MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION FOR ASSESSMENT OF GENETIC DIVERSITY AMONG SWEET POTATO (IPOMOEA BATATAS (L.) LAM) ACCESSIONS IN NIGERIA

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ABSTRACT

Assessment of genetic diversity is an essential component in germplasm characterization and utilization. Therefore, a study was undertaken to investigate the morphological and molecular characterization for assessment of genetic diversity of some sweetpotato accessions in Nigeria. Evaluation of the sweetpotato germplasm was carried out under rain-fed conditions using Randomized Completely Block Design (RCBD) with three replications at the Teaching and Research Farm of the Federal University of Technology, Owerri (FUTO) and at the National Root Crops Research Institute (NRCRI) Potato Programme, Kuru, Jos, Plateau State, North Central Nigeria during the 2018 cropping season. The molecular characterization was carried out at the Molecular laboratory of the Godfrey Okoye University, Enugu State in 2019. Thirty sweetpotato seeds were obtained from International Potato Center, Kumasi, Ghana, Mozambique and local germplasm of the National Root Crops Research Institute (NRCRI), Umudike, Umuahia, Abia State in Nigeria as well as sweetpotato vines from local farmers’ fields in Jos, Plateau State and Bauchi, in Bauchi State, Nigeria. These were investigated using Morphological and Molecular characterization approaches. The attributes for morphological, agronomic and nutritional characters were used to identify variations among the accessions. The results revealed that significant differences existed among the accessions (P<0.05) for the morphological and agronomic characters investigated. The first ten principal components with coefficient values greater than 1.0 together accounted for 97.68% of the total variation. Significant positive correlation was found between predominant flesh colour and storage root shape (r=0.722**, p<0.01), and also between predominant skin colour and mature leaf colour (r=0.831**, p<0.01). Total storage root yield had positive correlation with number of marketable roots, (r=0.788**, p<0.01), marketable weight/ha (r=0.99**, p<0.01) and unmarketable weight/ha (r=0.241*, p<0.05) but negative correlation with number of unmarketable roots, (r=-0.282, p<0.01). Cluster analysis based on the Unweighted Paired Grouped Arithmetic Average (UPGMA) grouped the accessions into three clusters for the morphological characters and four clusters for the molecular characters. Five Simple Sequence Repeats (SSR) primers used for the study detected polymorphism among the sweetpotato accessions. The primers detected a total of 18 alleles and the number of alleles per locus was 4 for IBR-19, IBR-286, IBR-297 and 3 for IBR-16 and IBR-242 with an average of 3.67 alleles per locus. The polymorphic information content (PIC) of the markers varied from 0.35 to 0.72 with an average of 0.497. Marker IBR-19 revealed the highest PIC of 0.72, while marker IBR-297 had the lowest PIC of 0.35. Observed heterozygosity ranged from 0.32 to 0.89 with a mean of 0.675 across the five SSR loci. Based on the genetic distances resulting from the analysis of the dendrogram for the combined morphological and molecular characters and also from the agronomic and nutritional characterization, twenty accessions were selected for in vitro and ex situ conservation and as core collection for future breeding and other agronomic programmes.

