GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North Korea
Heading date (Hd) is one of the main factors determining rice production and regional adaptation. To identify the genetic factors involved in the wide regional adaptability of rice, we conducted a genome-wide association study (GWAS) with 190 North Korean rice accessions selected for non-precocious...
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.1036747/full |
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| author | Chuluuntsetseg Jadamba Richie L. Vea Jung-Hoon Ryu Nam-Chon Paek Su Jang Joong Hyoun Chin Soo-Cheul Yoo Soo-Cheul Yoo |
| author_facet | Chuluuntsetseg Jadamba Richie L. Vea Jung-Hoon Ryu Nam-Chon Paek Su Jang Joong Hyoun Chin Soo-Cheul Yoo Soo-Cheul Yoo |
| author_sort | Chuluuntsetseg Jadamba |
| collection | DOAJ |
| description | Heading date (Hd) is one of the main factors determining rice production and regional adaptation. To identify the genetic factors involved in the wide regional adaptability of rice, we conducted a genome-wide association study (GWAS) with 190 North Korean rice accessions selected for non-precocious flowering in the Philippines, a low-latitude region. Using both linear mixed models (LMM) and fixed and random model circulating probability unification (FarmCPU), we identified five significant loci for Hd in trials in 2018 and 2019. Among the five lead single nucleotide polymorphisms (SNPs), three were located adjacent to the known Hd genes, Heading date 3a (Hd3a), Heading date 5 (Hd5), and GF14-c. In contrast, three SNPs were located in novel loci with minor effects on heading. Further GWAS analysis for photoperiod insensitivity (PS) revealed no significant genes associated with PS, supporting that this North Korean (NK) population is largely photoperiod-insensitive. Haplotyping analysis showed that more than 80% of the NK varieties harbored nonfunctional alleles of major Hd genes investigated, of which a nonfunctional allele of Heading date 1 (Hd1) was observed in 66% of the varieties. Geographical distribution analysis of Hd allele combination types showed that nonfunctional alleles of floral repressor Hd genes enabled rice cultivation in high-latitude regions. In contrast, Hd1 alleles largely contributed to the wide regional adaptation of rice varieties. In conclusion, an allelic combination of Hd genes is critical for rice cultivation across wide areas. |
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| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-10T15:07:03Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-0238122ae1de4e4f9c2f5a96a12fa54a2023-02-14T20:16:25ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-12-011310.3389/fgene.2022.10367471036747GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North KoreaChuluuntsetseg Jadamba0Richie L. Vea1Jung-Hoon Ryu2Nam-Chon Paek3Su Jang4Joong Hyoun Chin5Soo-Cheul Yoo6Soo-Cheul Yoo7Crop Molecular Breeding Laboratory, Department of Plant Life and Environmental Science, Hankyong National University, Anseong, South KoreaBureau of Plant Industry, National Seed Quality Control Services, San Mateo, Isabela PhilippinesCrop Molecular Breeding Laboratory, Department of Plant Life and Environmental Science, Hankyong National University, Anseong, South KoreaDepartment of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South KoreaDepartment of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South KoreaDepartment of Integrative Biological Sciences and Industry, Sejong University, Seoul, South KoreaCrop Molecular Breeding Laboratory, Department of Plant Life and Environmental Science, Hankyong National University, Anseong, South KoreaCarbon-Neutral Resources Research Center, Hankyong National University, Seoul, South KoreaHeading date (Hd) is one of the main factors determining rice production and regional adaptation. To identify the genetic factors involved in the wide regional adaptability of rice, we conducted a genome-wide association study (GWAS) with 190 North Korean rice accessions selected for non-precocious flowering in the Philippines, a low-latitude region. Using both linear mixed models (LMM) and fixed and random model circulating probability unification (FarmCPU), we identified five significant loci for Hd in trials in 2018 and 2019. Among the five lead single nucleotide polymorphisms (SNPs), three were located adjacent to the known Hd genes, Heading date 3a (Hd3a), Heading date 5 (Hd5), and GF14-c. In contrast, three SNPs were located in novel loci with minor effects on heading. Further GWAS analysis for photoperiod insensitivity (PS) revealed no significant genes associated with PS, supporting that this North Korean (NK) population is largely photoperiod-insensitive. Haplotyping analysis showed that more than 80% of the NK varieties harbored nonfunctional alleles of major Hd genes investigated, of which a nonfunctional allele of Heading date 1 (Hd1) was observed in 66% of the varieties. Geographical distribution analysis of Hd allele combination types showed that nonfunctional alleles of floral repressor Hd genes enabled rice cultivation in high-latitude regions. In contrast, Hd1 alleles largely contributed to the wide regional adaptation of rice varieties. In conclusion, an allelic combination of Hd genes is critical for rice cultivation across wide areas.https://www.frontiersin.org/articles/10.3389/fgene.2022.1036747/fullGWASphotoperiod sensitivityheading dateNorth Korean ricehaplotypingregional adaptation |
| spellingShingle | Chuluuntsetseg Jadamba Richie L. Vea Jung-Hoon Ryu Nam-Chon Paek Su Jang Joong Hyoun Chin Soo-Cheul Yoo Soo-Cheul Yoo GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North Korea Frontiers in Genetics GWAS photoperiod sensitivity heading date North Korean rice haplotyping regional adaptation |
| title | GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North Korea |
| title_full | GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North Korea |
| title_fullStr | GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North Korea |
| title_full_unstemmed | GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North Korea |
| title_short | GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North Korea |
| title_sort | gwas analysis to elucidate genetic composition underlying a photoperiod insensitive rice population north korea |
| topic | GWAS photoperiod sensitivity heading date North Korean rice haplotyping regional adaptation |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.1036747/full |
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