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Fabaceae: Caesalpinioideae) and Its Relation to Geography, Population Genetics and Morphology

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Fabaceae: Caesalpinioideae) and Its Relation to Geography, Population Genetics and Morphology Genome Relative genome size variation in the African agroforestry tree Parkia biglobosa (Fabaceae: Caesalpinioideae) and its relation to geography, population genetics and morphology Journal: Genome Manuscript ID gen-2019-0069.R2 Manuscript Type: Article Date Submitted by the 28-Jun-2019 Author: Complete List of Authors: Dobes, Christoph; Austrian Research Centre for Forests, Department of Forest Genetics Steccari, Irene; Austrian Research Centre for Forests, Department of Forest GeneticsDraft Köstenberger, Selina; Austrian Research Centre for Forests, Department of Forest Genetics Lompo, Djingdia; Centre National de Semences Forestieres genome size, morphometry, chromosome number, forestry, population Keyword: genetics Is the invited manuscript for consideration in a Special Not applicable (regular submission) Issue? : https://mc06.manuscriptcentral.com/genome-pubs Page 1 of 29 Genome 1 Relative genome size variation in the African agroforestry tree Parkia biglobosa (Fabaceae: 2 Caesalpinioideae) and its relation to geography, population genetics and morphology 3 4 Christoph Dobeš1,*, Irene Steccari1, Selina Köstenberger1, Djingdia Lompo2 5 6 1Austrian Research Centre for Forests, Department of Forest Genetics, Seckendorff-Gudent-Weg 8, A- 7 1131 Vienna 8 * corresponding author: phone +43 (1) 878 38 1265, fax +43 (1) 878 38 2250, email: 9 [email protected] 10 2 Centre National de Semences Forestieres, 01 BP 2682, Route de Kossodo, Ouagadougou, Burkina 11 Faso Draft 12 13 short title: Relative genome size in Parkia (Fabaceae) 14 1 https://mc06.manuscriptcentral.com/genome-pubs Genome Page 2 of 29 15 Abstract 16 Variation in genome size and in chromosome number can be linked to genetic, morphological and 17 ecological characteristics, and thus be taxonomically significant. We screened the relative genome size 18 (RGS) and counted the number of mitotic chromosomes in the African agroforestry tree Parkia 19 biglobosa, a widely distributed savannah species that shows conspicuous morphological clinal 20 variation and strong genetic structure, and tested for linkage of RGS variation to geography, leaf 21 morphology, and population genetic variation. An improved protocol for the preparation of 22 chromosomes was developed. The study is based on 58 individuals from 15 populations covering most 23 of the distribution range of the species. We observed differences in RGS among individuals of up to 24 10.2 %, with some of the individuals differing statistically in RGS from the bulk of screened 25 individuals. Most of the RGS variation was within populations whereas variation was unrelated to any 26 of the tested features of the species. ThoseDraft chromosome numbers which could be exactly established 27 were invariable 2n = 2x = 26. In conclusion, there was no evidence from the karyological data for 28 structured intra-specific taxonomic heterogeneity. 29 Keywords Africa, chromosome number, flow cytometry, forestry, morphometry, population genetics 30 2 https://mc06.manuscriptcentral.com/genome-pubs Page 3 of 29 Genome 31 Introduction 32 Variation in genome size, i.e. variation in the DNA-content of cell nuclei, is a commonly observed 33 phenomenon in plants (Bennett and Leitch 1995; Bennett and Leitch 2011) and generated by three 34 principal mechanisms: polyploidization, aneuploidization, and deletion or amplification of DNA. 35 Polyploidy refers to the presence of more than two basic chromosome sets (i.e. monoploid genomes: 36 (Greilhuber 2005b) within a cell nucleus and arises through the instantaneous addition of entire 37 chromosome sets (Ramsey and Schemske 1998). Aneuploidy results from chromosome 38 missegregation and refers to the deviation of chromosome number from a multiple of the monoploid 39 chromosome number due to non-balanced gain or loss of whole chromosomes (e.g. Compton 2011). 40 Finally, molecular mechanisms like transposon activation, unequal recombination between adjacent 41 repeated DNA motifs, or specific elimination of genes and DNA sequences (Leitch and Bennett 2004; 42 Soltis et al. 2009; Soltis and Soltis 1999) Draftpotentially change the DNA content of monoploid genomes 43 (or of single chromosomes; e.g. Bennetzen et al. 2005; Grover and Wendel 2010). An additional 44 cytological mechanism optionally involved in change of genome size is dysploidization, defined as the 45 stepwise change of the haploid – the meiotically reduced – chromosome number achieved through 46 fusion or fission of chromosomes. Resultant reduction or increase in the number of chromosomes 47 (descending and ascending dysploidy, respectively) can either occur with or without loss of 48 chromosomal fragments and therefore DNA (unbalanced and balanced rearrangements, respectively; 49 see reviews by Lysák and Schubert 2013; Schubert 2007; Weiss-Schneeweiss and Schneeweiss 2013). 