ABSTRACT
Genetic diversity among maize (Zea mays L.) landraces
reveals genetic backgrounds with respect to alleles, polymorphisms and
heterozygosities, as well as relationships among genotypes. There has always
been the need in Africa to identify useful alleles for maize improvement in a
wide genetic base yet little is done to search for diversity among existing
maize landraces. The IPGRI landraces of the IITA maize collection has neither
record of geographical origin nor information on genetic diversity. The
research objective was to estimate the level of genetic diversity, determine
relationships among the landraces, and reveal evolutionary processes that have
contributed to the genetic status of the population. A total of 60 landraces
and a check, „Obatanpa GH‟ were evaluated by agromorphological characterization
on 5 qualitative and 24 quantitative traits. Except for cob colour which was
least variable with 98.0 % white and 2.1 % red, a large variability was
observed for silk and grain colour, kernel texture and kernel arrangement
Kernel arrangement with fairly equal distribution of straight, regular,
irregular and spiral types was the most variable. On quantitative evaluation,
large variability was demonstrated for all traits except number of ears per
plant. Earliness ranged from 39 to 74 days with a mean of 54.8 ± 6.2 days to 50
% anthesis while days to 50 % silking covered 44 to 78 days and mean of 57.6 ±
6.3 days. Six early-maturing genotypes identified were TZm-149, TZm-1148,
TZm-1150, TZm-1157, TZm-1153, and TZm-1152. Mean anthesis-silking interval
revealed genotypes for drought tolerance having 1.2 to 1.4 days of
anthesis-silking interval in TZm-1188, TZm-1183, and TZm-1106. Many individual
plants of these accessions exhibited protogyny. Mean grain yield ranged from
2.16 ± 0.4 Mgha-1 to 6.19±1.7 Mgha-1 of which the best
performers with yield exceeding 4.2 Mgha-1 were TZm-1185, TZm-1142,
TZm-1213, TZm-1129, TZm-1143, TZm-1215, TZm-1150, TZm-1211, TZm-1152, TZm-1101,
TZm-1123, TZm-1100, TZm-1138, TZm-1112, TZm-1212, TZm-1130, TZm-1190, TZm-1118,
TZm-1106, TZm-1144, TZm-1122, TZm-1125, TZm-1117, TZm-1119 and TZm-1139. Low to
moderate broad sense heritability estimates of 0.00 for stay green and ear
weight to 0.68 and 0.69 for earliness were recorded. The medium to high
heritability estimates signify traits are under control of minimal additive and
some dominance gene effects for a slow pace in progress in breeding. Besides
the strong positive correlation of yield components with grain yield, all other
correlation coefficients with grain yield were weak and nonsignificant (P ≤ 0.05).
Genetic similarities ranged from 0.00 to 0.80 with a mean of 0.14±0.15
indicating extensive genetic diversity. The UPGMA cluster analysis grouped
genotypes into two main heterogeneous clusters, cluster I having
early-maturing, short plants with high grain yield and low anthesis-silking
intervals whereas cluster II was of tall plants with poor grain yield. The
first two principal components explained 85.0 % of the total variance with
large contributions from plant height, ear height, anthesis, silking, ear leaf
length, grain weight, grain yield, ear position, hundred kernel weight, kernel
length, and kernel width. SSR profiling of 64 IPGRI genotypes at 12 loci
produced a rate of polymorphism of 85.7 %, a total of 1,826 alleles ranging
from 108 to 216. The number of alleles per locus ranged 3 to 10 with mean of
5.64±2.15 indicating lots of variability. The mean observed heterozygosity of
0.36±0.18 was not significantly different from the expected heterozygosity of 0.69±0.08,
an indication of substantial mutation rate and polymorphism maintained by
balancing selection. The high heterozygosity is also suggestive of a historical
admixture event. Genetic distance by means of DICE similarity coefficient was
0.49±0.14. UPGMA clustering grouped the accessions into six clusters from which
hybridization could be exploited. The large variability, polymorphism, and heterozygosity
identified by both agromorphological and molecular assessments affirm the
existence of wide genetic diversity in the IPGRI genotypes and their possible
beneficial contributions if exploited in maize improvement programmes.
