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Open AccessArticle

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

1
Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
2
Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Korea
3
Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea
*
Authors to whom correspondence should be addressed.
Genes 2020, 11(5), 562; https://doi.org/10.3390/genes11050562
Received: 23 April 2020 / Revised: 11 May 2020 / Accepted: 14 May 2020 / Published: 18 May 2020
(This article belongs to the Special Issue Recent Advances in Genetics and Breeding of Major Staple Food Crops)
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. View Full-Text
Keywords: rice; yield; HYV; Tongil; indica; japonica; SNP; molecular breeding rice; yield; HYV; Tongil; indica; japonica; SNP; molecular breeding
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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.

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