Small-effect loci that fine-tune heading are responsible for the regional genetic diversity of Hokkaido rice varieties

Md. Imdadul Hoque; Shuntaro Sakaguchi; Masaki Takatori; Hiroshi Shinada; Naoya Yamaguchi; Tsutomu Nishimura; Masafumi Kinoshita; Yuji Kishima; Md. Imdadul Hoque; Shuntaro Sakaguchi; Masaki Takatori; Hiroshi Shinada; Naoya Yamaguchi; Tsutomu Nishimura; Masafumi Kinoshita; Yuji Kishima

doi:10.3934/agrfood.2025026

AIMS Agriculture and Food

2025, Volume 10, Issue 2: 523-542. doi: 10.3934/agrfood.2025026

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Research article

Small-effect loci that fine-tune heading are responsible for the regional genetic diversity of Hokkaido rice varieties

1.
Graduate School of Agriculture, Hokkaido University, Japan
2.
Kitami Agricultural Experimental Station, Hokkaido Research Organization, Japan
3.
Central Agricultural Experimental Station, Hokkaido Research Organization, Japan
4.
Kamikawa Agricultural Experimental Station, Hokkaido Research Organization, Japan

Received: 05 April 2025 Revised: 20 June 2025 Accepted: 25 June 2025 Published: 10 July 2025

Rice (Oryza sativa) is a domesticated crop widely grown from tropical to temperate regions. The complement of polymorphisms in locally adapted varieties (LAVs) of rice helps them acclimate to colder regions such as Hokkaido, a northern, high-latitude region of Japan. Although large-effect genetic variants have been characterized, small phenotypic effects arising from the limited genetic diversity present in LAVs have not been fully elucidated. We used 79 Hokkaido LAVs to investigate days to heading (DTH) over multiple years. Variance in the DTH caused by environmental variation ranged from 2.5 to 11.0 days. As the genome sequences of 70 Hokkaido LAVs are available, we looked for variation in four heading genes: Ghd7, OsPRR37, Hd1, and DTH8. Hokkaido LAVs mainly harbored nonfunctional alleles for Ghd7 and OsPRR37, thus suggesting that these alleles influence DTH by hastening heading. Hd1 and DTH8 had relatively small effects on the DTH of the Hokkaido varieties, which were comparable to the effects of the environment. Our previous studies that used recombinant inbred lines (RILs) between two Hokkaido varieties, A58 and Kitaake, suggested that another quantitative trait locus (QTL) for the DTH is present on chromosome 4 (qFDTH4). We mapped and evaluated the contribution of qFDTH4 to the DTH using 21 Hokkaido varieties, and detected a small effect compared to the effects of the four other genes. These findings indicate that small-effect QTLs maintain differences among LAVs and finely tune traits within the limited genetic variation of LAVs.
- cryptic variation,
- days to heading,
- locally adapted varieties,
- photosensitive genes,
- QTL,
- rice,
- small-effect locus
Citation: Md. Imdadul Hoque, Shuntaro Sakaguchi, Masaki Takatori, Hiroshi Shinada, Naoya Yamaguchi, Tsutomu Nishimura, Masafumi Kinoshita, Yuji Kishima. Small-effect loci that fine-tune heading are responsible for the regional genetic diversity of Hokkaido rice varieties[J]. AIMS Agriculture and Food, 2025, 10(2): 523-542. doi: 10.3934/agrfood.2025026

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Abstract

Rice (Oryza sativa) is a domesticated crop widely grown from tropical to temperate regions. The complement of polymorphisms in locally adapted varieties (LAVs) of rice helps them acclimate to colder regions such as Hokkaido, a northern, high-latitude region of Japan. Although large-effect genetic variants have been characterized, small phenotypic effects arising from the limited genetic diversity present in LAVs have not been fully elucidated. We used 79 Hokkaido LAVs to investigate days to heading (DTH) over multiple years. Variance in the DTH caused by environmental variation ranged from 2.5 to 11.0 days. As the genome sequences of 70 Hokkaido LAVs are available, we looked for variation in four heading genes: Ghd7, OsPRR37, Hd1, and DTH8. Hokkaido LAVs mainly harbored nonfunctional alleles for Ghd7 and OsPRR37, thus suggesting that these alleles influence DTH by hastening heading. Hd1 and DTH8 had relatively small effects on the DTH of the Hokkaido varieties, which were comparable to the effects of the environment. Our previous studies that used recombinant inbred lines (RILs) between two Hokkaido varieties, A58 and Kitaake, suggested that another quantitative trait locus (QTL) for the DTH is present on chromosome 4 (qFDTH4). We mapped and evaluated the contribution of qFDTH4 to the DTH using 21 Hokkaido varieties, and detected a small effect compared to the effects of the four other genes. These findings indicate that small-effect QTLs maintain differences among LAVs and finely tune traits within the limited genetic variation of LAVs.

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