TABLE OF CONTENTS
LIST OF TABLES
LIST OF FIGURES
LIST OF APPENDICES
LIST OF ABBREVIATIONS
ABSTRACT
CHAPTER ONE
1.0 INTRODUCTION
CHAPTER TWO
2.0 LITERATURE REVIEW
2.1 The role of maize in the
world‟s agricultural economy
2.2 Maize production and
consumption in Africa
2.3 Origin of maize
2.3.1 Cytological evidence
2.3.2 Isozyme evidence
2.3.3 Molecular evidence
2.4 Maize accessions and
landraces
2.5 Biology of maize
2.5.1 Morphology of maize
plant
2.5.2 Maize inflorescence
2.5.3 Pistillate flower
2.5.4 Fertilization and
embryogenesis
2.5.5 Growth stages of maize
plant
2.6 Maize research in Ghana
2.6.1 Maize breeding in Ghana
(varietal development)
2.7 Genetic diversity in
maize
2.8 Estimation of genetic
diversity
2.8.1 Agromorphological trait
evaluation
2.8.2 Estimation of diversity
by coancestry coefficients
2.8.3 Isozyme and storage
protein analysis
2.8.4. Assessment of genetic diversity
by molecular analysis
2.9 Measures of genetic
diversity
2.10 Determination of
relationships among genotypes
2.10.1 Genetic distance
2.11 Multivariate techniques
for interpretation of genetic distance
2.11.1 Cluster analysis
2.11.2 Bootstrapping
2.11.3 Principal components
analysis
CHAPTER THREE
3.0 MATERIALS AND METHODS
3.1 Plant Material
3.2 Location and conditions
of experimental site
3.3 Land preparation, planting
and experimental design
3.4 Data Collection
3.4.1 Morphological Data
3.5 Statistical analyses of
morphological data
3.5.1 Description of genetic
diversity
3.6 Genotypic and phenotypic
correlation and their standard error
3.7 Assessment of relationships
between genotypes
3.7.1 Data Standardization
3.7.2 Euclidean distance measurement
and cluster analysis
3.7.3 Cluster analysis
3.7.4 Bootstrapping
3.7.5 Principal components
analysis
3.8 Genetic diversity in
maize by means of SSR fingerprinting
3.8.1 SSR primer selection
3.8.2 Amplification and
detection of bands
3.9 Statistical analysis of
molecular data
3.9.1 Allele scoring and data
analysis
3.9.2 Estimation of genetic
diversity within populations
3.9.2.1 Rate of polymorphism
3.9.2.2 Average number of
alleles per locus (AP) or allele diversity
3.9.2.3 Polymorphic
information content or average expected heterozygosity
3.9.3 Estimation of genetic
diversity among populations
3.9.3.1 Genetic distance and
cluster analysis
CHAPTER FOUR
4.0 RESULTS AND DISCUSSION
4.1 Morphological Description
of Qualitative Traits
4.1.1 Qualitative trait
description
4.2 Means, standard
deviation, range and mean squares of quantitative traits of the IPGRI maize
landraces
4.2.1 Earliness in the IPGRI
landraces
4.2.2 Plant characteristics
4.2.3 Ear characteristics
4.2.4 Yield and yield
components
4.3 Heritability, phenotypic
variance and genotypic variance of 24 quantitative traits on the 60 IPGRI
genotypes and a check „Obatanpa GH‟
4.4 Phenotypic and genotypic
correlation of agro-morphological quantitative traits
4.5 Genetic distance and
cluster analysis of 60 IPGRI maize accessions held in IITA and a check,
“Obatanpa GH”
4.6 Principal components
analysis of morphological traits
4.7 Molecular diversity in
IPGRI maize accessions
4.8 Genetic similarity
estimates of molecular data
CHAPTER FIVE
5.0 CONCLUSIONS AND
RECOMMENDATIONS
5.1 Conclusion
5.2 Recommendations
REFERENCES
CHAPTER ONE
1.0 INTRODUCTION
Maize (Zea mays) is a member of the family Poaceae, the group
of crops known as the grasses, which includes wheat, barley, and rye. It is
generally believed that maize originated from Central America, specifically
Mexico where it was domesticated and spread rapidly around the globe through
trade routes (Matsuoka et al. 2002; Smith, 1998). Maize introduction to Africa
can be traced back to the 1500s by the Portuguese traders (Sinha, 2007). To
date, maize is grown in sub-Saharan Africa as the most important economic crop,
and is used as food, feed, and a raw material for many industrial products.
