Development and validation of microsatellite markers for Brachiaria ruziziensisobtained by partial genome assembly of Illumina single-end reads

Silva, Pedro I T; Martins, António A.; Gouvea, Ediene G.; Pessoa-Filho, Marco; Ferreira, Márcio Elias

doi:10.1186/1471-2164-14-17

Cited by 57 publications

(61 citation statements)

References 22 publications

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“…The PIC value in this study is within the range reported by Silva et al [14], Jungmann et al [15], and Vigan et al [16], but was lower than that found by Jungmann et al [17] and Pessoa-Filho et al [18]. Similarly, the average numbers of allele detected per loci (5.45) was in the range reported by Silva et al [14], Jungmann et al [15], and Vigan et al [16], but was about half and one-third of that reported by Jungmann et al [17] and Pessoa-Filho et al [18], respectively. However, these comparisons between studies may not be conclusive due to differences in types and number of germplasms and markers used among studies.…”

Section: Discussionsupporting

confidence: 91%

Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers

et al. 2017

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Brachiaria grass is an emerging forage option for livestock production in Kenya. Kenya lies within the center of diversity for Brachiaria species, thus a high genetic variation in natural populations of Brachiaria is expected. Overgrazing and clearing of natural vegetation for crop production and nonagricultural uses and climate change continue to threaten the natural biodiversity. In this study, we collected 79 Brachiaria ecotypes from different parts of Kenya and examined them for genetic variations and their relatedness with 8 commercial varieties. A total of 120 different alleles were detected by 22 markers in the 79 ecotypes. Markers were highly informative in differentiating ecotypes with average diversity and polymorphic information content of 0.623 and 0.583, respectively. Five subpopulations: International Livestock Research Institute (ILRI), Kitui, Kisii, Alupe, and Kiminini differed in sample size, number of alleles, number of private alleles, diversity index, and percentage polymorphic loci. The contribution of within-the-individual difference to total genetic variation of Kenyan ecotype population was 81%, and the fixation index (F ST = 0.021) and number of migrant per generation (Nm = 11.58) showed low genetic differentiation among the populations. The genetic distance was highest between Alupe and Kisii populations (0.510) and the lowest between ILRI and Kiminini populations (0.307). The unweighted neighbor-joining (NJ) tree showed test ecotypes grouped into three major clusters: ILRI ecotypes were present in all clusters; Kisii and Alupe ecotypes and improved varieties grouped in clusters I and II; and ecotypes from Kitui and Kiminini grouped in cluster I. This study confirms higher genetic diversity in Kenyan ecotypes than eight commercial varieties (Basilisk, Humidicola, Llanero, Marandú, MG4, Mulato II, Piatá and Xaraés) that represent three species and one three-way cross-hybrid Mulato II. There is a need for further collection of local ecotypes and their morphological, agronomical, and genetic characterizations to support Brachiaria grass breeding and conservation programs.

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Section: Discussionsupporting

confidence: 91%

Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers

et al. 2017

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“…The frequency, type and distribution of the 4,489 potential SSRs were also analyzed in the present study. Among the 4,489 SSRs, trinucleotide repeat motifs were the most abundant (3,868, 86.2 %) (Table 5), which is similar to the P. maximum transcriptome (86 %) [34] and the Brachiaria ruziziensis genome (85.2 %) [87], followed by dinucleotide (363, 8.09 %), tetranucleotide (173, 3.85 %), pentanucleotide (54, 1.20 %) and hexanucleotide (31, 0.69 %) repeat motifs. The total distribution of SSR motifs was similar to that determined for P. maximum [34], whereas in B. ruziziensis [87], tetranucleotide motifs were more abundant than dinucleotide motifs (Additional file 10).…”

