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

Abstract

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 p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by −log10(P) > 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.

Genome-wide association study (GWAS) with high-throughput SNP chip DNA markers identified novel genetic factors for mesocotyl elongation and seedling emergence in rice (Oryza sativa L.) using multiple GAPIT models

“…Mesocotyl elongation and seedling emergence are determinant factors conditioning the number of individuals present in the field. Since the advent of genome sequencing technologies, several techniques have been used to identify QTLs for mesocotyl elongation in rice, including QTL-sequencing (QTL-seq), GWAS ( Lu et al, 2016 ; Wang et al, 2021 ) or linkage or association mapping ( Edzesi et al, 2023 ; Feng et al, 2023 ), and employing diverse mapping populations/germplasm and various DNA marker systems ( Huang et al, 2022 ; Edzesi et al, 2023 ). Previous studies reported QTLs associated with mesocotyl elongation ( qMEL ) on almost all chromosomes of rice 1–5, 7, 9, 11, 12 ( Lee et al, 2012 ; Lu et al, 2016 ).…”