TABLE OF CONTENTS

Title Page i

Declaration ii

Certification iii

Dedication iv

Acknowledgments vi

Table of Contents vii

List of Tables xiii

List of Figures xv

List of Plates xvi

List of Abbreviations and Symbols xvii

Abstract xxi

CHAPTER 1: INTRODUCTION 1

CHAPTER 2: LITERATURE REVIEW 7

2.1 Origin, Distribution, Botany, and Evolution of Sweetpotato 7

2.1.1 Origin 7

2.1.2 Distribution 8

2.1.3 Botany 8

2.1.4 Evolution 10

2.2 Biology and Morphology of Sweetpotato 11

2.2.1 Growth habit 11

2.2.2 The Stem 11

2.2.3 The leaves and petiole 11

2.2.4 The Flowers 12

2.2.5 The Fruit and seed 13

2.2.6 The Storage roots 13

2.3 Agronomy of Sweetpotato 14

2.3.1 Climatic and Soil requirements 14

2.3.2 Propagation 14

2.3.3 Weeding and Earthing up 15

2.3.4 Mulching 15

2.3.5 Manure and Fertilizer application 16

2.3.6 Irrigation 16

2.3.7 Harvesting 17

2.3.8 Yield 18

2.3.9 Pest and Disease control 18

2.4 Trend in Global Production of Sweetpotato 19

2.5 Sweetpotato Virus Disease (SPVD) 21

2.6 Types of Sweetpotato Viruses 22

2.7 Methods of Detection for Sweetpotato Viruses 22

2.8 Control of Sweetpotato Virus Disease (SPDV) 23

2.9 Uses and Health Benefits of Sweetpotato 24

2.9.1 Human Food 24

2.9.2 Animal Feed 25

2.9.3 Industrial Uses 26

2.9.4 Health Benefits 26

2.10 Nutritional Composition of Sweetpotato 27

2.11 End-User Traits of Sweetpotato 28

2.11.1 Beta-Carotene Content 29

2.11.2 Dry Matter Content 30

2.11.3 Sugar Content 31

2.12 Genetic Diversity/Variation in Sweetpotato 32

2.13 Determination of Genetic Variation 34

2.14 Diversity Measurement 35

2.14.1 Morphological Characterization 35

2.14.2 Molecular Characterization 35

2.15 Genetic Distance 37

2.16 Calculation of Genetic Distances 37

2.17 Core Collections 38

2.18 Sweetpotato Studies Using Simple Sequence Repeat (SSR) Markers 39

2.19 Sweetpotato Breeding 39

2.20 Germplasm Characterization for Quality Traits 41

2.21 Application of Near Infrared Reflectance Spectroscopy (NIRS) in Rapid

Screening of Quality Traits 42

CHAPTER 3: MATERIALS AND METHODS 44

3.1 Experimental Site 44

3.2 Sources of planting materials 45

3.3 Method of Collection of Accessions 45

3.4 Field Experimentation 47

3.4.1 Nursery Management 47

3.4.2 Seed Treatment 47

3.4.3 Soil Sampling 47

3.4.4 Land Preparation 47

3.4.5 Planting and Fertilizer Application 48

3.4.6 Experimental Design 48

3.5 Evaluation of the Morphological Traits 48

3.5.1 Foliar Morphology Attributes 49

3.5.2 Storage Root Characters 50

3.6 Harvesting 53

3.7 Data Collection on Yield and Yield Components 53

3.8 Laboratory Experiment 54

3.8.1 Determination of Nutritional Quality Traits 54

3.9 Molecular Characterization Using SSR Markers 55

3.9.1 Sample Collection 55

3.9.2 DNA Extraction 56

3.9.3 Preparation of Agarose Gel 57

3.9.4 Determination of DNA Concentration 57

3.9.5 Agarose Gel Electrophoresis of the PCR Products 58

3.9.6 Amplification of Polymerase Chain Reaction (PCR) 59

3.9.7 Scoring and Statistical Analysis 60

3.10 Data Analysis 62

3.11 Estimation of Genetic Variability 64

CHAPTER 4: RESULTS AND DISCUSSION 66

4.1 Soil and Agrometeorological Data 66

4.2 Morphological Variations of the Sweetpotato Accessions Evaluated

in Jos and Owerri Locations 69

4.3 Analysis of Variance for Morpho-agronomic Characters of Sweetpotato

Accessions Evaluated in Owerri and Jos Locations 77

4.4 Principal Component Analysis (PCA) of the Morphological

Characters of Thirty Sweetpotato Accessions 83

4.4.1 Principal component analysis of morphological characters

of the Sweetpotato accessions from Jos. 83

4.4.2 Principal component analysis of morphological characters

of the Sweetpotato accessions from Owerri 86

4.4.3 Performance of the selected accessions from Jos 88

4.4.4 Principal Coordinate analysis of the Sweetpotato accessions 90

4.5 Estimation of Useful Genetic Parameters 92

4.5.1 Estimate of genetic variation for the agronomic and

nutritional traits of the sweetpotato accessions for Jos and Owerri 92

4.5.2 Variability, heritability and expected genetic advance for the

traits of the sweetpotato accessions for Jos and Owerri 95

4.6 Correlation Coefficient for the Sweetpotato Accessions 98

4.6.1 Correlation coefficients for the morphological characters of the

