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Molecular Characterization and Genetic Diversity of the Macaw Palm Ex Situ Germplasm Collection Revealed by Microsatellite Markers

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Molecular Characterization and Genetic Diversity of the Macaw Palm Ex Situ Germplasm Collection Revealed by Microsatellite Markers diversity Article Molecular Characterization and Genetic Diversity of the Macaw Palm Ex Situ Germplasm Collection Revealed by Microsatellite Markers Fekadu G. Mengistu 1,*, Sérgio Y. Motoike 2 and Cosme D. Cruz 3 1 Kulumsa Agricultural Research Center (KARC), Ethiopian Institute of Agricultural Research (EIAR), P.O.Box 489, Asella, Ethiopia 2 Departamento de Fitotecnia, Universidade Federal de Viçosa, Av. P.H. Rolfs, Campus, Viçosa, MG 36570-000, Brazil; [email protected] 3 Departamento de Biologia Geral, Universidade Federal de Viçosa, Av. P.H. Rolfs, Campus, Viçosa, MG 36570-000, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +251-0968-23-55-27; Fax: +251-022-331-1508 Academic Editor: Mario A. Pagnotta Received: 29 June 2016; Accepted: 9 October 2016; Published: 13 October 2016 Abstract: Macaw palm (Acrocomia aculeata) is native to tropical forests in South America and highly abundant in Brazil. It is cited as a highly productive oleaginous palm tree presenting high potential for biodiesel production. The aim of this work was to characterize and study the genetic diversity of A. aculeata ex situ collections from different geographical states in Brazil using microsatellite (Simple Sequence Repeats, SSR) markers. A total of 192 accessions from 10 provenances were analyzed with 10 SSR, and variations were detected in allelic diversity, polymorphism, and heterozygosity in the collections. Three major groups of accessions were formed using PCoA—principal coordinate analysis, UPGMA—unweighted pair-group method with arithmetic mean, and Tocher. The Mantel test revealed a weak correlation (r = 0.07) between genetic and geographic distances among the provenances reaffirming the result of the grouping. Reduced average heterozygosity (Ho < 50%) per locus (or provenance) confirmed the predominance of endogamy (or inbreeding) in the germplasm collections as evidenced by positive inbreeding coefficient (F > 0) per locus (or per provenance). AMOVA—Analysis of Molecular Variance revealed higher (48.2%) genetic variation within population than among populations (36.5%). SSR are useful molecular markers in characterizing A. aculeata germplasm and could facilitate the process of identifying, grouping, and selecting genotypes. Present results could be used to formulate appropriate conservation strategies in the genebank. Keywords: Acrocomia aculeata; biodiesel; domestication; genebank; genetic diversity; SSRs 1. Introduction Macaw palm (Acrocomia aculeata (Jacq.) (Lodd. ex Mart.))–Arecaceae (2n = 2x = 30) is commonly known as macaúba in Brazil [1]. This arborescent, spiny and single-stemmed palm is monoecious and self-compatible, and entomophily and anemophily forms of pollinations are reported [2]. It bears a mixed reproductive system, with a predominance of outcrossing [3,4]. The combination of the two pollination strategies with flexible reproductive systems suggests that A. aculeata can be highly successful in the colonization of new areas, as evidenced by the ample distribution of the species in the Neotropics. It is a very resilient palm and has abundant distribution in Brazil mainly in the regional States of Ceará, Minas Gerais, Mato Grosso, Mato Grosso do Sul, and São Paulo [2]. A. aculeata is little known globally, however, in recent years, it has raised interest due to its potential for social and economic use as an oil producer, considering that it is cited as one of the most important new sources of oil for biofuel [5,6]. It produces fruits yielding up to 25 t/ha corresponding Diversity 2016, 8, 20; doi:10.3390/d8040020 www.mdpi.com/journal/diversity Diversity 2016, 8, 20 2 of 12 Diversity 2016, 8, 20 2 of 13 toimportant about 4000 new kg sources of oil. The of oil solid for wastebiofuel is [5,6]. converted It prod touces charcoal fruits yielding and nutritious up to 25 cakes t/ha thatcorresponding can be used toto generate about 4000 energy kg of and oil. feedThe solid livestock waste as is wellconverted [7,8]. to The charcoal biochemical and nutritious properties cakes of thethat oil can are be provedused toto be generate suitable energy for the and cosmetic feed livestoc industryk as and well for [7,8]. biodiesel The biochemical production properties [9–11]. Moreover, of the oil this are palmproved has to be suitable for the cosmetic industry and for biodiesel production [9−11]. Moreover, this palm has environmental benefits as it can be fostered in impoverished soils and drought prevailing areas, which environmental benefits as it can be fostered in impoverished soils and drought prevailing areas, is a desirable trait for plants in order to rehabilitate