Working PaperArticleVersion 2This version is not peer-reviewed
Characterization of the Common japonica-Originated Genomic Regions in the High Yielding Varieties Developed from Inter-Subspecific Crosses in Rice (Oryza sativa L.)
Version 1
: Received: 23 April 2020 / Approved: 24 April 2020 / Online: 24 April 2020 (07:37:40 CEST)
Version 2
: Received: 30 April 2020 / Approved: 30 April 2020 / Online: 30 April 2020 (03:18:24 CEST)
Version 3
: Received: 11 May 2020 / Approved: 12 May 2020 / Online: 12 May 2020 (05:56:38 CEST)
Seo, J.; Lee, S.-M.; Han, J.-H.; Shin, N.-H.; Lee, Y.K.; Kim, B.; Chin, J.H.; Koh, H.-J. Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.). Genes2020, 11, 562.
Seo, J.; Lee, S.-M.; Han, J.-H.; Shin, N.-H.; Lee, Y.K.; Kim, B.; Chin, J.H.; Koh, H.-J. Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.). Genes 2020, 11, 562.
Seo, J.; Lee, S.-M.; Han, J.-H.; Shin, N.-H.; Lee, Y.K.; Kim, B.; Chin, J.H.; Koh, H.-J. Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.). Genes2020, 11, 562.
Seo, J.; Lee, S.-M.; Han, J.-H.; Shin, N.-H.; Lee, Y.K.; Kim, B.; Chin, J.H.; Koh, H.-J. Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.). Genes 2020, 11, 562.
Abstract
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. 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 the japonica-originated genomic regions on the nine chromosomes, although they were developed from different breeding programs. A panel of 94 varieties was classified into four varietal groups with 39 single nucleotide polymorphism (SNP) markers from 39 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 rice.
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Commenter: Joong Hyoun Chin
Commenter's Conflict of Interests: Author