thirty Sweetpotato accessions in Owerri, Imo State 98

4.6.2 Correlation coefficients for the morphological characters of the

thirty Sweetpotato accessions in Jos location 100

4.6.3 Correlation coefficients for the storage root characters of the Sweetpotato

accessions in Owerri, Imo State 102

4.6.4 Correlation coefficients for the storage root characters of the Sweetpotato

accessions in Jos location 104

4.7 Selection of highest performing Sweetpotato accessions based on

mean yield (t/ha) 106

4.8 Cluster analysis of the Sweetpotato accessions based on morphological

Characters 108

4.8.1 Cluster analysis of morphological characters of sweetpotato accessions

for Jos and Owerri. 108

4.8.2 Molecular cluster analysis (Dendrogram) based on molecular data 110

4.8.3 Comparison of morphological and molecular characterization (SSR DATA) 112

4.9 Molecular Characterization 114

4.9.1 Polymorphism of microsatellites used for the characterization

of the Sweetpotato accessions 114

4.10 Core Collection Determination and Mode of Selection 120

4.10.1 Selection based on clusters 120

4.10.2 Selection based on agronomic and nutritional characters 120

4.11 Discussion 123

CHAPTER 5: CONCLUSIONS AND RECOMMENDATIONS 131

5.1 Conclusions 131

5.2 Recommendations 133

References 134

Appendices 171

LIST OF TABLES

2.1	The world production of Sweetpotato (tons)	20
3.1	Sites of collection of the Sweetpotato accessions used in the study	46
3.2	Morphological traits measured among sweetpotato accessions	51
3.3	Sweetpotato microsatellite (SSR) primers used in the study	61
3.4	Format of analysis of variance for the study	63
4.1	Soil physical and chemical properties of the experimental sites in Jos and Owerri during the 2018 cropping season	67
4.2	Agro-meteorological data of the experimental site for Jos and Owerri in 2018 cropping season	68
4.3	Morphological characteristics of Sweetpotato accessions used in the study	70
4.4	Mean values of the morpho-agronomic characters of Sweetpotato accessions in Jos	81
4.5	Mean values of the morpho-agronomic characters of Sweetpotato accessions in Owerri	82
4.6	Eigen values and loading from principal component analysis of morphological characters in the Sweetpotato accessions from Jos	85
4.7	Eigen values and loading from principal component analysis of the agronomic and nutritional characters in the Sweetpotato accessions from Owerri	87
4.8	Performance of the selected accessions for beta-carotene, dry matter and sugar content.	89
4.9	Components of variance for agronomic and nutritional traits of the sweetpotato accessions in Jos	93
4.10	Components of variance for the agronomic and nutritional characters of the sweetpotato accessions in Owerri.	94
4.11 4.12	Genotypic and phenotypic coefficient of variation, heritability and genetic advance for the traits of Sweetpotato accessions from Jos Genotypic and phenotypic coefficient of variation, heritability and genetic advance for the traits of Sweetpotato accessions from Owerri	96 97
4.13	Correlation Coefficients (r) for the morphological characters of the thirty sweetpotato accessions in Jos location	99
4.14	Correlation Coefficients (r) for the morphological characters of the thirty sweetpotato accessions in Jos location	101
4.15	Correlation Coefficients (r) for the storage root characters of the thirty Sweetpotato accessions in Owerri location	103
4.16	Correlation Coefficients (r) for the storage root characters of the thirty Sweetpotato accessions in Jos location	105
4.17	Mean yield (t/ha) of the highest performing Sweetpotato accessions for Jos and Owerri locations	107
4.18	Characteristics of amplified fragments in the sweetpotato accessions using five SSR markers	116
4.19	List of core collections of Sweetpotato accessions considered for conservation	122

LIST OF FIGURES

1	Principal coordinate analysis of the thirty sweetpotato accessions from Jos and Owerri	91
2	Dendrogram of morphological characters of sweetpotato accessions in two locations (Owerri and Jos) based on Jaccard’s coefficient of similarity index using UPGMA	109
3	Dendrogram of sweetpotato accessions based on molecular character using Jaccard’s index genetic dissimilarity matrix	111
4	Dendrogram of the combined morphological and molecular data of the Sweetpotato accessions using Jaccard’s index genetic dissimilarity matrix	113

