{"id":5751,"date":"2026-02-19T21:15:10","date_gmt":"2026-02-19T13:15:10","guid":{"rendered":"https:\/\/transactions.nast.ph\/?p=5751"},"modified":"2026-03-26T15:35:09","modified_gmt":"2026-03-26T07:35:09","slug":"applications-of-molecular-marker-technology-in-the-philippine-rice-breeding","status":"publish","type":"post","link":"https:\/\/transactions.nast.ph\/?p=5751","title":{"rendered":"Applications of Molecular Marker Technology in the Philippine Rice Breeding"},"content":{"rendered":"\n

Edilberto D. Redona, L.R. Hipolito, L.S. Moreno, T.D. Ocampo and Samuel A. Ordonez, Jr.
Plant Breeding and Biotechnology Division
Philippine Rice Research Institute (Phil Rice)<\/p>\n\n\n\n

doi.org\/10.57043\/transnastphl.1999.5751<\/a><\/p>\n\n\n\n

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Abstract<\/strong><\/p>\n\n\n\n

There is an urgent need to increase the genetic yield potential of rice since past yield increases have been negated by unabated population growth and reduction in rice hectarage in many countries including the Philippines. Molecular marker technology promises to speed up and improve the overall efficiency of plant breeding and, hence, the attainment of higher yield potential. This paper describes efforts at PhilRice to use molecular marker-aided approaches for breeding direct-seeded and hybrid rice varieties, considered \u2018new frontier\u2019 varietal types for the next millennium. For hybrid rice breeding, the nuclear genome diversity of 22 cytoplasmic male-sterile (CMS) lines used as female parents for breeding hybrids in the Philippines were assayed at loci amplified by 20 microsatellite or simple-sequence repeat (SSR), 25 RAPD, and 10 amplified fragment length polymorphism (AFLP) primers or primer combinations. A high degree of polymorphism was detected in the CMS lines. Microsatellites and AFLPs appeared to be the most suited for DNA fingerprinting. Cluster analysis based on 222 molecular markers classified the CMS lines into nine groups. The groupings could guide hybrid rice breeders in developing genetically diverse and heterotic rice hybrids.<\/p>\n\n\n\n

To determine the utility of markers for predicting heterosis or hybrid vigor, the relationship of SSR heterozygosity and heterotic potential was studied for eight traits in 48 rice hybrids derived from 5 CMS and 10 male parents. Based on 43 microsatellite loci, the CMS and male parents clustered into 2 and 8 groups, respectively, at 75% level of genetic similarity. Microsatellite heterozygosity (based on all the markers used) and heterotic performance were significantly correlated for the number of tillers per plant and LAI when all F
1\u2019s were used in the analysis. Significant correlation were observed for maturity and number of tillers per plant between SSR polymorphism and heterosis relative to the male parent when only hybrids with positive heterosis for each trait were analyzed. Significant negative correlations were observed between heterozygosity and heterosis for maturity, harvest index, and grain yield, relative to the check varieties. Correlations for other traits were insignificant. The relationship of molecular marker heterozygosity and heterosis, therefore, appears to be complex and could vary with the traits and germplasm studied.<\/p>\n\n\n\n

For breeding direct-seeded rice, 25 quantitative trait loci (QTL) underlying seedling vigor (SV), one most important traits in direct-seeded rice culture, have been mapped through interval and single-point analyses to different rice chromosomes using restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers. To identify high-SV donors in local germplasm, 37 RAPDs flanking SV QTL were used as diagnostic probes to genotype 49 cultivars at 11 SV QTL. High-SV genotypes were identified in addition to known SV genetic donors and cluster analysis discriminated the 49 cultivars into eight major clusters. Newly identified high-SV genotypes such as Aus 257, Vandana, Dular WB, CG-14, CG-17, CG-20 and UG-20, that could possess alternative SV QTL alleles, have been used to develop crosses designed to concentrate favorable SV alleles in new populations that could be subjected to marker-aided selection.<\/p>\n<\/div>\n\n\n\n

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Keywords<\/h5>\n\n\n
breeding<\/a>, <\/span>direct seeding<\/a>, <\/span>hybrid<\/a>, <\/span>Molecular markers<\/a>, <\/span>rice<\/a><\/div><\/div>\n<\/div>\n\n\n\n
<\/object>TNP 1999 (21)_19_Applications of Molecular Marker Technology in the Philippine Rice Breeding<\/a>Download<\/a><\/div>\n","protected":false},"excerpt":{"rendered":"

Edilberto D. Redona, L.R. Hipolito, L.S. Moreno, T.D. Ocampo and Samuel A. Ordonez, Jr.<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[819],"tags":[946,948,947,949,198],"class_list":{"0":"post-5751","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-1999-technical-papers","7":"tag-breeding","8":"tag-direct-seeding","9":"tag-hybrid","10":"tag-molecular-markers","11":"tag-rice","12":"czr-hentry"},"_links":{"self":[{"href":"https:\/\/transactions.nast.ph\/index.php?rest_route=\/wp\/v2\/posts\/5751"}],"collection":[{"href":"https:\/\/transactions.nast.ph\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/transactions.nast.ph\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/transactions.nast.ph\/index.php?rest_route=\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/transactions.nast.ph\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=5751"}],"version-history":[{"count":3,"href":"https:\/\/transactions.nast.ph\/index.php?rest_route=\/wp\/v2\/posts\/5751\/revisions"}],"predecessor-version":[{"id":6072,"href":"https:\/\/transactions.nast.ph\/index.php?rest_route=\/wp\/v2\/posts\/5751\/revisions\/6072"}],"wp:attachment":[{"href":"https:\/\/transactions.nast.ph\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5751"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/transactions.nast.ph\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5751"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/transactions.nast.ph\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5751"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}