Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies
Multiparental mapping populations hold great potential for dissecting quantitative traits and rapidly identifying genetic determinants. We developed a japonica nested association mapping population, KNU_NAM, comprising 880 lines derived from ten recombinant inbred lines (RILs) families of prominent...
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Elsevier
2024-12-01
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| Series: | Current Plant Biology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2214662824000835 |
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| author | Bhagwat Nawade Sang-Ho Chu Sunhee Kim Chang-Yong Lee Jinsong Bao Yong-Jin Park |
| author_facet | Bhagwat Nawade Sang-Ho Chu Sunhee Kim Chang-Yong Lee Jinsong Bao Yong-Jin Park |
| author_sort | Bhagwat Nawade |
| collection | DOAJ |
| description | Multiparental mapping populations hold great potential for dissecting quantitative traits and rapidly identifying genetic determinants. We developed a japonica nested association mapping population, KNU_NAM, comprising 880 lines derived from ten recombinant inbred lines (RILs) families of prominent varieties and the elite Korean variety Shindongjin. Genetic characterization of KNU_NAM revealed 48,159 polymorphic SNPs, with family counts ranging from 18,787 to 42,578 and an average of 30,019 SNPs per family. Further molecular diversity analysis of KNU_NAM indicated reduced population structure and broad genetic diversity. Genome-wide association studies (GWAS) on five morphological traits identified 47 significant marker-trait associations (MTAs), with a set of 18 MTAs located on chromosome 9. Linkage disequilibrium (LD) block analysis of this region revealed 15 haplotypes and identified five key genes associated with panicle architecture: OsDEP1, OsEATB, OsLGD1, and OsSPL18. Additionally, two non-synonymous MTAs on chromosome 7 were located on the exon of OsPRR37/Ghd7.1, a gene associated with plant height, heading date, and grain number per panicle. Further phenotypic performance analysis of haplotypes from these hotspot regions revealed significant differences in the targeted traits. The study validates the potential of KNU_NAM and GWAS for high-resolution genetic mapping in rice breeding programs, highlighting the utility of these populations for enhancing genetic diversity and improving trait selection in rice. |
| format | Article |
| id | doaj-art-d7f46c5c4ff143d1a1b85a7c788f8bde |
| institution | DOAJ |
| issn | 2214-6628 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
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| series | Current Plant Biology |
| spelling | doaj-art-d7f46c5c4ff143d1a1b85a7c788f8bde2025-08-20T02:50:19ZengElsevierCurrent Plant Biology2214-66282024-12-014010040110.1016/j.cpb.2024.100401Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studiesBhagwat Nawade0Sang-Ho Chu1Sunhee Kim2Chang-Yong Lee3Jinsong Bao4Yong-Jin Park5Department of Plant Resources, Kongju National University, Yesan 32439, Republic of KoreaDepartment of Plant Resources, Kongju National University, Yesan 32439, Republic of KoreaDepartment of Industrial Engineering, Kongju National University, Cheonan 31080, Republic of KoreaDepartment of Industrial Engineering, Kongju National University, Cheonan 31080, Republic of KoreaInstitute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; Corresponding authors.Department of Plant Resources, Kongju National University, Yesan 32439, Republic of Korea; Corresponding authors.Multiparental mapping populations hold great potential for dissecting quantitative traits and rapidly identifying genetic determinants. We developed a japonica nested association mapping population, KNU_NAM, comprising 880 lines derived from ten recombinant inbred lines (RILs) families of prominent varieties and the elite Korean variety Shindongjin. Genetic characterization of KNU_NAM revealed 48,159 polymorphic SNPs, with family counts ranging from 18,787 to 42,578 and an average of 30,019 SNPs per family. Further molecular diversity analysis of KNU_NAM indicated reduced population structure and broad genetic diversity. Genome-wide association studies (GWAS) on five morphological traits identified 47 significant marker-trait associations (MTAs), with a set of 18 MTAs located on chromosome 9. Linkage disequilibrium (LD) block analysis of this region revealed 15 haplotypes and identified five key genes associated with panicle architecture: OsDEP1, OsEATB, OsLGD1, and OsSPL18. Additionally, two non-synonymous MTAs on chromosome 7 were located on the exon of OsPRR37/Ghd7.1, a gene associated with plant height, heading date, and grain number per panicle. Further phenotypic performance analysis of haplotypes from these hotspot regions revealed significant differences in the targeted traits. The study validates the potential of KNU_NAM and GWAS for high-resolution genetic mapping in rice breeding programs, highlighting the utility of these populations for enhancing genetic diversity and improving trait selection in rice.http://www.sciencedirect.com/science/article/pii/S2214662824000835Japonica riceBreedingNested-association mappingPanicle lengthGWASDiversity |
| spellingShingle | Bhagwat Nawade Sang-Ho Chu Sunhee Kim Chang-Yong Lee Jinsong Bao Yong-Jin Park Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies Current Plant Biology Japonica rice Breeding Nested-association mapping Panicle length GWAS Diversity |
| title | Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies |
| title_full | Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies |
| title_fullStr | Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies |
| title_full_unstemmed | Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies |
| title_short | Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies |
| title_sort | nested association mapping population in japonica rice development characterization and application in genome wide association studies |
| topic | Japonica rice Breeding Nested-association mapping Panicle length GWAS Diversity |
| url | http://www.sciencedirect.com/science/article/pii/S2214662824000835 |
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