LIST OF PLATES

1A Hastate leaf shape and yellowish-green leaf colour 71

1B Lobed leaf shape and green with purple edge colour 71

1C Lobed leaf shape and yellowish- green colour at immature stage,

green leaf at mature stage and green vine at mature stage 72

1D Hastate leaf shape with green leaf colour at mature stage and

purple leaf colour at immature stage 72

1E Triangular leaf shape with green leaf colour at mature stage 73

1F Cordate leaf shape, green leaf and green petiole colour at maturity stage 73

2A Cream colour of root flesh 74

2B Dark cream colour with pink spots scattered in the root flesh 74

2C Dark orange flesh colour with white spots scattered in the flesh 75

2D Orange root flesh colour 75

2E Long oblong root shape and cream root skin colour 76

2F Elliptic root shape and purple root skin colour 76

3A Simple Sequence Repeats Primer IBR- 19 image on visual gel 117

3B Simple Sequence Repeats Primer IBR-16 image on visual gel 117

3C Simple Sequence Repeats Primer IBR- 242 image on visual gel 118

3D Simple Sequence Repeats Primer IBR- 286 image on visual gel 118

3E Simple Sequence Repeats Primer IBR-297 image on visual gel 119

LIST OF ABBREVIATIONS AND SYMBOLS

AFLP -

A -

ANOVA -

Amplified fragment length polymorphism

Adenine

Analysis of Variance

bp -

Base pair(s)

BCIP -

BSA -

CGIAR -

5-bromo-4-chloro-3-indolyl phosphate

Bovine Serum Albumin

Consultative Group on International Agricultural Research

CIAT -

International Center for Tropical Agriculture

CIP -

International Potato Center

CTAB -

C -

^oC -

CV -

cm -

Cetyl trimethyl ammonium bromide

Cystosine

Degree Celsius

Coefficient of variation

Centimeter

DNA -

Deoxyribonucleic acid

dNTP -

dATP -

dCTP -

dGTP -

dTTP -

DW -

deoxyribonucleotide triphosphate

deoxyadenosine triphosphate

deoxycytidine triphosphate

deoxyguanosine triphosphate

deoxythymidine triphosphate

Dry weight

EDTA -

Ethylendiamine tetra-acetic acid

ELISA -

ECEC -

EMS -

Enzyme-linked immunosorbent assay

Exchangeable cation exchange capacity

Expected mean square

FAO -

Food and Agriculture Organization

G -

GA -

GCV -

s²e -

g -

s²g -

Guanine

Genetic advance

Genetic coefficient of variability

Environmental variance

Gram

Genotypic variance

ha -

h²b -

Hectare

Broad sense heritability

IBPGR - International Board for Plant Genetic Resources

IITA - LSD - Kg - K - m - Mbp - mg - min - ml - mm - MS - nM - ng - NARS -		International Institute for Tropical Agriculture Least significant difference Kilogram Selection intensity Meter Mega (or million) base pairs Milligram Minute Milliliter Millimeter Mean square Millimole Nanogram National Agricultural Research Systems
NTSYS -		Numerical taxonomy multivariate analysis system
OFSP -		Orange fleshed sweetpotatoes
PCA -		Principal Component Analysis
PCR - PC - PCV -		Polymerase chain reaction Principal coordinate Phenotypic coefficient of variability
PVP -		Polyvinylpyrrolidone
pH - s²p - % -		Hydrogen proton Phenotypic variance Percentage
	RAPD -RCBD -		Random amplified polymorphic DNA Randomized complete block design
	RFLP -		Restriction fragment length polymorphism
	RNA -		Ribonucleic acid
	RNAse -		Ribonuclease
	Rpm - r - SED -		Revolutions per minute Correlation coefficient Standard error of deviation
	SSR - SNP -		Simple sequence repeats Single Nucleotide Polymorphism
	Taq -		Thermophilus aquaticus
	TBE -		Tris borate EDTA
	Tris - Tm - SPVD - T - t - T-TBS - U - UPGMA - UV - WAP - µ l - X -		Tris (hydroxymethyl) aminomethane Annealing temperature Sweet potato virus disease Thymine ton Tris buffered saline supplemented with tween 20 Unit Unweighted pair group method of arithmetic average Ultraviolet Weeks after planting Microliter Sample mean

CHAPTER 1

INTRODUCTION

Sweetpotato (Ipomoea batatas [L.] Lam) is an important crop that is cultivated in 119 countries of the world for food, feed and industrial raw material (Scott and Ewell, 1993; FAOSTAT, 2013). The annual global production of sweetpotato is estimated at 110.7 million tones with about 15% from east and Central Africa (FAOSTAT, 2013).

