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Development and Characterization of SSR Markers for Trichloris Crinita Using Sequence Data from Related Grass Species

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Development and Characterization of SSR Markers for Trichloris Crinita Using Sequence Data from Related Grass Species SSRRev. FCAmarkers UNCUYO for. Trichloris2018. 50(1): crinita 1-16. ISSN impreso 0370-4661. ISSN (en línea) 1853-8665. Development and characterization of SSR markers for Trichloris crinita using sequence data from related grass species Desarrollo y caracterización de marcadores moleculares SSR para Trichloris crinita usando secuencias de gramíneas filogenéticamente cercanas Perla Carolina Kozub 1, Karina Barboza 2, Juan Bruno Cavagnaro 1, Pablo Federico Cavagnaro 2, 3 Originales: Recepción: 04/12/2017 - Aceptación: 07/05/2018 Abstract Trichloris crinita is among the most important native forage grasses in arid regions of America. Despite its importance, molecular resources and sequence data are extremely scarce in this species. In the present study, SSR markers were developed using available DNA sequences from grass taxa phylogenetically-related to Trichloris (Eleusine coracana, Cynodon dactylon and ‘Cynodon dactylon x Cynodon transvaalensis’). Marker transferability was evaluated in a panel of eight T. crinita of expected size in T. crinita, whereas transferability to other grass speciesaccessions ranged and from five 12closely-related (in Chloris castilloniana species. Of )the to 28105 SSRs SSR (in primer Eleusine pairs coracana evaluated,). Six 16 of theamplified 16 SSR products markers successfully transferred to T. crinita (37.5%) were polymorphic, and were further used to assess genetic diversity in eight T. crinita accessions. The analysis revealed a total of 23 SSR alleles (3.83 alleles/locus), allowing the discrimination of all T. crinita accessions, (and range) values for observed (Ho) and expected heterozygosity (He) were 0.53 (0.0-1.0)with pair-wise and 0.63 genetic (0.48-0.79), similarities respectively. ranging from 0.35 to 0.81 (Jaccard coefficient). Mean Keywords Chloridoideae • forage grass • genetic diversity • marker transferability • microsatellites 1 Universidad Nacional de Cuyo (UNCuyo). Facultad de Ciencias Agrarias (FCA). Instituto de Biología Agrícola de Mendoza (IBAM). Consejo Nacional de de Coria. Mendoza M5528AHB. Argentina. Investigaciones Científicas y Técnicas (CONICET). Almirante Brown 500. Chacras 2 SanConsejo Carlos. Nacional Mendoza de Investigaciones5567. Argentina. Científicas [email protected] y Técnicas (CONICET). Instituto 3 UniversidadNacional de NacionalTecnología de AgropecuariaCuyo. Facultad (INTA)de Ciencias E.E.A. Agrarias. La Consulta. Instituto Ex rutade Horticultura. 40 Km 96. Tomo 50 • N° 1 • 2018 1 P. C. Kozub et al. Resumen Trichloris crinita es una importante gramínea forrajera, nativa de regiones áridas del continente americano. A pesar de su importancia, no existen herramientas moleculares ni marcadores moleculares SSR (“simple sequence repeats”) a partir de secuencias nucleo- secuencias nucleotídicas disponibles para esta especie.Trichloris En este (Eleusine estudio, coracana se desarrollaron, Cynodon dactylon y ‘Cynodon dactylon x Cynodon transvaalensis’) y se evaluó su transferibilidad entídicas ocho de accesiones especies filogenéticamentede T. crinita y cinco cercanas especies a de gramíneas cercanamente emparen- esperado en T. crinita, mientras que la transferibilidad a otras especies varió entre 12 (entadas. Chloris De los castilloniana 105 pares de) y cebadores28 SSRs (en evaluados, Eleusine coracana16 amplificaron). De los productos 16 SSRs transferibles del tamaño a T. crinita, seis . - tieron diferenciarfueron todas polimórficos las accesiones y se de utilizaron T. crinita, para analizar el grado de diversidad entregenética pares en ocho de accesiones accesiones de de 0,35esta especiea 0,81 (Jaccard).El análisis Se reveló obtuvieron 23 alelos, valores los cuales medios permi de heterocigosidad observada y esperada de 0,53 y 0,63 respectivamente.con valores de similitud genética Palabras clave Chloridoideae • gramínea forrajera • diversidad genética • transferibilidad • microsatélites Introduction Trichloris crinita (Chloridoideae, phenotypes from natural populations, Poaceae) is one of the most important followed by their characterization based native grass species in arid regions of South on traits of interest, such as biomass America, due to its extensive area of distri- production (5), forage quality (7, 27), and bution (25), good forage quality (7, 27), drought resistance (12). Data from a recent and resistance to drought (13), tram- study (16), demonstrating that T. crinita is a pling and grazing by wild and domestic sexually-propagated autogamous species, animals (4). These characteristics and encourages the practice of conventional its competing aggressiveness among breeding strategies in the