Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations

Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were scr...

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Published in:Plants (Basel) 2023-07, Vol.12 (14), p.2743
Main Authors: Feng, Fangjun, Ma, Xiaosong, Yan, Ming, Zhang, Hong, Mei, Daoliang, Fan, Peiqing, Xu, Xiaoyan, Wei, Chunlong, Lou, Qiaojun, Li, Tianfei, Liu, Hongyan, Luo, Lijun, Mei, Hanwei
Format: Article
Language:English
Subjects:
Aquatic plants
Chromosomes
Confidence intervals
Crop production
Cultivars
Drought
dry direct sowing rice (DDSR)
Elongation
Gene loci
Genetic aspects
Genomes
Germination
Germplasm
Growth
GWAS
Identification and classification
Inbreeding
linkage mapping
mesocotyl elongation
Oryza sativa L
Quantitative trait loci
Rice
Seedlings
Seeds
Single-nucleotide polymorphism
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Summary:Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by -log ( ) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed.
ISSN:2223-7747
2223-7747
DOI:10.3390/plants12142743