The annual global production of sweetpotato is estimated at 110.7 million tons of which 15% is from East and Central Africa (FAOSTAT, 2013). It is a tropical American crop belonging to the family Convolvulaceae and a hexaploid, with chromosome number (2n=6x=90) and is considered the only species of Ipomoea that is of great economic importance (Austin, 1977). It originated in the tropics and has crossed the Pacific through Polynesia before the new world was discovered (Huaman, 1999; Zhang et al., 2000).It was introduced to Africa by explorers from Spain and Portugal during the 16th (Zhang et al., 2004). East Africa is the area that is considered as the secondary center of diversity based on the presence of large number of varieties (Gichuki et al., 2003). Sweetpotato is considered to be the seventh most important crop after wheat, maize, rice, potato, barley and cassava (FAO, 2011).

Sweetpotato is the seventh most important food crop after wheat, rice, maize, potato, barley and cassava (FAO, 2011). The crop is grown in all agro-ecologies, across all states in Nigeria and has been identified to be the fourth most important crop after Cassava, Yam and Cocoyam, (Okonkwo et al., 2009). In developing countries, it ranks fifth in terms of the economic value of production (Thottappilly and Loebenstein, 2009). In sub-Saharan Africa where the crop is grown on some 13.37 million hectares of land, it is the third most important root crop after cassava and yam (FAOSTAT, 2012). Despite the high production figures, yield has remained low in farmers’ fields with estimated average root yield of 3.0 tonnes/ha (FAOSTAT, 2015). In Nigeria, the production, marketing and utilization of sweetpotato have expanded to almost all the ecological zones within the past decade (NRCRI, 2009), and about 400,000 hectares of land are under sweetpotato cultivation.

Sweetpotato is one of the valuable crops that produce the highest quantity of root dry matter content which is used for human consumption. Starch is the major component which constitutes about 70% of the dry weight of sweetpotato, (Woolfe, 1992). According to Slafer and Savin (1994) and Mwanga et al., (2007), high dry matter is considered to be an important characteristic of a good sweetpotato variety. Storage root that contain high starch and low hexose contents are very important qualities that sweetpotato industry prefers (Slafer and Savin, 1994).

High starch and low soluble sugar contents has led to the reduction in the cost of sweetpotato processing which has been attributed to the absence of oxidation reactions, (McKibbin et al, 2006).

Sweetpotato has many positive attributes. It produces more carbohydrate per unit area per unit time than other root crops, has short production cycle, grows well in many agro ecologies, requires low inputs, and is fairly tolerant to production stresses such as high temperature, water deficits, insects, diseases and low soil fertility (Woolfe, 1992).

Nutritionally, its high levels of proteins, minerals and dietary fiber make it superior to most staples (Jaarsveld et al., 2005). Sweetpotato is an inexpensive source of β-carotene, anthocyanin, carbohydrate, vitamins and minerals. The orange-fleshed sweetpotato varieties are important sources of β-carotene which is the major precursor of vitamin A (Chassy et al., 2008), while the purple fleshed sweetpotato varieties contains a high content of anthocyanins and other polyphenolic components (Teowal et al., 2007; Steed and Truong, 2008). The quantity of β-carotene and anthocyanin in sweetpotato is as high as in carrot, pumpkin, Vaccinium species such as blueberry, cranberry, bilberry or red cabbage (Woolfe, 1992; Steed and Truong, 2008). Low et al., (2007) and Mcharo and La Bonte, (2007) reported that regular intake of one hundred grams of orange-fleshed sweetpotato varieties containing about 3 mg/100 g β-carotene on a fresh weight basis is adequate to meet the recommended daily allowance of vitamin A, and prevent deficiency of vitamin A in pregnant mothers, and also prevent blindness in children. Sweetpotato is known to have a low glycemic index, in that, the slow rate of digestion of its complex carbohydrate, lowers the rate of absorption of sugars into the blood stream. It is therefore, a suitable source of food for the diabetics (Willcox et al., 2009).

