GENETIC ANALYSIS OF SIMPLE SEQUENCE REPEAT MARKERS AND MORPHOLOGICAL TRAITS VARIATION IN LOWLAND, MID-ALTITUDE AND HIGHLAND AFRICAN MAIZE (Zea mays L.) ACCESSIONS

ABSTRACT
Genetic diversity is a valuable resource for improvement in crop productivity and trait performance. Maize (Zea mays L.) is an important food security crop in Africa constrained with low yield typically below world average. The forces of population escalation, diminishing arable land, and climate anomalies with their attendant low yield and crop loss arising from drought and emerging diseases indicate worsening food insecurity in Africa. However, genetic improvement in a wide genetic base is a relevant and logical strategy requiring availability of large reserve of alleles bearing these traits. This strategy necessitates studies into the well-adapted traditional African maize germplasm to identify, quantify, and explore the basis of variation in order to reveal the historical processes that have created and driven the level of variation for efficient exploitation. The main objective of this research was to investigate genetic diversity of maize originating from twelve countries, covering a wide geographical region in three mega environments in Africa, namely, lowland, mid-altitude and highland accessions. The accessions were tested under non-stressed environments in Ghana by evaluation of 29 agro-morphological traits on 35 genotypes, and 16 simple sequence repeat markers on 57 accessions held in IITA Genetic Resource Center. Accessions showed wide variations in silk color, kernel arrangement, principal grain color, and kernel texture except cob color. Significantly different mean squares and large coefficient of variation indicated substantial variation among the genotypes for all traits except anthesis-silking interval. Variability was highest in mid-altitude followed by lowland, and was least in the highland accessions. Being the most important traits, earliness and grain yield varied from 49 to 66 days to anthesis and 1.7 to 6.2 Mgha-1, respectively. Anthesis-silking interval varied from 2 to 6 days. The study identified a single early-maturing genotype TZm-1376, with strikingly short ASI of 2 days which also possessed high yield of 5.6 Mgha-1 in consonance to the improved check „‟Obatanpa GH‟‟ with yield of 6.3 Mgha-1.. Unusual combination of early-maturing yet high-yielding accessions were identified in ten genotypes TZm-4, TZm-41, TZm-270, TZm-1521, TZm-275, TZm-14, TZm-33 TZm-37, TZm-1367, and TZm-1376. Medium - maturing but high yielding genotypes which can be incorporated into breeding programs for improvement included TZm-1434, TZm-1356, TZm-1358 and TZm- 242. The broad sense heritability estimates were low for all traits in the accessions except earliness traits in the lowland genotypes. Significant (p≤ 0.01) positive genotypic correlations of grain yield with hundred kernel weight, kernel length, tassel length, and ear leaf width indicated that selection for these traits will lead to simultaneous increase in grain yield. Morphological genetic similarity measures ranged from 0.00 to 0.80 with overall mean of 0.26 indicating wide genetic variability among accessions. The African landraces were 23 %, 29 %, and 38 % similar in the mid-altitude, lowland and highland accessions which agreed with the level of variability revealed by the descriptive statistical measures. A total of 70 alleles ranging from 2-10 with a mean of 5.38 alleles per locus for the 14 SSR loci were identified. The total number of alleles generated across the loci was 1,908 over 57 accessions. Polymorphism Information Content ranged from 0.18 to 0.81 having an average of 0.64 and 93 % polymorphism rate. The high average expected heterozygosity of 0.64 indicates abundance of heterozygosity probably arising from historic admixture of two or more divergent populations. Molecular analysis revealed average dissimilarity coefficients of 0.70 for mid-altitude, 0.69 for lowland and 0.65 for highland accessions with an average of 0.70 ranging from 0.00 to 1.00. These were consistent with the low similarity values produced by the morphological analysis. The UPGMA produced four and three main clusters for agro-morphological and SSR analysis, respectively, confirmed by the principal components biplots. Potential good clusters for exploiting heterosis in maize breeding programs were identified. The study has revealed wide genetic diversity in the accessions to permit their utilization as sources of alleles for improvement in performance and productivity of maize in Africa.


CHAPTER ONE
INTRODUCTION
Maize (Zea mays L.) is a cereal belonging to the family Poaceae. It is believed to have originated from Central America, specifically Mexico (Gibson and Benson, 2002). It was first introduced to Africa by the Portuguese traders in the 16th century and has since become one of the continent‟s staple food crops making up more than 50% of the total caloric intake of local diets (Sinha, 2007). The diversified uses for food, feed, and as a major industrial raw material for many products, including adhesives, textile, paint, xylose, ethanol, biofuel and a binder for pharmaceuticals make maize a very important crop in the global economy.

