Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study

The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of...

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Bibliographic Details
Published in:Plants (Basel) 2024-01, Vol.13 (1), p.134
Main Authors: Ding, Xiaowen, Shi, Jubin, Gui, Jinxin, Zhou, Huang, Yan, Yuntao, Zhu, Xiaoya, Xie, Binying, Liu, Xionglun, He, Jiwai
Format: Article
Language:English
Subjects:
Alleles
Amino acids
Biosynthesis
Crop production
Frequency distribution
Gene mapping
Genes
Genetic aspects
Genetic control
Genome-wide association studies
Genomes
Germination
Germplasm
Growth
GWAS
haplotype
Haplotypes
Identification and classification
Phenotypes
Physiological aspects
Population studies
Proteins
protrusion percentage
QTL
Quantitative trait loci
Rice
Seed germination
Seeds
Signal transduction
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Summary:The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only was detected repeatedly two times. The candidate gene analysis showed that , and were the candidate genes for , and , respectively. The haplotype (Hap) analysis revealed that Hap1 of , Hap1 and 3 of and Hap2 and 5 of are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of is a favorable allele for the germination percentage; Hap3 of is an elite allele for seed germination; and Hap5 of is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice.
ISSN:2223-7747
2223-7747
DOI:10.3390/plants13010134