Preprint
Article

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

Submitted:

30 April 2020

Posted:

30 April 2020

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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.
Keywords: 
rice; yield; HYV; Tongil; indica; japonica; SNP; molecular breeding
Subject: 
Biology and Life Sciences  -   Agricultural Science and Agronomy
Copyright: This open access article is published under a Creative Commons CC BY 4.0 license, which permit the free download, distribution, and reuse, provided that the author and preprint are cited in any reuse.

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