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Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"

BACKGROUND: Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties. Tongil contributed to the self-sufficiency of staple food production in Korea during a period known as the `Korean Green Revolution'. We...

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Autores principales: Kim, Backki, Kim, Dong-Gwan, Lee, Gileung, Seo, Jeonghwan, Choi, Ik-Young, Choi, Beom-Soon, Yang, Tae-Jin, Kim, Kwang Soo, Lee, Joohyun, Chin, Joong Hyoun, Koh, Hee-Jong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer New York 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883996/
https://www.ncbi.nlm.nih.gov/pubmed/26224553
http://dx.doi.org/10.1186/s12284-014-0022-5
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author Kim, Backki
Kim, Dong-Gwan
Lee, Gileung
Seo, Jeonghwan
Choi, Ik-Young
Choi, Beom-Soon
Yang, Tae-Jin
Kim, Kwang Soo
Lee, Joohyun
Chin, Joong Hyoun
Koh, Hee-Jong
author_facet Kim, Backki
Kim, Dong-Gwan
Lee, Gileung
Seo, Jeonghwan
Choi, Ik-Young
Choi, Beom-Soon
Yang, Tae-Jin
Kim, Kwang Soo
Lee, Joohyun
Chin, Joong Hyoun
Koh, Hee-Jong
author_sort Kim, Backki
collection PubMed
description BACKGROUND: Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties. Tongil contributed to the self-sufficiency of staple food production in Korea during a period known as the `Korean Green Revolution'. We analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties. RESULTS: A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated for Tongil rice. Three parental accessions of Tongil rice, two indica types and one japonica type, were also sequenced at approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare varieties. The average SNP frequency of Tongil was 5.77 per kb. Genome composition was determined based on SNP data by comparing Tongil with three parental genome sequences using the sliding window approach. Analyses revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent. Copy numbers of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, and some yield-related QTLs or gene locations were also comparatively analyzed between Tongil and parental varieties using sequence-based tools. Each genetic factor was transferred from the parents into Tongil rice in amounts that were in proportion to the whole genome composition. CONCLUSIONS: Tongil was derived from a three-way cross among two indica and one japonica varieties. Defining the genome structure of Tongil rice demonstrates that the Tongil genome is derived primarily from the indica genome with a small proportion of japonica genome introgression. Comparative gene distribution, SSR, GO, and yield-related gene analysis support the finding that the Tongil genome is primarily made up of the indica genome. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12284-014-0022-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-48839962016-06-21 Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution" Kim, Backki Kim, Dong-Gwan Lee, Gileung Seo, Jeonghwan Choi, Ik-Young Choi, Beom-Soon Yang, Tae-Jin Kim, Kwang Soo Lee, Joohyun Chin, Joong Hyoun Koh, Hee-Jong Rice (N Y) Research BACKGROUND: Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties. Tongil contributed to the self-sufficiency of staple food production in Korea during a period known as the `Korean Green Revolution'. We analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties. RESULTS: A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated for Tongil rice. Three parental accessions of Tongil rice, two indica types and one japonica type, were also sequenced at approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare varieties. The average SNP frequency of Tongil was 5.77 per kb. Genome composition was determined based on SNP data by comparing Tongil with three parental genome sequences using the sliding window approach. Analyses revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent. Copy numbers of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, and some yield-related QTLs or gene locations were also comparatively analyzed between Tongil and parental varieties using sequence-based tools. Each genetic factor was transferred from the parents into Tongil rice in amounts that were in proportion to the whole genome composition. CONCLUSIONS: Tongil was derived from a three-way cross among two indica and one japonica varieties. Defining the genome structure of Tongil rice demonstrates that the Tongil genome is derived primarily from the indica genome with a small proportion of japonica genome introgression. Comparative gene distribution, SSR, GO, and yield-related gene analysis support the finding that the Tongil genome is primarily made up of the indica genome. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12284-014-0022-5) contains supplementary material, which is available to authorized users. Springer New York 2014-09-14 /pmc/articles/PMC4883996/ /pubmed/26224553 http://dx.doi.org/10.1186/s12284-014-0022-5 Text en © Kim et al.; licensee Springer. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
spellingShingle Research
Kim, Backki
Kim, Dong-Gwan
Lee, Gileung
Seo, Jeonghwan
Choi, Ik-Young
Choi, Beom-Soon
Yang, Tae-Jin
Kim, Kwang Soo
Lee, Joohyun
Chin, Joong Hyoun
Koh, Hee-Jong
Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
title Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
title_full Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
title_fullStr Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
title_full_unstemmed Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
title_short Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
title_sort defining the genome structure of `tongil' rice, an important cultivar in the korean "green revolution"
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883996/
https://www.ncbi.nlm.nih.gov/pubmed/26224553
http://dx.doi.org/10.1186/s12284-014-0022-5
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