Section: Resultsmentioning

confidence: 99%

Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas

et al. 2016

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Background Urochloa humidicola (Koronivia grass) is a polyploid (6x to 9x) species that is used as forage in the tropics. Facultative apospory apomixis is present in most of the genotypes of this species, although one individual has been described as sexual. Molecular studies have been restricted to molecular marker approaches for genetic diversity estimations and linkage map construction. The objectives of the present study were to describe and compare the leaf transcriptome of two important genotypes that are highly divergent in terms of their phenotypes and reproduction modes: the sexual BH031 and the aposporous apomictic cultivar BRS Tupi.ResultsWe sequenced the leaf transcriptome of Koronivia grass using an Illumina GAIIx system, which produced 13.09 Gb of data that consisted of 163,575,526 paired-end reads between the two libraries. We de novo-assembled 76,196 transcripts with an average length of 1,152 bp and filtered 35,093 non-redundant unigenes. A similarity search against the non-redundant National Center of Biotechnology Information (NCBI) protein database returned 65 % hits. We annotated 24,133 unigenes in the Phytozome database and 14,082 unigenes in the UniProtKB/Swiss-Prot database, assigned 108,334 gene ontology terms to 17,255 unigenes and identified 5,324 unigenes in 327 known metabolic pathways. Comparisons with other grasses via a reciprocal BLAST search revealed a larger number of orthologous genes for the Panicum species. The unigenes were involved in C4 photosynthesis, lignocellulose biosynthesis and flooding stress responses. A search for functional molecular markers revealed 4,489 microsatellites and 560,298 single nucleotide polymorphisms (SNPs). A quantitative real-time PCR analysis validated the RNA-seq expression analysis and allowed for the identification of transcriptomic differences between the two evaluated genotypes. Moreover, 192 unannotated sequences were classified as containing complete open reading frames, suggesting that the new, potentially exclusive genes should be further investigated.ConclusionThe present study represents the first whole-transcriptome sequencing of U. humidicola leaves, providing an important public information source of transcripts and functional molecular markers. The qPCR analysis indicated that the expression of certain transcripts confirmed the differential expression observed in silico, which demonstrated that RNA-seq is useful for identifying differentially expressed and unique genes. These results corroborate the findings from previous studies and suggest a hybrid origin for BH031.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3270-5) contains supplementary material, which is available to authorized users.

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“…Owing to the steady decrease in cost per sequenced nucleotide and increase in throughput data, NGS technologies have become a powerful approach for the high-throughput discovery of genes; they generate a large amount of sequence data for molecular marker identification (Iorizzo et al, 2011;Silva et al, 2013). Recently, de novo transcriptome assembly using Illumina sequences has been successfully developed and widely applied in various important plant species including rice, wheat, and maize (Lu and Lu.…”

Section: Discussionmentioning

confidence: 99%

Identification of novel and useful EST-SSR markers from de novo transcriptome sequence of wheat (Triticum aestivum L.)

2016

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ABSTRACT. Simple sequence repeats (SSRs) are highly informative, polymorphic, and co-dominant Mendelian markers that provide an important genomic resource for genetic research. Recently, the use of large-scale transcriptome sequence has become a reliable and efficient approach for the identification and development of new EST-SSR markers. In this study, 8389 potential SSRs with a minimum of five repetitions for all motifs were identified from 121,210 unigenes. Gene ontology analysis indicated that the unigenes containing SSR loci participate in various biological processes of regulation, growth, development, metabolism, and apoptosis in wheat. As in many other plants, trinucleotide repeats were found to be the most abundant repeat units with a frequency of 62.33%. A subset of 300 EST-SSRs was randomly selected for the applicability of EST-SSRs to be evaluated. Of the 300 primer pairs tested, 177 (59%) yielded unambiguous PCR products among five wheat cultivars. Using the Chinese Spring nullitetrasomic line, 131 of the 177 EST-SSR primer pairs yielded products and 178 loci were found to be located on all the 21 wheat chromosomes. These findings suggest that the novel EST-SSR markers, as a basis for future genetic linkage and gene tagging analysis, are a valuable tool for genetic mapping, marker assisted selection, and comparative genome analysis.

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Development and validation of microsatellite markers for Brachiaria ruziziensisobtained by partial genome assembly of Illumina single-end reads

Cited by 57 publications

References 22 publications

Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers

Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers

Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas

Identification of novel and useful EST-SSR markers from de novo transcriptome sequence of wheat (Triticum aestivum L.)

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