Maize is used as food for over 1.2 billion people in sub-Saharan Africa and
Latin America (FAO, 2011). Presently, maize makes up more than 50 % of the
total caloric intake (Sinha, 2007; McCann, 2005) and 53 % of the protein intake
of local diets (Bressani, 1991).
Global maize production is estimated to be 785 million metric
tons (MMT) with Africa producing about 51 million metric tons (6.5 %). Because
this quantity is not enough for the population, Africa imports 28 % deficit of
maize from other countries (IITA, 2012). Maize yield in developing countries
has been consistently lower than that in developed countries primarily due to
factors such as drought, use of landraces and old varieties. In contrast,
developed countries cultivate hybrids and improved varieties (Munsch, 2009).
Maize landraces in Africa are adapted to various
environments, from cold to hot, humid to drought, and on various elevations
(Taba and Twumasi-Afriyie, 2008).
Some landraces are still being used as local cultivars in
West and Central Africa, although the vast majority of the production areas are
planted with modern commercial varieties. These landraces, though are believed
to possess alleles for many important economic traits (Brandolini, 1969), they
have not been utilized as valuable germplasm for breeding modern maize
cultivars. For instance, more than 20 cultivars released in Ghana are bred from
the superior offspring from „Obatanpa GH‟ derived from Population 63 genotype
developed by the Crops Research Institute (CRI), Kumasi, Ghana in collaboration
with the International Institute of Tropical Agriculture (IITA), Ibadan; the
International Maize and Wheat Improvement Center (CIMMYT), Mexico; and the
Sasakawa Global 2000 (Badu-Apraku et al., 2006). Other cultivars in Ghana were
derived from International Institute of Tropical Agriculture (IITA) maize lines
(Sallah, 1998).
There appears to be dearth of information on the genotypic
composition of maize landraces in West and Central Africa, hence they have not
been utilized in maize improvement programs. Landraces are important genetic
resources which serve as sources of biotic and abiotic stress resistance,
yield, and disease resistance genes, quality and many useful agronomic
characteristics, and comprise high genetic variability and fitness to the
natural and anthropological environments where they have originated
(Brandolini, 1969). Consequently, landraces represent a unique and valuable
material for improvement of modern varieties adapted to changing environments
(Rao, 2004; Heslop-Harrison, 2002). In view of this, efforts must be made to
collect and conserve landraces and wild relatives for utilization in future
breeding programs.
To promote the efficient use of genetic variation in the
collection, information on genetic diversity and relationships within and among
cultivars, traditional populations and their wild relatives is essential
(Sidkar et al., 2010).
Considering the need to conserve plant genetic resources,
more than 800 tropical maize accessions have been collected and deposited at
the IITA Genetic Resource Center in Ibadan, Nigeria, with the collaboration of
local germplasm institutions in many countries in Africa and the International
Plant Genetic Resources Institute (IPGRI), Rome, Italy. This large number
presents challenges and demands for more efficient management and
cost-effective conservation. Management of germplasm collections encompasses
assessment of genetic diversity and construction of a core collection to
represent the variation within the group.
