Genome-wide association study of stem structural characteristics that extracted by a high-throughput phenotypic analysis "LabelmeP rice" in rice.
Plant J
; 119(4): 2080-2095, 2024 Aug.
Article
em En
| MEDLINE
| ID: mdl-38860937
ABSTRACT
Stem is important for assimilating transport and plant strength; however, less is known about the genetic basis of its structural characteristics. In this study, a high-throughput method, "LabelmeP rice" was developed to generate 14 traits related to stem regions and vascular bundles, which allows the establishment of a stem cross-section phenotype dataset containing anatomical information of 1738 images from hand-cut transections of stems collected from 387 rice germplasm accessions grown over two successive seasons. Then, the phenotypic diversity of the rice accessions was evaluated. Genome-wide association studies identified 94, 83, and 66 significant single nucleotide polymorphisms (SNPs) for the assayed traits in 2 years and their best linear unbiased estimates, respectively. These SNPs can be integrated into 29 quantitative trait loci (QTL), and 11 of them were common in 2 years, while correlated traits shared 19. In addition, 173 candidate genes were identified, and six located at significant SNPs were repeatedly detected and annotated with a potential function in stem development. By using three introgression lines (chromosome segment substitution lines), four of the 29 QTLs were validated. LOC_Os01g70200, located on the QTL uq1.4, is detected for the area of small vascular bundles (SVB) and the rate of large vascular bundles number to SVB number. Besides, the CRISPR/Cas9 editing approach has elucidated the function of the candidate gene LOC_Os06g46340 in stem development. In conclusion, the results present a time- and cost-effective method that provides convenience for extracting rice stem anatomical traits and the candidate genes/QTL, which would help improve rice.
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Fenótipo
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Oryza
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Caules de Planta
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Polimorfismo de Nucleotídeo Único
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Locos de Características Quantitativas
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Estudo de Associação Genômica Ampla
Idioma:
En
Revista:
Plant J
Assunto da revista:
BIOLOGIA MOLECULAR
/
BOTANICA
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
China