Rapid Identification of QTL for Mesocotyl Length in Rice Through Combining QTL-seq and Genome-Wide Association Analysis

Abstract

Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in direct-seeded rice. Thus, the identification of quantitative trait loci (QTL) associated with mesocotyl length (ML) could accelerate genetic improvement of rice for direct seeding cultivation. In this study, QTL sequencing (QTL-seq) applied to 12 F2 populations identified 14 QTL for ML, which were distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9 based on the Δ(SNP-index) or G-value statistics. Besides, a genome-wide association study (GWAS) using two diverse panels identified five unique QTL on chromosomes 1, 8, 9, and 12 (2), respectively, explaining 5.3–14.6% of the phenotypic variations. Among these QTL, seven were in the regions harboring known genes or QTLs, whereas the other 10 were potentially novel. Six of the QTL were stable across two or more populations. Eight high-confidence candidate genes related to ML were identified for the stable loci based on annotation and expression analyses. Association analysis revealed that two PCR gel-based markers for the loci co-located by QTL-seq and GWAS, Indel-Chr1:18932318 and Indel-Chr7:15404166 for loci qML1.3 and qML7.2 respectively, were significantly associated with ML in a collection of 140 accessions and could be used as breeder-friendly markers in further breeding.

Integrated QTL Mapping, Meta-Analysis, and RNA-Sequencing Reveal Candidate Genes for Maize Deep-Sowing Tolerance

“…Different crop species have evolved diverse organs to adapt to deep-sowing stressors, including elongated mesocotyl in rice ( Oryza sativa L.) [ 10 ] and elongated coleoptile in wheat ( Triticum aestivum L.) [ 11 ] and barley ( Hordeum vulgare L.) [ 12 ]. These structures help the emergence of the shoot tips and the first internode from the embryo to the soil surface; the co-elongated mesocotyl and coleoptile in maize send the buds to the soil surface [ 13 , 14 ], where natural light represses the continued elongation of mesocotyl and coleoptile and induces leaf expansion [ 7 , 15 ].…”

Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping

“…Mutants of OsPAO5 synthesize more ethylene and produce lower amounts of H 2 O 2 , resulting in a longer mesocotyl, faster seedling emergence, and higher yield potential [ 18 ]. According to the result of GWAS from other authors, eight and five high-confidence candidate genes known to be related to mesocotyl elongation were identified on chromosomes 1(2), 3,4,6,7(2),9 and 1, 3, 5, 9, 12, respectively were involved in the biological metabolism of phytohormones, cell elongation and division [ 19 , 20 ].…”

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

“…Liu et al (2020) reported 16 unique loci for mesocotyl elongation through a GWAS [16]. Wang et al (2021) identified 14 QTLs for mesocotyl elongation via QTL sequencing using 12 F 2 populations, and five unique QTLs with a GWAS using two diverse panels [17]. Gothe et al (2022) also identified eight QTLs for mesocotyl elongation using a GWAS [18].…”