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

Abstract

Background Rice is one of the most important food crops in the world and mainly cultivated in paddy field by transplanting seedlings. However, increasing water scarcity due to climate change, labor cost for transplanting, and competition from urbanization is making this traditional method of rice production unsustainable in the long term. In the present study, we mined favorable alleles for mesocotyl elongation length (MEL) by combining the phenotypic data of 543 rice accessions with genotypic data of 262 SSR markers through association mapping method. Results Among the 543 rice accessions studied, we found 130 accessions could elongate mesocotyl length under dark germination condition. A marker-trait association analysis based on a mixed linear model revealed eleven SSR markers were associated with MEL trait with p-value less than 0.01. Among the 11 association loci, seven were novel. In total, 30 favorable marker alleles for MEL were mined, and RM265-140 bp showed the highest phenotypic effect value of 1.8 cm with Yuedao46 as the carrier accession. The long MEL group of rice accessions had higher seedling emergence rate than the short MEL group in the field. The correlation coefficient (rGCC−FSC = 0.485**) between growth chamber condition (GCC) and field soil condition (FSC) showed positive relationship and highly significant (P < 0.01) indicating that the result obtained in GCC could basically represent that obtained under FSC. Conclusion Not every genotype of the rice possesses the ability to elongate its mesocotyl length under dark or deep sowing condition. Mesocotyl elongation length is a quantitative trait controlled by many gene loci, and can be improved by pyramiding favorable alleles dispersed at different loci in different germplasm into a single genotype.

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

“…In contrast to previous reports, qMEL2 is a novel QTL associated with the control mesocotyl elongation in rice. The physical position of qMEL2 indicates no overlapping region with previously reported mesocotyl-related QTLs in rice ( Redona et al, 1996 ; Cai et al, 2002 ; Lee et al, 2012 ; Edzesi et al, 2023 ). The qMEL2 , a major mesocotyl QTL explaining nearly 37.5% of the observed phenotypic variance, harbors a set of genes proposed to have diverse molecular functions or be involved in biological processes such as transcription factor activity ( Os02g26430 , encoding a WRKY42 transcription factor, TF), growth and development ( Os02g26490 , no apical meristem (NAM) domain-containing protein, zinc-ribbon domain-containing protein ( Os02g26560 ), a Ubiquitin carboxyl-terminal hydrolase ( Os02g26550 ), a Serine carboxypeptidase homologue ( OsSCP7 , Os02g26480 ), and a gene encoding the Wiskott-Aldrich syndrome protein (WAS, Os02g26370 : a conserved domain analysis revealed that this gene has no functional conserved domain.…”

“…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 ).…”

An orchestrated ethylene–gibberellin signaling cascade contributes to mesocotyl elongation and emergence of rice direct seeding

“…Sowing under a certain depth of soil can protect seeds from adverse environmental conditions, improve nutrient‐use efficiency, and enhance lodging resistance (Sandhu et al, 2019; Wang et al, 2019). However, seedlings must be able to emerge from this soil and, unfortunately, most modern rice cultivars have poor emergence vigor following direct seeding, leading to higher seed usage and resource costs (Edzesi et al, 2023). Previous studies showed that the mesocotyl, a structure between the basal part of the seminal root and the coleoptile node of seedlings, provides vigor when pushing the shoot tip through the soil surface and is essential for the uniform emergence of direct‐seeded rice (Lee et al, 2017; Zhan et al, 2020).…”