Mapping QTLs using High-Density SNPs Genotyped by Sequencing Reveals Novel Potential Regions Underlying Maize Root Morphological Traits at Seedling Stage

Abstract

Maize (Zea mays L.) root system plays a crucial role in plant fixation and the acquisition of nutrients and water essential for growth and development. Herein, 179 recombinant inbred lines (RILs) obtained from a cross between P014 × E1312 were genotyped via genotyping-by-sequencing (GBS) and phenotyped for root related-traits at 5 and 15 days after germination (dag) under controlled conditions. Quantitative trait locus (QTL) mapping based on high-density GBS-SNPs bin map was performed, and an overall number of 14 QTLs with a phenotypic variance explained (PVE) ranging from 1.78 to 16.05% were identified. The QTL co-localization was detected at each of the two time-points, and one major QTL region on chromosome 4 was found to be significantly associated with multiple traits, including root projected area (PRA), root surface area (SUA), shoot dry weight (SDW), and total plant biomass (TPB). Compared to previous root-related studies, QTLs located in chromosomal bins 2.09 (qROT5d-2-1), 4.05 (qPRA5d-4-1, qSUA5d-4-1, qSDW15d-4-1, qTPB15d-4-1), 7.06 (qTRL15d-7-1), and 8.09 (qSDW5d-8-1) were found to be novel. Two candidate genes GRMZM2G109056 and GRMZM2G053458, associated with root dry weight trait on chromosome 1, were verified for expression level, and the results showed significantly different expression levels between the two outer parental accessions in primary roots at all evaluated time-points. Thus, the identified loci and genes could play an important role in maize molecular breeding for high yielding varieties. © 2021 Friends Science Publishers

Genome-wide association screening and verification of potential genes associated with root architectural traits in maize (Zea mays L.) at multiple seedling stages

“…This SNP was also in LD with qTRL17-1 [ 19 ] and 9d LRL7-1 [ 24 ]. Remarkably, the cluster qTRL v1 -10-1 and qRBN v1 -10-1 associated with total root length and root branching number at V1 stage collocated consistently with the QTL qTRL 5d -10-1 regulating total root length detected recently by Moussa et al [ 45 ] within the same population using 5 days old seedlings. This chromosomal region can, therefore, be considered as a special noteworthy locus that can directly be used in marker-assisted selection programs.…”

“…The linkage map contained 4235 high-quality SNP markers covering a total length of 1514.57 cM distributed for 10 linkage groups [ 45 ]. Using inclusive composite interval mapping method with LOD ≥ 2.5 as a threshold, a total of eight substantial QTLs with a phenotypic variance explained ranging from 6.44 to 8.83 % were detected across the three stages (Table 5 ).…”

“…The mapping population consisted of 179 RILs developed by a cross between the female parent P014 and the male parent E1312 and continuous inbreeding for 9 generations. P014 line was known to possess a larger and thicker root system with significantly higher root dry weight, total root length, surface area, projected area, average root diameter, and root tips as compared to E1312 line [ 45 ]. Genetically pure seeds from both populations were produced at the Jilin Agricultural University’s experimental field in summer 2019.…”