capita (Kariuki, 2015), loss of yield due to MLN threatens food and economic security of the many households’ dependent on maize cultivation. In addition, 90% of commercial varieties of maize grown in eastern Africa region are susceptible to MLN (Manje, 2015). Managing MLN is multifaceted.
The use of closed seasons such as use of gap years between planting seasons in Kenya may not be a viable solution for smallholder farmers (Kariuki, 2015). Use of chemical pesticides to manage the virus vectors may not be affordable to the resource-constrained small-holder farmers and may have undesirable effects on the environment. Use of chemicals to contain spread of SCMV is also difficult due to the non-persistent manner of virus spread by the aphids. MCMV has also been shown to be seed transmitted a very low rates (Sanchez et al., 1994). A long term and sustainable approach could involve the use of germplasm with resistance to viruses causing MLN disease.
1.3 Justification
The best approach to manage MLN and viruses causing the disease is use of resistant varieties. Development of new varieties is crucial (Makone et al., 2014). However, this requires that sources of resistance are continuously identified and then deployed into adapted maize varieties. In 2013, KALRO together with CIMMYT set up a MLN screening site in Naivasha. In efforts to identify resistant maize germplasm, about 95,000 maize genotypes sourced from different organizations assessed for their response to MLN reported high susceptibility (Mahuku et al., 2015). To manage MLN, it’s important to identify sources of resistance to the singular viruses namely SCMV and MCMV and also MLN since SCMV presence exacerbates symptom severity of MCMV resulting in higher yield losses. This should be followed by knowing the nature and manner of inheritance of the resistance to facilitate deployment of such resistance in maize breeding programs and in development of superior varieties. Commercial seed companies can use these materials to develop tolerant or resistant maize varieties and avail them to farmers thus ensure food security and income to households.
1.4. Main objective
The major goal of this study was to contribute towards control of MLN disease by finding of sources of resistance to Sugarcane mosaic virus that will be useful in breeding programs.
1.4.1 Specific objectives
1. To identify maize germplasm with resistance to Sugarcane mosaic virus.
2. To determine the nature and number of genes conferring resistance to Sugarcane mosaic virus among F2 segregating populations.
1.4.2 Hypothesis
1. Maize varieties with resistance to SCMV exist among the available germplasm.
2. Resistance to Sugarcane mosaic virus in maize is provided by single genes with major effect.
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