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

Jeonghwan Seo,Hee-Jong Koh,Yoon Kyung Lee,Joong Hyoun Chin,Na-Hyun Shin,So-Myeong Lee,Jae-Hyuk Han,Backki Kim

doi:10.3390/genes11050562

Jeonghwan Seo, Hee-Jong Koh + Show 6 more

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https://doi.org/10.3390/genes11050562

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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. 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.

Highlights

There are two subspecies in cultivated rice (Oryza sativa), indica and japonica
Indica rice is known to be adaptable to tropical regions, while japonica rice is grown in temperate regions
To analyze the genomic composition of the high-yielding varieties (HYVs) derived from indica–japonica crosses, the whole genomes of HYVs and four varieties were sequenced on the Illumina platform

Summary

Introduction

There are two subspecies in cultivated rice (Oryza sativa), indica and japonica. Indica rice is known to be adaptable to tropical regions, while japonica rice is grown in temperate regions. Japonica varieties are known to have relatively low yield potentials, as compared to indica varieties. To improve the yield potential of japonica rice, inter-subspecific crosses between indica and japonica have been conducted by conventional rice breeders [2]. As a result of these efforts, several high-yielding varieties (HYVs) have been developed from indica-japonica crosses. One of the greatest historical successes of indica–japonica crosses was the development of Tongil, an HYV, in Korea. Tongil showed a 30% higher yield than those of the conventional japonica varieties. By growing Tongil rice, self-sufficiency in staple food in Korea was possible in 1977 [3]. There were important trade-offs in growing Tongil, such as cold intolerance, Genes 2020, 11, 562; doi:10.3390/genes11050562 www.mdpi.com/journal/genes

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