Mining and validation of novel simple sequence repeat (SSR) markers derived from coconut (Cocos nucifera L.) genome assembly.

Autor: Caro RES; Institute of Plant Breeding (IPB), College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Los Baños, Laguna, Philippines.; Philippine Genome Center - Program For Agriculture, Livestock, Fisheries and Forestry, University of the Philippines Los Baños, College, Los Baños, 4031, Laguna, Philippines., Cagayan J; Institute of Plant Breeding (IPB), College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Los Baños, Laguna, Philippines.; Philippine Genome Center - Program For Agriculture, Livestock, Fisheries and Forestry, University of the Philippines Los Baños, College, Los Baños, 4031, Laguna, Philippines., Gardoce RR; Institute of Plant Breeding (IPB), College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Los Baños, Laguna, Philippines., Manohar ANC; Institute of Plant Breeding (IPB), College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Los Baños, Laguna, Philippines. acmanohar@up.edu.ph., Canama-Salinas AO; Institute of Plant Breeding (IPB), College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Los Baños, Laguna, Philippines., Rivera RL; Philippine Coconut Authority - Zamboanga Research Center, San Ramon, 7000, Zamboanga City, Philippines., Lantican DV; Institute of Plant Breeding (IPB), College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Los Baños, Laguna, Philippines., Galvez HF; Institute of Plant Breeding (IPB), College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Los Baños, Laguna, Philippines.; Philippine Genome Center - Program For Agriculture, Livestock, Fisheries and Forestry, University of the Philippines Los Baños, College, Los Baños, 4031, Laguna, Philippines., Reaño CE; Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Los Baños, Laguna, Philippines.
Jazyk: angličtina
Zdroj: Journal, genetic engineering & biotechnology [J Genet Eng Biotechnol] 2022 May 16; Vol. 20 (1), pp. 71. Date of Electronic Publication: 2022 May 16.
DOI: 10.1186/s43141-022-00354-z
Abstrakt: Background: In the past, simple sequence repeat (SSR) marker development in coconut is achieved through microsatellite probing in bacterial artificial chromosome (BAC) clones or using previously developed SSR markers from closely related genomes. These coconut SSRs are publicly available in published literatures and online databases; however, the number is quite limited. Here, we used a locally established, coconut genome-wide SSR prediction bioinformatics pipeline to generate a vast amount of coconut SSR markers.
Results: A total of 7139 novel SSR markers were derived from the genome assembly of coconut 'Catigan Green Dwarf' (CATD). A subset of the markers, amounting to 131, were selected for synthesis based on motif filtering, contig distribution, product size exclusion, and success of in silico PCR in the CATD genome assembly. The OligoAnalyzer tool was also employed using the following desired parameters: %GC, 40-60%; minimum ΔG value for hairpin loop, -0.3 kcal/mol; minimum ΔG value for self-dimer, -0.9 kcal/mol; and minimum ΔG value for heterodimer, -0.9 kcal/mol. We have successfully synthesized, optimized, and amplified 131 novel SSR markers in coconut using 'Catigan Green Dwarf' (CATD), 'Laguna Tall' (LAGT), 'West African Tall' (WAT), and SYNVAR (LAGT × WAT) genotypes. Of the 131 SSR markers, 113 were polymorphic among the analyzed coconut genotypes.
Conclusion: The development of novel SSR markers for coconut will serve as a valuable resource for mapping of quantitative trait loci (QTLs), assessment of genetic diversity and population structure, hybridity testing, and other marker-assisted plant breeding applications.
(© 2022. The Author(s).)
Databáze: MEDLINE
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