Rapeseed (Brassica napus L.) is a major winter crop in the Yangtze River Basin, China, with sown area of 6.6 million hectares and annual production of 13.5 million tons1,2. Along with technology advancement and labour costs rise, the cultivate patterns of rapeseed is gradually changed into no-tillage direct seeding3. Recent years, the late direct seeding area for rapeseed is continuously increased as the intensive cropping development. However, since the temperature at late sowing time in China are frequently below 10°C, the direct sowing of rapeseed growth are easily affected due to low germination rates and seedling under low-temperature conditions4. Low-temperature limits seed germination and seedling growth, which ultimately affect yields4,5. The germination stage of rapeseed is sensitive to temperatures below 10°C6,7. Low-temperature during germination stage is an important problem for rapeseed cultivation. Selecting superior varieties of rapeseed with a high rate of low-temperature germination (LTG) has become an important breeding goal under late direct seeding cultivation.
Different cultivars respond differently to low-temperature, and the differences are largely controlled by genetic factors. The LTG ability of crops is a complex trait that controlled by quantitative trait loci (QTLs)4,5,8. Lots of QTL mapping studies for LTG have been conducted in crops, such as rice, maize, soybean and wheat9,10,11,12,13,14,15. In rapeseed, there was a wide genotypic variation of LTG for many studies16,17, and a few QTLs associated with low-temperature stress during seed germination and seedling stages were reported. Xian et al. (2017)4 identified several different expressed genes associated with low-temperature 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 genome-wide association study (GWAS). Except that, to our knowledge, the genetic study of rapeseed germination under low-temperature is still rare. To date, very few markers associated with LTG have been developed for rapeseed breeding. Thus, it is critical to find and identify new LTG QTLs for further fine-mapping or molecular breeding to accelerate breed low-temperature tolerant varieties of rapeseed during seed germination stage.
QTL associated with interest traits can be identified through different QTL mapping approaches including QTL-seq, which is an effective approach via bulked segregant analysis (BSA) using next-generation sequencing (NGS) for mapping QTL18. QTL-seq has been successfully used to rapidly identify QTLs for different traits in some field crops, such as spikelet fertility under heat stress in rice19, plant height in wild soybean20, cold tolerance in wild rice21, etc. In this study, we employed the F2:3 populations, derived from two inbred lines Huyou21 (tolerant to low-temperature stress) and 3429 (susceptible to low-temperature stress), to detect the QTL related to rapeseed LTG by QTL-seq method. The goals of this study were to: (i) analyze seed germination of this population under low-temperature; (ii) identify QTL for LGT from this population by QTL-seq method; (iii) develop simple sequence repeat (SSR) markers of the LTG QTLs for further fine-mapping or molecular breeding.