Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.)

Abstract

Low temperature inhibits rapid germination and successful seedling establishment of rapeseed (Brassica napus L.), leading to significant productivity losses. Little is known about the genetic diversity for seed vigor under low-temperature conditions in rapeseed, which motivated our investigation of 13 seed germination- and emergence-related traits under normal and low-temperature conditions for 442 diverse rapeseed accessions. The stress tolerance index was calculated for each trait based on performance under non-stress and low-temperature stress conditions. Principal component analysis of the low-temperature stress tolerance indices identified five principal components that captured 100% of the seedling response to low temperature. A genome-wide association study using ~8 million SNP (single-nucleotide polymorphism) markers identified from genome resequencing was undertaken to uncover the genetic basis of seed vigor related traits in rapeseed. We detected 22 quantitative trait loci (QTLs) significantly associated with stress tolerance indices regarding seed vigor under low-temperature stress. Scrutiny of the genes in these QTL regions identified 62 candidate genes related to specific stress tolerance indices of seed vigor, and the majority were involved in DNA repair, RNA translation, mitochondrial activation and energy generation, ubiquitination and degradation of protein reserve, antioxidant system, and plant hormone and signal transduction. The high effect variation and haplotype-based effect of these candidate genes were evaluated, and high priority could be given to the candidate genes BnaA03g40290D, BnaA06g07530D, BnaA09g06240D, BnaA09g06250D, and BnaC02g10720D in further study. These findings should be useful for marker-assisted breeding and genomic selection of rapeseed to increase seed vigor under low-temperature stress.

QTLs Detection for Low-Temperature Germination in Rapeseed by QTL-seq and Linkage Mapping Approach

“…Whereas the rapeseed germination is easily affected by low-temperature with the delay of seeding times 4 . Low-temperature sensitively at the germination stage is a major challenge for rapeseed cultivation under the late direct-seeding conditions in China 4,7 . It is a breeding goal to select varieties with well germination under both optimal and stressed conditions to adapt the changing temperature under late direct seeding cultivation.…”

“…In our study, the position of the QTL (qLTGA9-1) on chromosome A09 was mapped around 30.2-Mb apart from each other based on the physical position of linkage markers on ZS11 genome sequence 25 . GWAS mapping from Luo et al (2021) 7 showed the candidate genes to be around the 3.0-Mb position on chromosome A09 based on ZS11 genome sequence 25 related to seed vigor under low-temperature. As the physical distance between the locus and the QTL we identi ed was more than 27 Mb probably rules out, we believe that the QTLs including qLTGC1-1 we found were novel in rapeseed for LTG.…”

“…Low-temperature limits seed germination and seedling growth, which ultimately affect yields 4,5 . The germination stage of rapeseed is sensitive to temperatures below 10°C 6,7 . Low-temperature during germination stage is an important problem for rapeseed cultivation.…”

“…Xian et al (2017) 4 identi ed several different expressed genes associated with lowtemperature tolerance in rapeseed through transcriptome analysis. Luo et al (2021) 7 detected 22 QTLs associated with low-temperature tolerance during seed germination and seedling stages through genomewide association study (GWAS). Except that, to our knowledge, the genetic study of rapeseed germination under low-temperature is still rare.…”

QTL mapping for low temperature germination in rapeseed

“…The late direct seeding area under rapeseed has continuously increased in recent years, with intensive cropping development. Meanwhile, rapeseed is sensitive to temperatures below 10 °C at germination 4 , 5 . The temperature at late sowing time in China is generally below 10 °C, which leads to a low germination rate and seedling in rapeseed 6 , which ultimately affects yield 6 , 7 .…”