Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L. collections in West Africa using simple sequence repeats marker

Abstract

Knowledge of genebank and on-farm genetic diversity, particularly in an introduced crop species, is crucial to the management and utilization of the genetic resources available. Microsatellite markers were used to determine genetic diversity in 574 accessions of cacao, Theobroma cacao L., representing eight groups covering parental populations in West Africa, genebank, and farmers' populations in Nigeria. From the 12 microsatellite markers used, a total of 144 alleles were detected with a mean allelic richness of 4.39 alleles/locus. The largest genetic diversity was found in the Upper Amazon parent population (H nb =0.730), followed by the 1944 Posnette's Introduction (H nb =0.704), and was lowest in the Local parent population (H nb =0.471). Gene diversity was appreciably high in the farmers' populations (H nb =0.563-0.624); however, the effective number of alleles was lower than that found in the genebank's Posnette's population. Fixation index estimates indicated deficiency of heterozygotes in the Upper Amazon and the Local parent populations (F is = 0.209 and 0.160, respectively), and excess of heterozygotes in the Trinitario parent population (F is =−0.341). The presence of inbreeding in the Local parent populations and substructure (Wahlund effect) in the Upper Amazon were suggested for the deficiency of heterozygotes observed. Non-significant genetic differentiation observed between the genebank's and farmers' populations indicated significant impact of national breeding programs on varieties grown in farmers' plantations. From this study, we showed that appreciable genetic diversity was present in on-farm and field genebank collections of cacao that can be exploited for crop improvement in West Africa. Suggestions for future conservation of on-farm genetic diversity and local landraces are further discussed.

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping

“…The physical location of each marker loci was determined by comparing microsatellite flanking sequences and their primers against a recently published, high-resolution cacao genome (Motamayor et al 2013) using both BLAST and e-PCR (Altschul et al 1990;Schuler 1997). All base-pair positions reported in this study indicate a physical location on this reference genome, which was built from the Matina 1-6 cultivar, the most common cultivated type of cacao and belonging to the Amelonado diversity group (Aikpokpodion et al 2009;Efombagn et al 2008;Motamayor et al 2013Motamayor et al , 2003. These physical locations are consistent with their locations on a previously published composite genetic map .…”

Defining Genetic Diversity in the Chocolate Tree, Theobroma cacao L. Grown in West and Central Africa

“…Cocoa is the single largest non-oil export earning commodity for Nigeria. In comparison with other agricultural commodities, cocoa makes the largest non-oil contribution to the nation's economic development and accounted for 65% of total agricultural export in 2004 (Aikpokpodion, 2007). In Cameroon, it is estimated that some four million people depend on cocoa and coffee for their livelihood.…”

“…Since the first successful introduction of 'Amelonado' cacao, Lower Amazon Forastero type into West Africa in the late 19 th century, there has been series of additional germplasm introductions as reviewed by (Bartley, 2005;Aikpokpodion, 2009 (Toxopeus, 1964). Efforts to increase genetic variability in the base population in response to outbreaks of disease epidemic had provided impetus for germplasm introduction into Africa.…”

“…Consequently, new introductions were made in 1944 from Upper Amazon Forastero materials collected by F. J. Pound into the West African Cocoa Research Institute headquarters in Tafo, Ghana and Ibadan in Nigeria (Aikpokpodion et al, 2009). Due to the precocity of these materials, they were widely distributed for replanting of cut out plantations and by late 1950s, some 11 selected Upper Amazon types have been used to produce second and third generations of Amazon known as "F 3 Amazon" or "Mixed Amazon" distributed to farmers (Knight and Rogers 1955).…”

“…Due to the precocity of these materials, they were widely distributed for replanting of cut out plantations and by late 1950s, some 11 selected Upper Amazon types have been used to produce second and third generations of Amazon known as "F 3 Amazon" or "Mixed Amazon" distributed to farmers (Knight and Rogers 1955). By 1961, some 60,000 ha in Ghana and an estimated 21 million seedlings had been distributed by the government of the Western Region to plant some 9,500 ha in Nigeria (Aikpokpodion 2009). Several hybrid varieties involving crosses with local Amelonado, Trinitario, and some Criollo materials were also developed from these materials in Ghana (Lockwood and Gyamfi 1979), Nigeria (Atanda and Jacobs 1974), and Cote d'Ivoire (Besse 1975;N'Goran et al 1992).…”