50 Genome size variation can be a driver or at least has been identified as an associate of 51 evolutionary divergence. Each of the mentioned principal mechanisms causing genomic modification 52 thus were shown to be linked to patterns of differentiation: monoploid genome size was found to vary 53 with ecological preferences (Jakob et al. 2004; Reeves et al. 1998) or tolerances (Macgillivray and 54 Grime 1995) although the causality of the association often remained elusive or speculative (Schmuths 55 et al. 2004; Slovák et al. 2009; Šmarda and Bureš 2006; Suda et al. 2007a). Large differences in 56 genome size among crossing partners furthermore can cause sterility of the progeny this way reducing 57 gene flow (Levin 2002). Chromosomal structural rearrangements (with or without change of the 3 https://mc06.manuscriptcentral.com/genome-pubs Genome Page 4 of 29 58 number of chromosomes) and ploidy variation can both introduce barriers to gene flow and thus 59 promote diversification of cytologically differentiated populations and contribute to speciation (Coyne 60 and Orr 2004; Levin 1975; Levin 2002). Finally, although aneuploidy is usually a transient condition – 61 because it changes the genetic balance within a genome –, presence of extra chromosomes like B 62 chromosomes has been shown to be associated with the expression of specific functional plants traits 63 of evolutionary importance like asexual reproduction via seeds (Sharbel et al. 2004). 64 Variation in genome size and/or chromosome number becomes taxonomically significant, if 65 associated with some degree of morphological (or genetic) and ecological differentiation (Murray 66 2005). Genome size can both help to discover taxonomic heterogeneity and be a first clue to 67 understand the mechanisms of associated cytological barriers to gene flow. For instance two 68 subspecies of the New Zealand grass Lachnagrostis littoralis (Hack.) Edgar (both with 2n = 8x = 56 69 chromosomes) have been recognized basedDraft on a 23 % difference in genome size (Murray et al. 2005), 70 a variation which clearly coincided with morphological and ecological differences (Edgar 1995). 71 Different dysploid chromosome numbers can serve as diagnostic characters in species which otherwise 72 only show cryptic morphological divergence (e.g. the species pair Pulmonaria obscura Dumort. – P. 73 officinalis L. from the Boraginaceae: Dobeš and Vitek 2000; Sauer 1975). Finally, the importance of 74 difference in ploidy per se (i.e. autopolyploidy) only relatively recently has been fully acknowledged. 75 Several examples demonstrate that the diploid parents and their autopolyploid descendants might 76 qualify as species of their own right since they possess distinct geographic ranges (e.g. Cosendai et al. 77 2011; Soltis 1984), can be distinguished morphologically (Chansler et al. 2016; Hodálová et al. 2007; 78 Marhold 1999), and are largely reproductively isolated via cytological and other barriers (Hardy et al. 79 2001; Zohary and Nur 1959). 80 In the following, we asked if morphological and molecular differentiation in the African 81 agroforestry tree Parkia biglobosa is paralleled by divergence in relative nuclear genome size (RGS), 82 i.e. if RGS could be used as a predictor of taxonomic heterogeneity. We (1) estimated RGS using flow 83 cytometry for 15 populations from throughout most of the distribution range of the species and (2) 84 correlated estimates to the geographic origin of populations (distances among populations) and 4 https://mc06.manuscriptcentral.com/genome-pubs Page 5 of 29 Genome 85 affiliation to major genetic groups as identified by Lompo et al. (2018) and to the leaf morphology of 86 individuals, the latter analysed within the present study. We (3) further aimed to optimize the protocol 87 for preparing root tips for counting chromosomes in mitotic divisional plates and to provide new 88 chromosome counts. 89 Materials and Methods 90 Study system 91 Parkia biglobosa (Jacq.) R. Br. ex G. Don (Fabaceae, subfamily Caesalpinioideae, inclusively 92 Mimosoideae: Stevens 2001), the African locust bean or in French néré, is one of the most important 93 indigenous agroforestry trees of Western and Central Africa (Ouedraogo 1995). Although in the 94 majority of the Caesalpinioideae genera karyotypes evolved without change of the base chromosome 95 number x = 13 characterizing the subfamily (Santos et al. 2012), three different chromosome numbers 96 have been reported for P. biglobosa whichDraft appear to be based on analyses of five accessions or reports 97 (2n = 22, 24: Uyoh et al. 2011, 2n = 24: Mangenot and Mangenot 1957, 2n = 26: Miege 1960a). 98 Additionally, spread citations either refer to these counts
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