Sweetpotato has many industrial applications (Lin et al., 2007). It is an industrial source of starch and alcohol (Rahman et al., 2003), yielding 30–50 % more starch than rice, corn and wheat sources measured under the same conditions (Wang, 1984). Its high grade starch is suitable for food and pharmaceutical industries, and has been used in textile, paper, cosmetics, insulating and adhesive industries (Rahman et al., 2003; Veeraragavathatham et al., 2007) and has great potential for bio fuel production (Mays et al., 1990).

Systematic plant breeding and the efficient use of agricultural inputs has generally led to the increase in crop productivity during the last century (Warburton et al., 2002). However, increase in productivity has led to the decrease in genetic diversity within gene pools (Fernie et al., 2006) due to a compounding factor such as inbreeding.

This trend is particularly difficult among vegetatively propagated crops like sweetpotato and in particular landraces which have a diverse genetic base but are rarely integrated into the plant breeding programs due to their low production.

A large number of sweetpotato cultivars exist varying in taste, food value, root size and shape (Bashaasha et al., 1995). This has mainly arisen through natural hybridization and selection. Farmers usually identify varieties by their local names and prefer to grow more than one cultivar for various reasons such as varietal preference, lack of enough planting materials of any one cultivar, food security, spreading of yield over time, and guarding against losses from storage and pests or diseases (Kapinga et al., 1995). The identification and characterization of these landraces is important for purposes of conservation of genetic diversity.

Morphological characterization is an important step in the assessment of sweetpotato diversity, but has certain limitations due to morphological plasticity and parallel evolution (Prakash and He, 1996). Therefore, genetic differences exhibited as presence/absence of polymorphisms that exist among accessions can be combined with phenotypic analyses to augment germplasm characterization. Morphological characterization has been used extensively on various crop plants in the assessment of genetic diversity in many places of the world (Lacroix et al., 2005; and K’Opondo, 2011). Despite the environmental influences on plant morphology, this direct inexpensive and easy to use method of estimation was perceived as the strongest determinant of the agronomic value and taxonomic classification of plants (Li et al., 2009) and the first step in the assessment of genetic diversity. On sweetpotato, this tool has been used successfully to analyze genetic diversity necessary for the germplasm conservation, to reduce accession number by identification and elimination of duplicates and to enhance crop breeding (Huaman, 1992 and Yada et al., 2010a).

Sweetpotato morphological descriptors have been variously used (Mbithe et al. 2016 and Su et al., 2016) and proven useful for preliminary evaluation of accessions due to their considerable discriminatory power, but the present trend is to use molecular marker based characterization as a complementary tool to validate morphological characterization findings (Changadeya et al., 2012a and Malviya et al., 2012).

Molecular markers have increasingly been employed to investigate sweetpotato genetic diversity for germplasm conservation and genetic enhancement (Ochieng et al., 2015 and Naidoo et al., 2016). Simple sequence repeats (SSR) are considered to be the most efficient markers for genetic diversity studies in many plants (Rakoczy-Trojanowska and Bolibok, 2004) including sweetpotato (Zhang et al., 2000). This is because of their high levels of allelic variation and their co-dominant character, which means that they deliver more information per unit assay than any other marker system (Rakoczy-Trojanowska and Bolibok, 2004). These markers are highly polymorphic, co-dominant, and can easily be detected on high-resolution gels.

Successful conservation of any given gene pool is largely dependent on understanding the diversity and its distribution in a given region (Zhang et al., 1999). Studying the diversity of important crops enables identification of land marks for in situ germplasm conservation, the creation of core genotypes for genetic analysis and the extension of knowledge, useful for breeding programs, therefore, an accurate assessment of the levels of genetic diversity in sweetpotato is invaluable for various purposes including identification of diverse parental combinations to develop segregating progenies with maximum genetic variability for further selection (Barrette and Kidwell, 1998).

The objectives of the study are to:

1. Evaluate the extent of morphological diversity among sweetpotato accessions from different areas of collection in Nigeria.

2. Ascertain the level of genetic diversity among the sweetpotato accessions using simple sequence repeats (SSRs) molecular markers.

3. Determine the nutritional components of sweetpotato accessions.

4. Assess the correlation between genetic distance estimates of sweetpotato accessions based on morphological traits and molecular markers selection.

5. Select core collection of sweetpotato accessions for conservation and future breeding work.

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