Characterization of Grain Amaranth (Amaranthus spp.) Germplasm in South West Nigeria Using Morphological, Nutritional, and Random Amplified Polymorphic DNA (RAPD) Analysis

Pamela Akin-Idowu, Michael Gbadegesin, Uterdzua Orkpeh, Dorcas Ibitoye, Oyeronke Odunola
2016 Resources  
Efficient utilization of plant genetic resources for nutrition and crop improvement requires systematic understanding of the important traits. Amaranthus species are distributed worldwide with an interesting diversity of landraces and cultivars whose leaves and seeds are consumed. Despite their potential to enhance food security and economic livelihoods, grain amaranth breeding to improve nutritional quality and adoption by farmers in sub-Saharan Africa is scanty. This study assessed the
more » ... assessed the variation among 29 grain amaranth accessions using 27 phenotypic (10 morphological and 17 nutritional) characters and 16 random amplified polymorphic DNA (RAPD) primers. Multivariate analysis of phenotypic characters showed the first four principal components contributing 57.53% of observed variability, while cluster analysis yielded five groups at 87.5% similarity coefficient. RAPD primers generated a total of 193 amplicons with an average of 12.06 amplicons per primer, 81% of which were polymorphic. Genetic similarities based on Jaccard's coefficient ranged from 0.61 to 0.88. The RAPD-based unweighted pair group method with arithmetic mean dendrogram grouped the accessions into nine clusters, with the same species clustering together. RAPD primers distinguished the accessions more effectively than phenotypic markers. Accessions in the different clusters as obtained can be exploited for heterotic gain in desired nutritional traits. Resources 2016, 5, 6 2 of 15 increasing interest over recent decades [6] [7] [8] . Grain amaranth has been gaining worldwide acceptance as a crop rich in high-quality protein (13%-19% of dry weight) and its remarkable essential amino acid balance which is close to the optimum protein reference pattern in the human diet according to FAO/WHO requirements [9] [10] [11] . Grain amaranth is also an excellent source of minerals, vitamins A, C, and E [12] [13] [14] . Considering its agronomic and nutritional importance, amaranth has potential to broaden the food base in sub-Saharan Africa [15] ; therefore, attention should be given to the cultivation, genetic improvement, and sustainable utilization of this promising crop in the region. Amaranth is a self-pollinated crop, but wide variation in genotypes exists due to varying amounts of outcrossing and frequent interspecific and inter-varietal hybridization [1, 16] . Amaranths also exhibit tremendous diversity related to their wide adaptability to different eco-geographic situations [17] . Genotype identification in amaranth had been a long term challenge [18] due to the close relationships that exists within the genus. Knowledge of genetic diversity and trait variations in populations is useful in plant breeding and for developing ex situ conservation strategies of plant genetic resources [19] [20] [21] . Plant phenotype is commonly used for estimating genetic diversity as it provides a simple way of quantifying genotypic variation. However, the efficiency of estimating genetic differences using morphological traits is largely limited by uncontrollable environmental factors and distinctness. Molecular-based analyses overcome many limitations of morphological and biochemical trait-based procedures and have been used variously in determining genetic diversity [22, 23] . Various types of molecular markers are utilized to evaluate DNA polymorphism. Random Amplified Polymorphic DNA (RAPD), a PCR (polymerase chain reaction)-based technique has considerable advantage for studying plant genome characterizations because it is simple, relatively inexpensive, utilizes arbitrary primers, and randomly samples a potentially large number of loci in a less complex pattern [1, 24, 25] . Even though RAPD is criticized for low reproducibility, this is overcome by optimization of the reaction and maintenance of stringent conditions [26, 27] . RAPD analyses has been employed for several plant species in relation to development of genetic conservation and improvement strategies, including the study of genetic diversity, taxonomic delimitations, and evolutionary relationships in Amaranthus species [1, 17, 28, 29] . Grain amaranth remains a largely underexploited crop for grain purposes in sub-Saharan Africa despite the potential as a hardy field crop with generally excellent nutritional qualities. However, research aimed at its genetic improvement and agronomic adoption in sub-Saharan Africa is almost non-existent. A number of accessions of amaranth have been introduced that have acclimatized well in the region, but evaluation of agronomic and nutritional traits in the peculiar agro-ecologies of the region has not been conducted. The availability of genetic variation among and within the different accessions for these traits provides great scope for crop improvement through selection and other breeding methods to develop desired genotypes. Thus, insight into the genetic variation within and among the available amaranth genotypes in relation to the morphological and nutritional traits as revealed by RAPD markers is necessary. Such empirical knowledge will facilitate strategic marker-assisted selection (MAS) breeding, as well as enhance effective genetic resources exploration, conservation, management, and utilization of Amaranthus species in future breeding programs. The aim of this work was therefore to study the genetic variation observable in 29 Amaranthus accessions in the agro-ecology of South West Nigeria using phenotypic traits of agronomic and nutritional significance, and RAPD markers. The goal is to provide an insight for further utilization of RAPD markers to characterize and identify quantitative trait loci (QTLs) for agronomic and nutritional quality in amaranth genotypes bred for adoption in sub-Saharan agro-ecologies. Subsequently, RAPDs adjacent to important QTLs will be used in marker-assisted selection (MAS) of breeding lines. Resources 2016, 5, 6 3 of 15
doi:10.3390/resources5010006 fatcat:cg6cqdro5bdana7usa4ehuhkvu