Micropropagation of Jatropha curcas superior genotypes and evaluation of clonal fidelity by target region amplification polymorphism (TRAP) molecular marker and flow cytometry

Pelargonium was a priority genera collected by the Ornamental Plant Germplasm Center (OPGC) until a recent reorganization. To preserve genetic diversity for future breeders, OPGC collects heirloom cultivars, breeding lines, and wild species. The current Pelargonium collection at OPGC consists primarily of cultivars originating from P. ×hortorum and P. ×domesticum. Target region amplification polymorphism (TRAP) has the advantage of producing a large number of markers through use of sequence information that is already available. Our first goal was to determine the feasibility of TRAP for the analysis of this large collection, so that in the future the most diverse genotypes may be retained. To achieve this goal, we first modified existing DNA extraction techniques to account for the high levels of phenolic compounds present in some Pelargonium species by combining several washes to remove the phenolics with the addition of high levels of antiphenolic compounds. Second, we evaluated the TRAP procedure using the DNA isolated from 46 accessions. For 44 accessions, one or two primer combinations generated enough fragments to discriminate each of the accessions, and similar clades were produced by cluster analysis of the polymorphic fragments amplified by different primer combinations. All the scorable fragments were polymorphic, for one primer combination there were 148 markers from one image and the other produced 160 markers on two images. These results demonstrate that TRAP is an effective method for molecular characterization of ornamental collections.

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Respon Pertumbuhan dan Fisiologi Aksesi Jarak Pagar (Jatropha curcas Linn) dalam Kondisi Cekaman Kekeringan di Pembibitan

Buletin Agrohorti ◽

10.29244/agrob.4.3.298-301 ◽

2016 ◽

Vol 4 (3) ◽

pp. 298

Author(s):

Fajar Utama ◽

. Hariyadi

Keyword(s):

Molecular Marker ◽

Jatropha Curcas

Jatropha (Jatropha curcas Linn) merupakan salah satu bahan baku popular untuk menghasilkan bahan bakar biodiesel. Kendala yang sering terjadi, yaitu lahan yang tersedia untuk menanam Jatropha adalah lahan marjinal sehingga penting untuk mengetahui toleransi aksesi jarak pagar terhadap kekeringan. Penelitian dilakukan di Rumah Kaca, Cikabayan, Dramaga IPB. Pengujian klorofil dilakukan di laboratorium Molecular Marker, Spectrofotometry dan UV-Vis, Departemen Agronomi dan Hortikultura, Institut Pertanian Bogor. Penelitian dimulai bulan Juli 2011 dan berakhir Maret 2012. Rancangan yang digunakan adalah Rancangan Acak Kelompok (RAK) faktorial dua faktor, yaitu aksesi dan uji cekaman dengan ulangan tiga kali. Faktor pertama yang diamati adalah toleransi terhadap kekeringan yang dilakukan pada tiga taraf, yaitu 30%, 55%, dan 80% kadar air tanah kapasitas lapang. Faktor kedua yang diamati adalah 10 aksesi jathropa yang telah dievaluasi, diantaranya IP-3M, Jatim 013, Jatim 045, NTT 065, NTT 080, NTB 019, NTB 047, NTB 116, Sulawesi 72 dan Sulawesi 117. Berdasarkan uji klorofil a dan b yang telah dilakukan, aksesi Jatim 045 menunjukkan perlakuan dengan hasil terbaik (toleransi tertinggi terhadap kekeringan), sedangkan dari uji skor toleransi tertinggi terhadap kekeringan antara 35% dan 80% kapasitas lapang ditunjukkan oleh NTT 065 aksesi dan toleransi tertinggi terhadap kekeringan di antara 55% dan 80% kadar air tanah ditunjukkan oleh aksesi Jatim 045 dan NTB 047.

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Improved reliability in production of maize inbred lines by the combination of the R1-navajo marker with flow cytometry or microsatellite genotyping

Cereal Research Communications ◽

10.1007/s42976-020-00054-9 ◽

2020 ◽

Vol 48 (4) ◽

pp. 423-430

Author(s):

F. Rádi ◽

K. Török ◽

M. Nagymihály ◽

A. Kereszt ◽

D. Dudits

Keyword(s):

Flow Cytometry ◽

Molecular Marker ◽

Early Stage ◽

Doubled Haploids ◽

Inbred Lines ◽

Hybrid Population ◽

Initial Population ◽

Seed Selection ◽

Root Tips ◽

Haploid Inducer

AbstractDoubled haploid (DH) technology is an essential component in producing inbred lines for a competitive maize (Zea mays L.) breeding program. The R1-navajo (R1-nj) gene provides phenotypic marker that insures only variable reliability for seed selection of haploid embryos. Therefore, in the present study we outline a complex protocol for early stage genome size determination that integrates the phenotypic screening with the flow cytometry of nuclei from root tips and with the use of DNA isolated from seedlings for molecular marker-based genotyping. In a representative experiment with three genotypes, only 59% of the color marker pre-selected seeds were confirmed to be haploid by cytometric analysis of nuclei isolated from root tips. As a novel tool we have identified the UMC1152 SSR marker being polymorphic between the haploid inducer line (K405) and the K4390 hybrid as parents to screen seedlings pre-selected with the R1-navajo marker. Using this molecular marker, alleles characteristic for the inducer K405 line could not be detected in 83% of seedlings previously selected as haploid candidate. Seedlings identified as haploids were exposed to 0.06% colchicine solution for rediploidization. This procedure resulted in doubled haploids with 3% frequency relative to the initial population as it was quantified by the number of mature maize plants with fertile tassel. The described complex approach can support safer identification of haploids at early seedling stage in a hybrid population derived from crossing with a haploid inducer line.

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Target Region Amplification Polymorphism (TRAP) for Assessing Genetic Diversity and Relationships Among Cultivated Populations of Dendrobium officinale

Journal of Biobased Materials and Bioenergy ◽

10.1166/jbmb.2020.1999 ◽

2020 ◽

Vol 14 (5) ◽

pp. 624-631

Author(s):

Bingzhong Ding ◽

Benhou Zhang ◽

Chao Li ◽

Qingyun Xue ◽

Wei Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Dendrobium Officinale ◽

Target Region ◽

Target Region Amplification Polymorphism ◽

Rare And Endangered Species ◽

Upgma Dendrogram ◽

Rare And Endangered ◽

Cultivated Populations ◽

High Level

Dendrobium officinale (Orchidacesae) is one of the rare and endangered species of herbs in China. Therefore, it will be beneficial to investigate the genetic diversity and relationships of cultivated populations of D. officinale for quality improvement. In this study, eight target region amplification polymorphism (TRAP) primer combinations were selected from fifty-four combinations, which were designed based on the related genes of the polysaccharides and alkaloids. A total of 148 fragments were scored in nine cultivated populations of D. officinale, including 130 (87.84%) polymorphic fragments. The analysis of genetic diversity revealed high level of genetic diversity in cultivated populations of D. officinale (H = 0.4125, I = 0.5985). Based on analysis of genetic structure, there was a moderate variation (Gst = 0.4706) and lower gene flow (Nm = 0.5625) among the cultivated populations due to some isolated measures, and domestication of excellent cultivars. Moreover, UPGMA dendrogram and Principal Coordinate Analysis (PCoA) indicated that nine cultivated populations were divided into four major groups. The results suggested that genetic relationships were associated with geographical germplasm sources instead of cultivation locations. Therefore, TRAP markers can be effectively employed to analyze genetic diversity and relationships among cultivated populations of D. officinale.

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