Cargando…
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...
Autores principales: | , , , , , , , , , , |
---|---|
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 |
_version_ | 1782434318940897280 |
---|---|
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. |
format | Online Article Text |
id | pubmed-4883996 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Springer New York |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT kimbackki definingthegenomestructureoftongilriceanimportantcultivarinthekoreangreenrevolution AT kimdonggwan definingthegenomestructureoftongilriceanimportantcultivarinthekoreangreenrevolution AT leegileung definingthegenomestructureoftongilriceanimportantcultivarinthekoreangreenrevolution AT seojeonghwan definingthegenomestructureoftongilriceanimportantcultivarinthekoreangreenrevolution AT choiikyoung definingthegenomestructureoftongilriceanimportantcultivarinthekoreangreenrevolution AT choibeomsoon definingthegenomestructureoftongilriceanimportantcultivarinthekoreangreenrevolution AT yangtaejin definingthegenomestructureoftongilriceanimportantcultivarinthekoreangreenrevolution AT kimkwangsoo definingthegenomestructureoftongilriceanimportantcultivarinthekoreangreenrevolution AT leejoohyun definingthegenomestructureoftongilriceanimportantcultivarinthekoreangreenrevolution AT chinjoonghyoun definingthegenomestructureoftongilriceanimportantcultivarinthekoreangreenrevolution AT kohheejong definingthegenomestructureoftongilriceanimportantcultivarinthekoreangreenrevolution |