A comprehensive and precise set of intervarietal substitution lines to identify candidate genes and quantitative trait loci in oilseed rape (Brassica napus L.)

Abstract

A set of intervarietal substitution lines were developed in rapeseed by recurrent backcrossing and marker-assisted selection and employed for mapping both qualitative and quantitative traits. Intervarietal substitution lines (ISLs) may be assembled into advanced secondary mapping populations that have remarkable potential for resolving trait loci and mapping candidate genes. To facilitate the identification of important genes in oilseed rape (canola, Brassica napus), we developed 89 ISLs using an elite cultivar 'Zhongyou 821' (ZY821) as the recipient and a re-synthesized line 'No.2127' as the donor. In the whole process of ISLs development, the target chromosome segments were selected based on the genotypes of 300 microsatellite markers evenly distributed across the genome. Eighty-nine ISLs fixed at BCF were genotyped by sequencing using double digestion to survey the lengths of target substitution segments from the donor parent and the background segments from the recurrent parent. The total length of the substituted chromosome segments was 3030.27 Mb, representing 3.56 × of the Darmor-bzh reference genome sequence (version 4.1). Gene mapping was conducted for two qualitative traits, flower colour and seed-coat colour, and nine quantitative traits including yield- and quality-related traits, with 19 QTLs identified for the latter. Overlapping substitution segments were identified for flower colour and seed-coat colour loci, as well as for QTLs consistently detected in 2 or 3 years. These results demonstrate the value of these ISLs for locus resolution and subsequent cloning, targeted mutation or editing of genes controlling important traits in oilseed rape.

High‐throughput phenotyping accelerates the dissection of the dynamic genetic architecture of plant growth and yield improvement in rapeseed

“…Two QTLs for PC1_SV‐6 and PC3_SV‐9 in 2016‐2017 overlapped with the QTLs on chromosome A02 for seed number per silique, which was scored from the field in the same population (Yang et al , 2018). In addition, QTLs for PC6_SV‐2, AC_SV‐1 and R_SV‐1 in 2015–2016 and for PAR_TV‐11 in 2016‐2017 also overlapped with the QTLs on chromosome A09 for seed number per silique, which was also scored from the field (Yang et al , 2018).…”

“…Two QTLs for PC1_SV‐6 and PC3_SV‐9 in 2016‐2017 overlapped with the QTLs on chromosome A02 for seed number per silique, which was scored from the field in the same population (Yang et al , 2018). In addition, QTLs for PC6_SV‐2, AC_SV‐1 and R_SV‐1 in 2015–2016 and for PAR_TV‐11 in 2016‐2017 also overlapped with the QTLs on chromosome A09 for seed number per silique, which was also scored from the field (Yang et al , 2018). Notably, of the eight i‐traits selected as indicators to predict the final grain yield (Figure 1a), the QTLs for FDNIC_TV‐7 and GPA_TV‐7 as well as H_SV‐12 colocalized with QTLs on chromosomes A07 and A05, respectively, for final yield assessed in the same greenhouse (Figure 5b).…”

“…In our study, a rapeseed ISL population that included 89 lines and its recurrent parent Zhongyou 821 (ZY821) (nine repeats) (Yang et al , 2018) was used for phenotyping in the HRPF. All lines were first planted in a two‐row plot, with ten plants in each row, in the experimental field of Huazhong Agricultural University (Wuhan, Hubei Province, China).…”

“…The detailed characteristics of substituted chromosome segments of the ISL population are described in a previous study (Yang et al , 2018). In brief, the 89 ISLs were genotyped using the GBS approach, and 4214 SNP markers were found across the 19 chromosomes.…”

“…High‐throughput genotyping approaches, including single nucleotide polymorphism (SNP) Illumina Infinium array, genotyping by sequencing (GBS) and resequencing‐based genotyping, have been established in rapeseed (Chen et al , 2013; Clarke et al , 2016; Wang et al , 2018). Based on these resources, substantial amounts of SNPs, insertions/deletions (InDels) and presence and absence variations (PAVs) have been identified in various permanent populations, such as recombinant inbred lines (RILs), double haploids (DHs), intervarietal substitution lines (ISLs), and in nested association mapping (NAM) and natural populations (Chen et al , 2013; Hu et al , 2018; Luo et al , 2015; Song et al , 2020; Yang et al , 2016; Yang et al , 2018). In contrast, the development of phenotyping technology is very slow in rapeseed and is still dominated by traditional manual scoring.…”