Joint genome-wide association and transcriptome sequencing reveals a complex polygenic network underlying hypocotyl elongation in rapeseed (Brassica napus L.)

Abstract

Hypocotyl elongation is considered an important typical seedling trait contributing directly to an increase in and stabilization of the yield in Brassica napus, but its molecular genetic mechanism is poorly understood. In the present study, hypocotyl lengths of 210 lines were measured in an illuminated culture room. A genome-wide association study (GWAS) was performed with 23,435 single nucleotide polymorphisms (SNPs) for hypocotyl length. Three lines with long hypocotyl length and three lines with short hypocotyl length from one doubled haploid line (DH) population were used for transcriptome sequencing. A GWAS followed by transcriptome analysis identified 29 differentially expressed genes associated with significant SNPs in B. napus. These genes regulate hypocotyl elongation by mediating flowering morphogenesis, circadian clock, hormone biosynthesis, or important metabolic signaling pathways. Among these genes, BnaC07g46770D negatively regulates hypocotyl elongation directly, as well as flowering time. Our results indicate that a joint GWAS and transcriptome analysis has significant potential for identifying the genes responsible for hypocotyl elongation; The extension of hypocotyl is a complex biological process regulated by a polygenic network.

An Endeavor of ‘Deep-underground Agriculture’: Deep-underground Storage in a Gold Mine Impacts the Germination of Canola (Brassica Napus L.) Seeds

“…In general, we found that biomass gradually increased as storage depth and duration were extended regardless of the packaging method used. Furthermore, biomass and hypocotyl length showed similar variation with storage time, which is similar to the results reported by (Luo et al, 2017). Therefore, the lengthening of the hypocotyl with storage depth and duration may explain the observed increase in biomass accumulation.…”

“…The elongation of the hypocotyl is a crucial feature of the seedling stage; with better development of the seedling, a satisfactory yield can be obtained (Luo et al, 2017). In the present study, the maximum hypocotyl length usually appeared after more extended storage periods for seeds in both envelopes and sealed packages.…”

“…In contrast, over long-term storage periods at deeper storage depths, greater hypocotyl length and biomass accumulation were observed (i.e., 227 days at 690 or 1,410 m). For canola, hypocotyl length and biomass accumulation are closely related to the nal yield (Li et al, 2019;Luo et al, 2017), which is the concern of most producers. Therefore, to increase hypocotyl length and biomass accumulation, storing seeds in a deeper location for a shorter period would be reasonable.…”

QTL analysis of shoot elongation before winter in relation to vernalization requirement in the doubled haploid population L16 × Express617 (Brassica napus L.)

“…Enhanced hypocotyl elongation is like enhanced epicotyl (shoot) elongation before winter presumably related to reduced frost tolerance. Hypocotyl elongation has not been measured in the present studies, but in a genome wide association study Luo et al (2017) suggested candidate gene BnaC07g46770D among others as a negative regulator of hypocotyl elongation and of flowering time. In the present study, no significant QTL for shoot elongation was detected on C07 in the autumn and in the spring-sown environment.…”

Transcriptome profiling based on Illumina- and SMRT-based RNA-seq reveals circadian regulation of key pathways in flower bud development in walnut

“…Circadian clocks fine-tune physiology and behaviour to match the environmental day/night cycle [39,40]. The plant circadian clock generates daily and even seasonal rhythms in an orderly succession of physiological processes including stomatal opening, leaf movement, hypocotyl elongation, photosynthesis and carbon metabolism, resistance to abiotic and biotic stresses, and flowering time [15,33,[41][42][43][44][45]. Expression analysis of critical genes helped to dissect the genetic basis of important traits, such as floral in hickory [46] and Persian walnut [47].…”