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Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)

The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The...

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Autores principales: Seo, Jeonghwan, Lee, So-Myeong, Han, Jae-Hyuk, Shin, Na-Hyun, Lee, Yoon Kyung, Kim, Backki, Chin, Joong Hyoun, Koh, Hee-Jong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7290844/
https://www.ncbi.nlm.nih.gov/pubmed/32443496
http://dx.doi.org/10.3390/genes11050562
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author Seo, Jeonghwan
Lee, So-Myeong
Han, Jae-Hyuk
Shin, Na-Hyun
Lee, Yoon Kyung
Kim, Backki
Chin, Joong Hyoun
Koh, Hee-Jong
author_facet Seo, Jeonghwan
Lee, So-Myeong
Han, Jae-Hyuk
Shin, Na-Hyun
Lee, Yoon Kyung
Kim, Backki
Chin, Joong Hyoun
Koh, Hee-Jong
author_sort Seo, Jeonghwan
collection PubMed
description The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.
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spelling pubmed-72908442020-06-19 Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.) Seo, Jeonghwan Lee, So-Myeong Han, Jae-Hyuk Shin, Na-Hyun Lee, Yoon Kyung Kim, Backki Chin, Joong Hyoun Koh, Hee-Jong Genes (Basel) Article The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice. MDPI 2020-05-18 /pmc/articles/PMC7290844/ /pubmed/32443496 http://dx.doi.org/10.3390/genes11050562 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Seo, Jeonghwan
Lee, So-Myeong
Han, Jae-Hyuk
Shin, Na-Hyun
Lee, Yoon Kyung
Kim, Backki
Chin, Joong Hyoun
Koh, Hee-Jong
Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)
title Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)
title_full Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)
title_fullStr Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)
title_full_unstemmed Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)
title_short Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)
title_sort characterization of the common japonica-originated genomic regions in the high-yielding varieties developed from inter-subspecific crosses in temperate rice (oryza sativa l.)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7290844/
https://www.ncbi.nlm.nih.gov/pubmed/32443496
http://dx.doi.org/10.3390/genes11050562
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