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GISH-Based Comparative Genomic Analysis in Urochloa P. Beauv

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GISH-Based Comparative Genomic Analysis in Urochloa P. Beauv Molecular Biology Reports (2020) 47:887–896 https://doi.org/10.1007/s11033-019-05179-7 ORIGINAL ARTICLE GISH‑based comparative genomic analysis in Urochloa P. Beauv. Caio T. R. Corrêa1 · Nathalia G. Z. Bonetti1 · Sanzio C. L. Barrios2 · Cacilda B. do Valle2 · Giovana A. Torres1 · Vânia H. Techio1 Received: 10 September 2019 / Accepted: 31 October 2019 / Published online: 16 November 2019 © Springer Nature B.V. 2019 Abstract The genus Urochloa P. Beauv. [syn. Brachiaria (Trin.) Griseb.] comprises species of great economic relevance as forages. The genomic constitution for the allotetraploid species Urochloa brizantha (cv. Marandu) and Urochloa decumbens (cv. Basi- lisk) and the diploid Urochloa ruziziensis was previously proposed as BBB1B1, B1B1B2B2 and B2B2, respectively. Evidence indicates U. ruziziensis as the ancestral donor of genome B2 in U. decumbens allotetraploidy, but the origin of the genomes B and B 1 is still unknown. There are diploid genotypes of U. brizantha and U. decumbens that may be potential ancestors of the tetraploids. The aim of this study was to determine the genomic constitution and relationships between genotypes of U. brizantha (2x and 4x), U. decumbens (2x and 4x) and U. ruziziensis (2x) via genomic in situ hybridization (GISH). Additionally, chromosome number and genome size were verifed for the diploid genotypes. The diploids U. brizantha and U. decumbens presented 2n = 2x = 18 chromosomes and DNA content of 1.79 and 1.44 pg, respectively. The GISH analysis revealed high homology between the diploids U. brizantha and U. decumbens, which suggests relatively short divergence time. The GISH using genomic probes from the diploid accessions on the tetraploid accessions’ chromosomes presented similar patterns, highlighting the genome B1 present in both of the tetraploids. Based on GISH results, the genomic consti- tution was proposed for the diploid genotypes of U. brizantha (B1B1) and U. decumbens (B1′B1′) and both were pointed as donors of genome B1 (or B1′), present in the allotetraploid genotypes. Keywords Brachiaria · Genomic composition · Polyploidy · Cytogenomic analysis Abbreviations H3K9me2 Dimethylation of the lysine residue at 9th GISH Genomic in situ hybridization position on the N-terminal tail of histone 3 RAPD Random amplifcation of polymorphic DNA FISH Fluorescent in situ hybridization CTAB Cetyltrimethylammonium bromide rDNA Ribosomal DNA gDNA Genomic DNA SSC Saline sodium citrate TNT Tris-NaCl-Tween-20 Introduction DAPI 4′,6-Diamidino-2-phenylindole H3K4me2 Dimethylation of the lysine residue at 4th The genus Urochloa P. Beauv. [syn. Brachiaria (Trin.) position on the N-terminal tail of histone 3 Griseb.] comprises approximately 135 species distributed in tropical and subtropical regions, mainly in East Africa, which is considered as their center of origin [1]. Urochloa This study is part of C.T.R. Correa’s thesis and the abstract can species are the most commonly used forages in Brazil, repre- be found in the repository: http://repos itori o.ufa.br/jspui /handl e/1/33642 . senting 85% of the cultivated pastures (99 Mha). The species of greatest economic importance are Urochloa brizantha * Vânia H. Techio (Hoschst. ex A. Rich) R.D. Webster, Urochloa decumbens [email protected] (Stapf) R.D. Webster, Urochloa humidicola (Rendle) Mor- Urochloa ruziziensis 1 Department of Biology/DBI – Plant Cytogenetics rone & Zuloaga and (R. Germ. & C.M. Laboratory, Federal University of Lavras (UFLA), P.O. Evrard) Morrone & Zuloaga [2]. Box 3037, Lavras, Minas Gerais, Brazil Due to the extensive use of Urochloa species in livestock 2 Embrapa Gado de Corte – Campo Grande, Campo Grande, nutrition and their wide adaptation and distribution, new Mato Grosso do Sul, Brazil Vol.:(0123456789)1 3 888 Molecular Biology Reports (2020) 47:887–896 cultivars have been pursued through genetic breeding to points to U. ruziziensis as the ancestral donor of genome overcome actual cultivar limitations [3]. Part of the current B2, whereas the origin of the genomes B and B1 is unknown breeding programs are focused in the production of inter- and eligible candidates would be diploid genotypes of U. specifc hybrids with the species U. brizantha, U. decum- brizantha and U. decumbens. bens and U. ruziziensis [2]. These three species are known Additional GISH analysis including diploid genotypes to form an agamic complex, in which U. brizantha and U. may contribute to validate the genomic constitution pro- decumbens are predominantly apomictic tetraploids and U. posed by Paula et al. [18], as well as to assist in the investi- ruziziensis is a sexual diploid [4]. gation of the ancestral genomes involved in the polyploidi- The phylogenetic relationships between the agamic com- zation process and the genomic relationships between the plex species demonstrate some controversy. Morphological diploid and tetraploid genotypes. Thus, the aims of this analysis have grouped U. brizantha, U. decumbens and U. study were to determine the genomic constitution and the