species. Along other native grasses (22), have led to with this, the possibility of developing a widespread utilization of T. crinita in molecular markers for assisting selection range grazing and revegetation projects in may accelerate T. crinita breeding goals. arid environments (24). Molecular resources in T. crinita are Despite its importance, advances in very scarce. To date, only two studies genetic research and breeding of T. crinita regarding the use of molecular markers have been limited, mainly due to the in this species have been published scarcity of molecular resources and the fact that the species mode of reproduction was unknown until very recently. The genetic(5, 16). Thediversity first study,in a T. publishedcrinita germplasm in 2006, main approach used to improve T. crinita collectionused AFLP (4), markers whereas for a characterizingmore recent has been the selection of interesting study by Kozub et al. (2017) used simple 2 Revista de la Facultad de Ciencias Agrarias SSR markers for Trichloris crinita sequence repeats (SSR) markers for Objectives inferring about the mode of reproduction of this species. The present work reports 1) To develop SSR markers for on the development and evaluation, at Trichloris crinita using sequence data various levels, of the SSR markers used in from Eleusine and Cynodon species. the latter report. 2) To evaluate marker transferability SSRs are robust and informative across T. crinita-related taxa. PCR-based markers and they are generally 3) To assess SSR polymorphism and genetic diversity in T. crinita accessions. level of polymorphism, reproducibility andfavored codominant over AFLPs dueinheritance to their higher(18). These markers have been successfully Materials and methods used for multiple genetic and breeding purposes in many crop species, including Source of sequence data, microsatellites grapevine (19), carrot (6), alfalfa (12) and search and primer design soybean (3). However, the development All the available genomic of SSR markers generally requires DNA sequences (GSS) of Eleusine coracana sequence data to search and detect SSR (633 sequences; 0.4 Mbp), Cynodon dactylon (404 sequences; 0.2 Mbp) SSR. In the case of T. crinita, using sequence and ‘Cynodon dactylon x Cynodon databasesmotifs, and to design identify primers SSRs is flankingnot feasible the transvaalensis’ (92 sequences; 0.04 Mbp) since very few sequences are available for were downloaded from the NCBI database the species (only 34 T. crinita sequences on April 15, 2016. These species were are available at the NCBI database). selected based on their phylogenetic The use of sequence data from related proximity to T. crinita and the availability taxa for developing SSR markers in a of sequences in the database. species lacking sequence information has been widely used in plants, with program MISA (31). Only perfect micro- variable degrees of success, generally satellites,SSR motifs with awere basic identified motif of 2-6 using nt, andthe increasing success rate with the phylo- a minimum length of 12 nt (for di-, tri-, genetic proximity between SSR donor and tetranucleotides), 15 nt (for pentanu- and target species (15). This approach cleotides), and 18 nt (for hexanucleotides) has been particularly successful in the were considered. Poaceae family, where SSR markers were The position of the detected SSRs in developed for numerous orphan species, the genomic sequence was recorded, and using sequences from economically important cereal crops (34, 35). This designed. These SSR loci were selected strategy may also be effective for becauseprimers theypairs had flanking larger number105 SSRs of repeat were developing SSR markers for T. crinita units, as this feature has been associated using the available sequence data from with higher polymorphism rate (6). phylogenetically related genera, such as Eleusine and Cynodon. Tomo 50 • N° 1 • 2018 3 P. C. Kozub et al. For primer design, the software Primer3 v.4.0.0 (32) was used, using parameters to generate amplicons 2 μl 10 × DNA polymerase buffer, 1.6 μl of 200-500 bp, and primer length of dNTPs (2.5 mM each), 1 μl 5μM of each 22-30 nt with Tm of 55-62°C and GC wereprimer, programmed 0.3 μl Taq aspolymerase follows: initial at 3 dena U/μl- content of 30-50 %. Other parameters turationand 2.5 μl at of 94°C genomic for 30DNA. sec, Thermocyclers followed by used the program default values. 40 cycles of 94°C for 45 sec, appropriate annealing temperature for 30 sec, and 72°C Plant materials Trichloris crinita accessions Agarose (3%) gel electrophoresis used for 1 min; and a final step of 72°C for 4 min. (CynodonEight dactylon, Eleusine coracana, for visualization of the amplicons. A 100 bp Eleusineand five indica, related Chloris grass gayana species, and ladderethidium (Invitrogen) bromide (4 was ul/100 used ml as of size TAE marker. buffer) Chloris castilloniana) from the Germplasm Denaturing
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