Genetic diversity analysis reveals genetic backgrounds and
relationships of germplasm, and provides strategies to establish, utilize, and
manage crop germplasm (Roussel et al., 2004; Brown-Guedira et al., 2000). It
also offers the basis for devising future strategies for crop improvement,
cultivar development, conservation, and sustainable use of crop germplasm for
long-term crop improvement and reduction of vulnerability in plants to
diseases. Measurement of genetic diversity is useful for enhancing genetic
variation in base populations.
Despite the many benefits of genetic diversity analyses,
there have been few reports of detailed assessment of genetic diversity among
the African maize germplasm compared to the collections of other regions. For
example, temperate maize genotypes such as the U.S. Corn Belt germplasm (Smith et
al., 1997; Hallauer et al., 1988;
Goodman and Stuber, 1983 ), North America (Smith, 1986;
Goodman and Stuber, 1983; Kahler et al., 1983), European maize genotypes
(Hartings et al., 2008; Messmer et al., 1993;1992 ), France maize genotypes
(Dubreuil et al., 1996) and Japanese maize inbred lines (Enoki et al., 2002)
are fully classified into heterotic groups. Similarly, thousands of tropical
maize germplasm at CIMMYT are listed to be evaluated (Warburton et al., 2005;
2002; Xia et al., 2005, 2004; Reif et al., 2003a, 2003b).
These efforts have led to the assignment of lines into
heterotic groups for hybrid maize development, as well as identification of
desirable traits for future breeding programs.
Records available on genetic diversity in African maize
include assessment of few germplasm from Ethiopia (Legesse et al., 2007; Beyene
et al., 2006), Ghana (Obeng-Antwi, 2007), Zimbabwe, Zambia and Malawi
(Magorokosho, 2006), and six other countries in West Africa (Sanou et al.,
1997). There is therefore the urgent need to study the genetic diversity in the
African maize collection.
Since the 1970‟s, African maize has undergone changes arising
from hybridization with genotypes of plant introductions from the U.S.A. and
CIMMYT, Mexico with the aim of producing improved cultivars (Morris et al.,
1999). An example is „Obatanpa GH‟, an open pollinated variety (OPV) and a
quality protein maize (QPM) developed by the Crops Research Institute (CRI),
Kumasi, Ghana in collaboration with the International
Institute of Tropical Agriculture (IITA), Ibadan; the
International Maize and Wheat Improvement Center (CIMMYT), Mexico; and the
Sasakawa Global 2000 (SG 2000) (Badu-Apraku et al. 2006). As these practices
are carried out, gene flow and genetic erosion are inevitable. Some elite
African inbred lines and accessions have also contributed to maize improvement
in exotic lines, as they are reported to demonstrate good yield potential,
disease resistance, and overall favorable agronomic performance (Mwololo et al,
2012). Among these are few TZi accessions of International Institute of
Tropical Agriculture, Ibadan, together with Institut National de la Recherche
Agronomique (INRA), Cameroon (Nelson and Goodman, 2008).
These point to the fact that there is useful distribution of
genes in the African maize germplasm awaiting to be utilized to transform maize
improvement in Africa. Assessment of the extent and distribution of genetic
variation within plant populations has the capacity to increase the
understanding of the historical processes underlying the genetic diversity. It
can reveal both novel genes waiting to be exploited, as well as identify
heterotic groups. This information finds uses in breeding for trait improvement
and for management of the large number of germplasm in repositories.
Little is known about the genetic backgrounds and
relationships including the geographical origins of the accessions collected by
IPGRI and held by the Genetic Resource Center of IITA. In response to the lack
of information on the geographical distribution of the IPGRI accessions, this
research project was designed to reveal its potential exploitation in breeding
programs.
In order to reveal the genetic backgrounds and relationships
including variability within and among the IPGRI accessions, it is required
that a combination of approaches such as morphological trait evaluation and
molecular genotyping be applied to identify genes, reveal the richness of
allelic polymorphisms, partition the population into heterotic groups, and
identify a set of genotypes which maximize their diversity.