The demand for maize around the world is increasing. In 2010/11 world maize consumption was forecast to rise to 830 million metric tons (mmt), representing 2% increase in the previous year‟s forecast while production in the same period was 823 mmt. Over the years, demand for maize has increased, without commensurate increase in supply. While the International Food Policy Research Institute (IFPRI, 2003) projected a demand of 852 mmts by 2020, the actual consumption of maize was 868 mmt in 2011/2012 , with a new projection of over 1,000 mmt by 2018/2019 (International Grain Council, 2013). With this tendency of consumption exceeding production, as well as actual consumption surpassing projections, the need to target improvement in maize productivity has become more important than ever. In sub-Saharan Africa, demand is expected to double from 27 mmt in 1995 to about 52 mmt by 2020 (Pingali and Pandey, 2000). As demand for maize increases around the world, there has been a commensurate increase in the acreage planted, as well as tremendous efforts by many countries to increase productivity of maize (CIMMYT, 1994). Prior to 2001, average maize yield of 0.9 to 1.2 t/ha was recorded for sub-Saharan Africa which is just below a quarter of the global average of 5.5 t/ha, and about a sixth of the average yield of 7.8 t/ha in the U.S.A. (FAOSTAT, 2006).

In recent years, impressive advancements in maize productivity have been achieved through conventional breeding in West and Central Africa raising the productivity from 1.2 t/ha to 3-5 t/ha. To support this, the Food and Agricultural Organization (FAO) reported that in 2005 six countries in Africa produced twice the amount consumed, while eight other countries imported 5-35% and 11 countries also imported 57-100% of the maize consumed in their respective countries (FAO, 2007). Nevertheless, maize yield in West/Central Africa still remains below the world average.

The key constraints to crop production globally are limited land and water resources, expanding population and abiotic and biotic stresses. In sub-Saharan Africa, the disparity in maize productivity is exacerbated by nutrient poor soils, drought, disease, and use of unimproved seed. The great demand for maize of both quality and quantity requires more rapid genetic improvement. Efforts have to be made to increase maize yield in Africa.

Genetic improvement of any crop begins with an evaluation of the genetic diversity present in the germplasm. Genetic diversity estimates provide valuable information for classification of germplasm for guidance in performing crosses in crop improvement programmes. It also provides the basis for devising strategies for conservation and sustainability. In the current climate variability phenomena, the need for developing genotypes having less vulnerability to drought, pest and disease resistance traits combined with high yield in a wide genetic base is relevant. Genetic diversity information is useful for identification of useful genes among germplasm, for inbred line development, for assignment of inbred lines into heterotic groups, and for identification of testers.

To date only few reports of detailed assessment of genetic diversity among the accessions adapted to sub-Saharan Africa are documented. Genetic diversity studies on Ethiopian maize genotypes were reported by Beyene et al. (2006) and Legesse et al. (2007). In Ghana, Obeng-Antwi (2007) reported genetic diversity estimates of 90 landraces. Oppong et al. (2014) worked on genetic characterization of Ghanaian maize landraces using microsatellite markers. Some 294 Zimbabwe, Zambia and Malawi maize genotypes were evaluated for genetic diversity estimates (Magorokosho, 2006). Sanou et al. (1997) determined the diversity in some West African maize genotypes by means of isozyme diversity.

In contrast, genetic diversity among maize germplasm in North America (James et al., 2002; Bretting et al., 1990; Smith 1986; Goodman and Stuber, 1983 and Kahler et al., 1983.), in CIMMYT (Warburton et al., 2005; 2002; Xia et al., 2005; Carvalho et al., 2002), in Europe (Hartings et al., 2008; Okumus, 2007), and Asia (Enoki et al., 2002; Yuan et al., 2000) have been evaluated. As a result of this lack of information, maize breeding efforts in sub-Saharan Africa is seriously limited. To date, old breeding materials, and few newly developed inbred lines have been culled from CIMMYT lines, producing maize of narrow genetic base. While landraces are known to possess many useful alleles for crop improvement, the utilization of African landraces in breeding programs have not been exploited. For example, the popular maize genotype, „Obatanpa GH‟ which is in the pedigree of many of the maize cultivars produced in Ghana was bred from CIMMYT Population 63 maize of Mexican origin (Badu-Apraku, 2006).

„Obatanpa GH‟ (Reg. no. CV-1, PI 641711), a tropically adapted, intermediate maturing, open-pollinated cultivar was developed by the Crops Research Institute (CRI), Kumasi, Ghana in collaboration with the International Institute of Tropical Agriculture (IITA), the International Maize and Wheat Improvement Center (CIMMYT), and the Sasakawa Global 2000. „Obatanpa GH‟ is a white dent and flint endosperm Quality Protein Maize (QPM) with elevated levels of lysine and tryptophan and was first released by CRI, Ghana in 1992 as „Obatanpa‟ to help improve the protein nutritional status and the health of a large population of low-income groups in sub- Saharan Africa who depend on maize as a major component of their dietary protein intake (Sallah, 1998).

