Molecular-Genetic Foundations of Rice Domestication: Control of Seed Shattering, Grain Size, and Pericarp Coloration

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Abstract

Domestication of rice (Oryza sativa L.), one of the five earliest cereal crops, gave rise to a characteristic “domestication syndrome” marked by loss of natural seed dispersal, enlargement and colour change of the caryopsis, shortening of seed dormancy, and transition to an annual life cycle. Archaeological, physiological-genetic and molecular evidence is synthesised here to summarise the mechanisms underlying these key agronomic traits. Reduced seed shattering is linked to mutations andallelic diversification at loci SH4, qSH1, SH5, SHAT1, CPL1, OsSh1/ObSH3, ObSH11, NPC1, OSH15, GRF4 and OsLG1/SPR3, which govern formation and degradation of the spikelet abscission layer. Grain size is determined by QTL GW2, GS3, GS5 and TGW6, modulating cell division and endosperm development and thus shaping thousand-grain weight and yield. Pericarp pigmentation is controlled by Rc and Rd together with the Kala1–Kala3–Kala4 cassette; structural rearrangements in theKala4 promoter trigger ectopic expression of a bHLH factor and anthocyanin accumulation, whereas a 14-bp deletion in Rc converted most cultivars to the white-grained type and was later functionally restored via CRISPR/Cas9. Collectively, these findings provide a genetic foundation for targeted improvement of yield, harvestability and nutritional quality in modern rice breeding.

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About the authors

Nikita A. Mirgorodskii

Sirius University of Science and Technology

Author for correspondence.
Email: i@nmirgorodskij.ru
ORCID iD: 0009-0005-6662-0741
SPIN-code: 1057-6260
Russian Federation, 1 Olimpiiskii av., Sirius Federal Territory, 354340

Sofya A. Slezova

Sirius University of Science and Technology

Email: slezovas@mail.ru
Russian Federation, 1 Olimpiiskii av., Sirius Federal Territory, 354340

Nadezhda A. Dobarkina

Sirius University of Science and Technology

Email: n.dobarkina@yandex.ru
ORCID iD: 0009-0009-4283-519X
Russian Federation, 1 Olimpiiskii av., Sirius Federal Territory, 354340

Tatiana V. Matveeva

Saint Petersburg State University; All-Russian Research Institute of Plant Protection

Email: radishlet@gmail.com
ORCID iD: 0000-0001-8569-6665
SPIN-code: 3877-6598
Scopus Author ID: 7006494611

Dr. Sci. (Biology), Professor

Russian Federation, Saint Petersburg; Saint Petersburgcity, Pushkin

Elena A. Andreeva

Saint Petersburg State University

Email: a.andreeva@spbu.ru
ORCID iD: 0000-0002-9326-3170
SPIN-code: 7269-8240

Cand. Sci. (Biology)

Russian Federation, Saint Petersburg

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