degraded pastures or for agroforestry practices [12]. which is a desirable trait for plants in order to rehabilitate degraded pastures or for agroforestry Hence, A. aculeata can be a suitable option for production of biodiesel among the common food-based practices [12]. Hence, A. aculeata can be a suitable option for production of biodiesel among the oleaginous plants such as soya bean, sunflower, and oil palms [13]. common food-based oleaginous plants such as soya bean, sunflower, and oil palms [13]. It is not commercially cultivated like the domesticated Arecaceae palms such as Elaeis guineensis, It is not commercially cultivated like the domesticated Arecaceae palms such as Elaeis guineensis, Cocus nucifera Enterpe oleraceae Cocus nucifera,, and and Enterpe oleraceae,, whichwhich are important elements elements in in the the Brazilian Brazilian savannah, savannah, and and presentpresent great great genetic genetic diversity diversity in in natural natural populations populations [5 [5,14,15].,14,15]. The The palm’s palm's genetic genetic diversity diversity suffers suffers by predatoryby predatory extractivism, extractivism, unsustainable unsustainable land use,land anduse, climate and climate change change [16,17]. [16,17]. Hence, Hence, genetic genetic resource conservationresource conservation and its sustainable and its sustainable use have paramount use have importanceparamount forimportance future genetic for future improvement. genetic Aimprovement. central point inA itscentral sustainable point in conservation its sustainable is theconservation knowledge is ofthe the kn geneticowledge diversityof the genetic present indiversity genebank present collection in genebank and potential collection exploitation and pote ofntial the exploitation genetic materials of the bygenetic breeding materials programs. by Thebreeding germplasm programs. characterization The germplasm and speciescharacterization genetic diversity and species could genetic be effectively diversity integrated could be by moleculareffectively analyses. integrated by molecular analyses. Therefore,Therefore, we we characterized characterized andand studiedstudied the ge geneticnetic diversity diversity of of the the macaw macaw palm palm germplasm germplasm collectionscollections in in a genebanka genebank using using microsatellites microsatellites (Simple (Simple Sequence Sequence Repeats—SSRs) Repeats—SSRs) [18 [18,19].,19]. SSRs SSRs are are well knownwell known molecular molecular markers markers for their for potentially their potentially high information high information content andcontent versatility and versatility as molecular as toolsmolecular in germplasm tools in characterization germplasm characterization [20,21]. They are [20,21]. often co-dominant, They are often highly co-dominant, reproducible, highly frequent inreproducible, most eukaryotes frequent and are in quitemost useful eukaryotes in various and aspectsare quite of molecularuseful in geneticvarious studiesaspects [ 22of, 23molecular]. Another aimgenetic was tostudies study [22,23]. the distribution Another aim of was the geneticto study diversity the distribution and in particularof the genetic if a diversity correlation and exists in betweenparticular the if genetic a correlation and the exists geographic between distances the gene andtic ifand distinct the geographic genetic groupings distances are and formed if distinct among populations.genetic groupings These resultsare formed will among be useful populations. in future conservationThese results activities.will be useful in future conservation activities. 2. Experimental Section 2. Experimental Section 2.1. Plant Material and DNA Isolation 2.1. Plant Material and DNA Isolation Leaf samples from 192 A. aculeata germplasm accessions were obtained from the ex situ plant collection,Leaf macaúbasamples from Active 192 Genebank,A. aculeata germplasm situated in accessions Araponga were (S2040 obtained 01, W423115), from the Stateex situ of plant Minas Gerais,collection, Brazil. macaúba Theaccessions Active Genebank, were originated situated in from Araponga seeds collected(S2040 01, in W423115), six regional State states of Minas of the countryGerais, (FigureBrazil. 1The) and accessions germinated were using originated a pre-germination from seeds collected protocol in as six described regional in states patent of INPIthe 014070005335country (Figure [24]. 1) The and accessions germinated represent using a 10 pre-germination provenances having protocol a total as described of 41 populations in patent coded INPI as BGP014070005335 and 3–5 individuals [24]. The accessions were considered represent per 10 population provenances (Table having1). a total of 41 populations coded as BGP and 3– 5 individuals were considered per population (Table 1). Figure 1. Map shows the six geographical states in Brazil, where the original plant materials were Figure 1. Map shows the
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