{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T02:22:34Z","timestamp":1771554154388,"version":"3.50.1"},"reference-count":154,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2019,1,8]],"date-time":"2019-01-08T00:00:00Z","timestamp":1546905600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"HarvestPlus; Rural Development Administration, Republic of Korea; Research University Grant,Universiti Kebangsaan Malaysia","award":["HarvestPlus-5302; Plant Molecular Breeding Center, No. PJ PJ01319603;DCP-2017-004-2"],"award-info":[{"award-number":["HarvestPlus-5302; Plant Molecular Breeding Center, No. PJ PJ01319603;DCP-2017-004-2"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Colored rice is rich in nutrition and also a good source of valuable genes\/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p &lt; 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.<\/jats:p>","DOI":"10.3390\/genes10010030","type":"journal-article","created":{"date-parts":[[2019,1,9]],"date-time":"2019-01-09T03:06:06Z","timestamp":1547003166000},"page":"30","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice"],"prefix":"10.3390","volume":"10","author":[{"given":"Gwen Iris","family":"Descalsota-Empleo","sequence":"first","affiliation":[{"name":"International Rice Research Institute (IRRI), Laguna 4031, Philippines"},{"name":"University of the Southern Mindanao, Kabacan, Cotabato 9407, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abd Aziz Shamsudin","family":"Noraziyah","sequence":"additional","affiliation":[{"name":"Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian Paul","family":"Navea","sequence":"additional","affiliation":[{"name":"International Rice Research Institute (IRRI), Laguna 4031, Philippines"},{"name":"Nousbo Corp. #4-107, 89 Seohoro, Gwonsun, Suwon 16614, Gyeonggi, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chongtae","family":"Chung","sequence":"additional","affiliation":[{"name":"Chungcheongnam-do Agricultural Research and Extension Services, 167, Chusa-ro, Shinam-myeon, Yesan-gun 32418, Chungcheongnam-do, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9042-0612","authenticated-orcid":false,"given":"Maria Stefanie","family":"Dwiyanti","sequence":"additional","affiliation":[{"name":"International Rice Research Institute (IRRI), Laguna 4031, Philippines"},{"name":"Applied Plant Genome Laboratory, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reuben Jacob Dicen","family":"Labios","sequence":"additional","affiliation":[{"name":"International Rice Research Institute (IRRI), Laguna 4031, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0530-7020","authenticated-orcid":false,"given":"Asmuni Mohd","family":"Ikmal","sequence":"additional","affiliation":[{"name":"Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7581-5501","authenticated-orcid":false,"given":"Venice Margarette","family":"Juanillas","sequence":"additional","affiliation":[{"name":"International Rice Research Institute (IRRI), Laguna 4031, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mary Ann","family":"Inabangan-Asilo","sequence":"additional","affiliation":[{"name":"International Rice Research Institute (IRRI), Laguna 4031, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amery","family":"Amparado","sequence":"additional","affiliation":[{"name":"International Rice Research Institute (IRRI), Laguna 4031, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8129-7226","authenticated-orcid":false,"given":"Russell","family":"Reinke","sequence":"additional","affiliation":[{"name":"International Rice Research Institute (IRRI), Laguna 4031, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Casiana M. Vera","family":"Cruz","sequence":"additional","affiliation":[{"name":"International Rice Research Institute (IRRI), Laguna 4031, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3932-8639","authenticated-orcid":false,"given":"Joong Hyoun","family":"Chin","sequence":"additional","affiliation":[{"name":"Department of Integrative Bio-Industrial Engineering, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B.P. Mallikarjuna","family":"Swamy","sequence":"additional","affiliation":[{"name":"International Rice Research Institute (IRRI), Laguna 4031, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,1,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Awika, J.M. (2011). 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