Detection of a novel locus involved in non-seed-shattering behaviour of Japonica rice cultivar, Oryzasativa ‘Nipponbare’

Tsujimura, Yuki; Sugiyama, Shôhei; Otsuka, Kotaro; Htun, Than Myint; Numaguchi, Koji; Castillo, Cristina; Akagi, Takashi; Ishii, Takashige; Ishikawa, Ryo

doi:10.1007/s00122-019-03376-3

Cited by 10 publications

(10 citation statements)

References 22 publications

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“…However, the ILs having mutations at both qSH3 and sh4 slightly inhibited the abscission layer formation, resulting in reduced seed-shattering behaviour (Inoue et al 2015 ; Ishikawa et al 2022 ). In our previous study, we reported qCSS3 , a novel locus involved in reducing seed shattering in the japonica cultivar Nipponbare (Tsujimura et al 2019 ). Studies of these loci suggested that a loss of seed shattering in cultivated rice can be established by the combination of variations at several loci with specific and common mutations among cultivars.…”

Section: Introductionmentioning

confidence: 99%

Detection of novel loci involved in non-seed-shattering behaviour of an indica rice cultivar, Oryza sativa IR36

et al. 2023

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Asian rice (Oryza sativa) was domesticated from O. rufipogon, and reduced seed-shattering behaviour was selected to increase yields. Two seed-shattering loci, qSH3 and sh4, are involved in reducing seed shattering in both japonica and indica rice cultivars, while qSH1 and qCSS3 are likely specific to japonica cultivars. In indica cultivars, qSH3 and sh4 fail to explain the degree of seed shattering, as an introgression line (IL) of O. rufipogon W630 carrying domesticated alleles at qSH3 and sh4 still showed seed shattering. Here we analysed differences in seed-shattering degree between the IL and the indica cultivar IR36. The values for grain detachment in the segregating population between the IL and IR36 were continuous. Based on QTL-seq analysis using the BC1F2 population between the IL and IR36, we detected two novel loci, qCSS2 and qCSS7 (QTLs for the Control of Seed Shattering in rice on chromosomes 2 and 7), which contributed to the reduced seed shattering in IR36. We further investigated the genetic interaction of qCSS2 and qCSS7 under the presence of qSH3 and sh4 mutations in O. rufipogon W630 and found that IL carrying IR36 chromosomal segments covering all four loci are required to explain seed-shattering degree in IR36. Since qCSS2 and qCSS7 were not detected in previous studies on seed shattering in japonica, their control may be specific to indica cultivars. Therefore, they are important to understanding the history of rice domestication as well as to adjusting the seed-shattering degree of indica cultivars to maximise their yield.

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Section: Introductionmentioning

confidence: 99%

Detection of novel loci involved in non-seed-shattering behaviour of an indica rice cultivar, Oryza sativa IR36

et al. 2023

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“…To identify the rest of the gene(s), an approach that involves fixing the known QTL(s) in the segregating population would be effective for exploring and uncovering the novel QTL(s). Based on this approach, we recently detected QTL for the Control of Seed Shattering in rice on chromosome 3 (qCSS3), a novel locus involved in a loss of seed shattering in japonica rice cultivar O. sativa Nipponbare (Tsujimura et al 2019). Once all the mutations related to a loss of seed shattering are clarified, information on the causal mutations would be very useful to understand the change in the degree of seed shattering conferred by each locus and their additive effects in combination.…”

Section: What Traits Were Targeted For Selection In Early Rice Domestication?mentioning

confidence: 99%

Genetic evaluation of domestication-related traits in rice: implications for the archaeobotany of rice origins

Ishikawa

Castillo

Fuller

2020

Archaeol Anthropol Sci

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Domestication is the process in which preferred genetic changes in wild plants and animals have been selected by humans. In other words, domesticated plants have become adapted to being part of human-managed ecosystems. Asian cultivated rice, Oryza sativa L., is one of the most important crops in the world and is known to have been domesticated from its wild ancestor, O. rufipogon. Many morphological changes in cultivated rice have been beneficial to humans in terms of increased efficiency of cultivation and yield that supported the development of human civilisations. The genetic mechanisms of these changes have been extensively studied since rice genome sequences were determined, and based on genome analyses, the origin of rice has been widely discussed. Most of the domestication-related traits and genes are, however, often evaluated based on the genetic background of cultivated rice, leading to misinterpretation of rice domestication. Here, we review several genetic changes and discuss the importance of evaluating these traits in the wild rice genetic background to understand the process of rice domestication. In this review, we also provide a phenotypic evaluation of domestication-related traits.

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“…Other genes such as SH5 and SSH1/SNB are also believed to have large influences on seed shattering by interacting with qSH1 (Jiang et al 2019a;Yoon et al 2014). Mutagenesis and transgenic methods have been frequently used to illustrate the function and mechanisms of these genes, which affected seed shattering through modifications on AZ formation or lignin deposition in the AZ regions (Jiang et al 2019a;Lv et al 2018;Tsujimura et al 2019).…”

Section: Introductionmentioning

confidence: 99%

Architecture of paleas and lemmas dominates seed shattering trait in naked oat (Avena nuda)

Zhang

Han

et al. 2023

CEREAL RESEARCH COMMUNICATIONS

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Seed shattering in naked oat (Avena nuda) is a severe problem, resulting in significant yield losses. In the present study, the seed-shattering rates were characterized in a set of 177 naked oat cultivars and lines. Eight cultivars with different seed-shattering rates were studied in several morphological and physiological traits that may be related to seed shattering at different developmental stages. Three types of paleas, viz. boat type, defect type and flaky type, were identified at the dough stage, and the proportion of the boat-type paleas were found to positively correlate with seed shattering. In a following scaling-up morphological study on paleas and lemmas in 32 cultivars with different seed-shattering rates, the length, width and the thickness of paleas and lemmas were investigated, and the ratio of the bottom/medium thickness of both paleas and lemmas showed high association with seed shattering tolerance in naked oat. These indicate that the architecture of paleas and lemmas has a particularly obvious correlation with seed shattering in naked oat. More intriguingly, a unique zigzag pattern of the cell wall was found in lemma tissues of naked oat, which may increase the toughness and strength of lemmas and help with seed retention.

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Detection of a novel locus involved in non-seed-shattering behaviour of Japonica rice cultivar, Oryzasativa ‘Nipponbare’

Abstract: A novel locus, qCSS3, involved in the non-seed-shattering behaviour of Japonica rice cultivar, 'Nipponbare', was detected by QTL-seq analysis using the segregating population with the fixed known seed-shattering loci.

Cited by 10 publications

References 22 publications

Detection of novel loci involved in non-seed-shattering behaviour of an indica rice cultivar, Oryza sativa IR36

Detection of novel loci involved in non-seed-shattering behaviour of an indica rice cultivar, Oryza sativa IR36

Genetic evaluation of domestication-related traits in rice: implications for the archaeobotany of rice origins

Architecture of paleas and lemmas dominates seed shattering trait in naked oat (Avena nuda)

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