Working Paper Article Version 3 This version is not peer-reviewed

Characterization of the Common japonica-Originated Genomic Regions in the High Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate 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)

A peer-reviewed article of this Preprint also exists.

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.). Genes 2020, 11, 562.

Journal reference: Genes 2020, 11, 562
DOI: 10.3390/genes11050562

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. 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.

Subject Areas

rice; yield; HYV; Tongil; indica; japonica; SNP; molecular breeding

Comments (1)

Comment 1
Received: 12 May 2020
Commenter: Joong Hyoun Chin
Commenter's Conflict of Interests: Author
Comment: Title and the contents revised after getting the comments from the reviewers. 
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