Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species.

Autor: Hechanova SL; Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines., Bhattarai K; Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines.; Institute of Crop Science (ICropS), College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, Los Baños, Laguna, Philippines., Simon EV; Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines.; Institute of Crop Science (ICropS), College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, Los Baños, Laguna, Philippines., Clave G; Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines., Karunarathne P; Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines.; Institute of Crop Science (ICropS), College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, Los Baños, Laguna, Philippines., Ahn EK; National Institute of Crop Science, Rural Development Administration (RDA), Suwon, 16429, Republic of Korea., Li CP; Taiwan Agricultural Research Institute (TARI), Council of Agriculture, Taichung City, Taiwan., Lee JS; National Institute of Crop Science, Rural Development Administration (RDA), Suwon, 16429, Republic of Korea., Kohli A; Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines., Hamilton NRS; Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines., Hernandez JE; Institute of Crop Science (ICropS), College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, Los Baños, Laguna, Philippines., Gregorio GB; Institute of Crop Science (ICropS), College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, Los Baños, Laguna, Philippines., Jena KK; Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines.; School of Biotechnology, KIIT Deemed University, Bhubaneswar, Odisha, India., An G; Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea., Kim SR; Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines. s.r.kim@irri.org.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2021 Apr 26; Vol. 11 (1), pp. 8962. Date of Electronic Publication: 2021 Apr 26.
DOI: 10.1038/s41598-021-88533-9
Abstrakt: Wild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a "genetic reservoir" for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.
Databáze: MEDLINE
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