ruziziensis, indicating high similarity between the three chromosome homology/homoeology relationship between species and closer proximity between the frst two [5, 6]. genotypes of U. ruziziensis (2x), U. brizantha (2x and 4x) Molecular phylogenies and dendrograms corroborate with and U. decumbens (2x and 4x), via GISH. the grouping of these three species, but they difer regarding the interrelations within the group. Studies based on RAPD markers [7, 8] and chloroplastid genes [9] agree with the Materials and methods morphological data on the closer proximity between U. bri- zantha and U. decumbens. According to Pessoa-Filho et al. Plant material [9], U. ruziziensis lineage would have diverged from the other two 5.67 mya, followed by a more recent divergence The experiment was conducted with the diploid accessions between the other two, approximately 1.6 mya. In contrast, of U. brizantha [B105 (2n = 2x = 18)] and U. decumbens Triviño et al. [10], in a study of genetic diversity and popu- [D04 (2n = 2x = 18)], from Embrapa Beef Cattle, munici- lation structure based on microsatellites, verifed a closer pality of Campo Grande, Mato Grosso do Sul State, Bra- proximity between U. decumbens and U. ruziziensis, in rela- zil and the commercial cultivars U. ruziziensis [cultivar tion to U. brizantha. It is worth noting that the majority of Kennedy (2n = 2x = 18)], U. brizantha [cultivar Marandu these studies used mostly polyploid genotypes and cultivars, (2n = 4x = 36)] and U. decumbens [cultivar Basilisk with the exception of U. ruziziensis, which is exclusively (2n = 4x = 36)]. diploid and a single diploid genotype of U. decumbens used in Triviño et al. [10] analysis. Slide preparation Similarly, cytogenetic studies tend to assess predomi- nantly polyploid species, considering its prevalence in the Root tips were collected and pretreated with cycloheximide genus (specially tetraploids) and in cultivated pastures [3]. (12.5 mg/l) for 2 h at room temperature. Subsequently, they Chromosome numbers in Urochloa range from 2n = 14 to were washed in distilled water and fxed in ethanol/ace- 2n = 90, and the most frequently observed basic chromosome tic acid (3:1) solution. Cell wall digestion was performed number is x = 9. Regarding the agamic complex species, with an enzyme solution consisting of cellulase Onozuka cytotypes (intraspecifc variation on chromosome number) R10 (0.7%), cellulase Sigma-Aldrich (0.7%), pectolyase were reported for U. brizantha (2n = 18, 36, 45 and 54) and Sigma-Aldrich (1%) and cytohelicase Sigma-Aldrich (1%) U. decumbens (2n = 18 and 36) [11, 12]. for 90 min at 37 °C. Slides were prepared according to the Meiotic studies on tetraploids cultivars of U. brizantha fame-drying technique [21], with adaptations. (cv. Marandu) e U. decumbens (cv. Basilisk) and hybrids revealed several abnormalities typical from allopolyploids, GISH e.g., asynchronic chromosome segregation, intragenomic pairing and presence of multivalents and micronucleus Genomic DNA (gDNA) from U. brizantha (B105), U. [13–17]. More recently, the allotetraploidy was confrmed decumbens (D04) and U. ruziziensis was isolated using via genomic in situ hybridization (GISH) and a proposal CTAB protocol [22]. The genomic probes were labeled by for genomic composition was presented for U. brizantha nick translation with digoxigenine-12-dUTP. The GISH was (BBB1B1), U. decumbens (B1B1B2B2) and U. ruziziensis performed by hybridizing gDNA of the diploid genotypes (B2B2) [18]. The authors have also demonstrated that the reciprocally and on the tetraploid cultivars (Fig. 1). three genomes (B, B 1 and B2) are homoeologous and that Previously selected slides were denatured in 70% for- U. decumbens and U. ruziziensis share one genome, which mamide at 85 °C for 1 min and 25 s, followed by dehydra- highlights the greater proximity between the two species, as tion in alcohol series (70, 90 and 100%) for 5 min each. The proposed in previous studies [10, 11, 19, 20]. This scenario hybridization mixture containing formamide (50%), dextran 1 3 Molecular Biology Reports (2020) 47:887–896 889 Fig. 1 Schematic of GISH prob- ing in Urochloa species. Aes- terisk—genomes determined by Paula et al. [18] sulfate (10%), 2x saline sodium citrate (SSC) bufer (pH 7.0) Results and 50 to 100 ng of probe was denatured at 95 °C for 8 min and applied to the slides. Hybridization process took place The accessions B105 (U. brizantha) and D04 (U. decum- in humid chamber at 37 °C for 24 to 48 h. No blocking DNA bens) were both confrmed with 18 chromosomes and pre- was used. sented nuclear DNA content (2C) of 1.79 and 1.44 pg, Probes were detected using anti-digoxigenin conjugated respectively. with rhodamine after washes in 2x SSC bufer at 42 °C (80.7% GISH+ signals varied in the extension of hybridiza- of estringency) and 1× tris-NaCl-Tween-20 (TNT). The chro- tion region (centromeric/pericentromeric and interstitial mosomes were stained with 4′,6-diamidino-2-phenylindole regions or fully hybridized chromosomes) on chromo- (DAPI)/Vectashied and images were captured by QImaging somes within the same set and between diferent acces- Retiga EXi CCD camera attached to a fuorescence micro- sions (Figs.
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