The Plant Genetic Resources Research Institute (PGRRI) in Ghana has in store some 400 maize accessions collected in 1991. The International Institute of Tropical Agriculture, Nigeria, also has over 800 maize accessions collected from many agroecological zones in Africa (www.iita.org, verified March 04, 2015). Evaluation of the genetic diversity estimates within the large African maize germplasm has the potential to reveal useful alleles for future maize breeding programs.

The markers commonly used in genetic diversity studies include morphological trait evaluation, isozyme and molecular markers. Accurate estimation of genetic diversity requires the use of very efficient marker protocols that detect fine genetic differences between the accessions. Maize breeders in India, as in most developing countries, have differentiated accessions mainly on the basis of major morphological characters such as plant height, anthocyanin pigmentation of various plant parts, tassel type, tassel branching, number of days to flowering, ear characteristics, cob colour, grain colour and grain type (Virk and Witcombe, 1997). Although morphological descriptions are important for ascertaining the agronomic utility of germplasm, such descriptions are not very reliable because of complex genotype×environment interactions that require assessment in multiple environments (Enoki, 2002; Smith and Smith, 1989), are time-consuming, labour-intensive and require large populations (Botha and Venter, 2000). Isozyme analysis is relatively simple and less costly compared with molecular marker analysis; however inadequate genomic coverage, relatively low levels of polymorphism, developmental regulation and pleiotropic effects impose major constraints in effectively using these markers in genotype differentiation and analysis of genetic diversity (Dubreuil et al., 1996; Smith and Smith, 1986).

Molecular markers have proved to be more powerful tools in genetic diversity and mapping studies. The available molecular markers include Random Amplified Polymorphic DNA (RAPDs), Restriction Fragment Length Polymorphism (RFLPs), Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Repeats (SSR), Sequence Tagged Sites (STS) and Single Nucleotide Polymorphisms (SNPs)

Among the different types of PCR- based DNA markers available for diverse applications in maize breeding, SSR markers (microsatellites) are often preferred because they are less costly, simple to prepare, offer greater reliability and reproducibility and more effective than the other markers (Smith et al., 1997). The SSR markers are robust, codominant, hypervariable, abundant, and uniformly dispersed in plant genomes. Senior and Heun (1993) reported that SSR loci provide a high level of polymorphism in maize. Pejic et al. (1998) and Smith et al. (1997) reported of good correlation between SSR and RFLP diversity and pedigree-based measurements. Moreover, the efficiency of SSRs can be increased by running multiplexed reactions under automated electrophoresis conditions (Mitchell et al., 1997).

Genetic diversity study among the African maize inbred lines present in the CIMMYT Centers in Ethiopia and Zimbabwe has been determined using SSR markers (Legesse et al., 2007). Menkir et al. (2004) assessed the genetic relationships among tropical mid-altitude inbred lines developed in Nigeria and Cameroon, using AFLP and SSR markers. Beyenne et al. (2006) evaluated genetic diversity of traditional Ethiopian highland maize accessions by SSR markers. Reif et al. (2003) determined the genetic distance and heterosis in tropical maize populations by means of SSR markers. The genetic diversity estimates among maize accessions originating from Zambia, Zimbabwe, and Malawi were determined by SSRs (Magorokosho, 2006).

Reif et al., (2004) determined genetic diversity within and among CIMMYT maize populations of tropical, subtropical, and temperate germplasm by means of SSR markers. Warburton et al. (2008) estimated genetic diversity in CIMMYT non-temperate maize germplasm, including landraces, open pollinated varieties, and inbred lines using SSRs. Equivalent information on genetic diversity among West and Central African maize accessions is not available, hence they have not formed part of maize breeding programs in Africa.


The main objective of this research is to estimate genetic diversity and groupings among fifty-seven maize accessions originating from three ecological zones in Africa, viz, lowland, mid-altitude and highland regions. The specific objectives include:

Assessment of genetic diversity by means of morphological trait markers

Assessment of genetic diversity by means of SSR profiling

Determination of groupings within the maize collection for the purpose of hybrid breeding

Hypothesis of current research is based on two themes delineated as:

Over a long period of time, forces of evolution including mutation, recombination, selection, migration, and genetic drift have introduced allelic variation in the African maize germplasm pool

That the allelic variation can be estimated from marker polymorphisms 

Justification
The information on genetic diversity study among the maize germplasm in Africa will be useful for identification of useful genotypes for enhancing the performance of commercial cultivars in future breeding programs, for application in organizing and managing the germplasm in Genetic Resource Centers, for widening the genetic base of the gene pool, and for identification of heterotic groups for hybrid breeding. Effective plant breeding and crop improvement programs for food security depend on the availability of genetic diversity information.

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Item Type: Ghanaian Project Material  |  Attribute: 146 pages  |  Chapters: 1-5
Format: MS Word  |  Price: GH50  |  Delivery: Within 30Mins.
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