Information regarding genetic diversity of breeding materials
especially landraces is indispensable for maize improvement. Genetic diversity
of maize has usually been assessed based on morphological data characterization
using descriptors (Goodman and Bird, 1977), and pedigree analysis through
estimation of coancestry coefficients (Malécot, 1948).
Collecting and analyzing data by this technique is
inexpensive in developing countries where labour cost is considerably low.
Morphological evaluation is relatively simple and does not require sophisticated
technology. Despite the simplicity, these descriptors alone present several
limitations such as high demand of time and labour intensiveness.
Again, morphological characters are often influenced by
environment, hence are limited in their reliability. In contrast, molecular
markers such as SSRs (Warburton et al., 2002), AFLP (Beyene et al., 2006),
RFLPs (Dubreuil et al., 1999) and SNPs (Yu et al., 2011) have proven to be
powerful in discriminating among accessions. They are immune to environmental
effects and have high heritability. Among these, SSRs have been widely used for
the study of diversity including population structure and demographic history of domesticated species because of their
high level of allelic diversity over RFLPs, AFLPs, or SNPs loci (McGregor et al.,
2000; Powell et al., 1996). They are highly polymorphic, reliable (Smith et al.,
1997), easy to generate, have low cost, are highly repeatable (Warburton et al.,
2002), and are suitable for large-scale investigations as needed for the
characterization of genetic resources (Powell et al., 1996). Molecular markers
are therefore superior to morphological and biochemical markers because they
are more efficient and sensitive in detection of distinct differences arising
from mutations among genotypes at DNA level (Melchinger et al., 1991). They are
however expensive and demand sophisticated equipment.
In a morphological study involving twenty-two traits Ruiz de
Galaretta and Alvarez (2001) evaluated 100 landraces of maize from Northern
Spain and came up with seven groups having promising breeding values. Beyene et
al. (2005) researched into 62 traditional Ethiopian highland maize using
morphological traits and molecular profiling by encompassing AFLPs and SSRs and
concluded that variability existed among the selected genotypes. Hartings et al.
(2008) reported a large genetic heterogeneity among 54 maize landraces
originating from Italy on the basis of morphological and AFLP analyses and
revealed four major clusters relating to their geographical origin.
Rebourg et al. (2001) examined genetic variation among 130
European traditional maize populations and split them into six groups on the
basis of morphological and molecular analyses. Analysis of 294 landraces
originating from Malawi, Zambia, and Zimbabwe using 34 phenotypic traits
partitioned the set into three non-overlapping groups by cluster analysis (Magorokosho, 2006). Obeng-Antwi
(2007) performed genetic diversity study on 92 maize landraces from Ghana and
observed a large variability among accessions within groups (96 %) rather than
among groups using AFLPs and agromorphological traits. Studies by the various
researchers confirm the effectiveness of the combined use of morphological
evaluation and molecular genotyping.
Therefore for a comprehensive study of the IPGRI genotypes
held in IITA with little passport data the combined techniques must be applied
to reveal their useful characteristics in terms of allele diversity, unique
genotypes worth incorporating in breeding programs, relationships among the
genotypes, as well as their evolutionary history.
The main goal of this study was to estimate the level of
genetic diversity and relationships among the tropical IPGRI maize landraces in
the IITA germplasm repository.
The specific objectives are:
(1) To determine
genetic variation in the IPRGI population by means of agromorphological traits
evaluation
To investigate the heritability, genotypic and phenotypic
correlations among the IPGRI maize genotypes
To estimate genetic diversity of the IPGRI genotypes using
SSR profiling
To assemble the IPGRI population into groups on the basis of
genetic distance
To determine the allele diversity and heterozygosity among
the genotypes
That, the IPGRI maize landraces in IITA repository with
little passport data are genetically diverse and contain alleles that can be
exploited for maize improvement especially in Sub-Saharan Africa.
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