Statistics of genetic linkage map information.

Seed density per silique (SD) is an important agricultural trait and plays an important role in the yield performance of Brassica napus L. (B. napus). In this study, a genetic linkage map was constructed using a double haploid (DH) population with 213 lines derived from a cross between a low SD line No. 935 and a high SD line No. 3641, and a total of 1,098,259 SNP (single-nucleotide polymorphisms) markers and 2,102 bins were mapped to 19 linkage groups. Twenty-eight QTLs for SD were detected on chromosomes A02, A04, A05, A09, C02, C03, C06, and C09 of B. napus, of which eight QTLs were on chromosome A09 and explained 5.89%-13.24% of the phenotypic variation. Furthermore, a consistent QTL for SD on chromosome A09, cqSD-A9a, was identified in four environments by QTL meta-analysis, explaining 10.68% of the phenotypic variation. In addition, four pairs of epistatic interactions were detected in the DH population via QTL epistasis analysis, indicating that SD is controlled not only by additive effects but also by epistatic effects that play an important role in spring B. napus., but with little environmental effect. Moreover, 18 closely linked SSR markers for cqSD-A9a were developed, as a result, it was mapped to a 1.86Mb (7.80–9.66 Mb) region on chromosome A09. A total of 13 differentially expressed genes (DEGs) were screened in the candidate interval by RNA-seq analysis, which were differentially expressed in buds, leaves and siliques both between and siliques both between two parents and two pools of extremely high-SD and low-SD lines in the DH population. Three of 13 DEGs were possible candidate genes that might control SD: BnaA09g14070D, which encodes a callose synthase that plays an important role in development and stress responses; BnaA09g14800D, a plant synaptic protein that encodes a membrane component; and BnaA09g18250D, which is responsible for DNA binding, transcriptional regulation, and sequence-specific DNA binding and is involved in the response to growth hormone stimulation. Overall, these results lay a foundation for fine mapping and gene cloning for SD in B. napus.每角果种子密度（Seed density per silique, SD）是一项重要的农艺性状，对甘蓝型油菜（Brassica napus L., B. napus）的产量表现具有关键作用。本研究以低SD品系935号与高SD品系3641号杂交构建的包含213个株系的双单倍体（double haploid, DH）群体为材料，构建了遗传连锁图谱；共将1098259个单核苷酸多态性（single-nucleotide polymorphisms, SNP）标记与2102个bin位点定位至19个连锁群。在甘蓝型油菜的A02、A04、A05、A09、C02、C03、C06及C09染色体上，共检测到28个控制SD的数量性状位点（Quantitative Trait Locus, QTL），其中8个QTL位于A09染色体，可解释5.89%~13.24%的表型变异。进一步通过QTL元分析，在4个环境中均检测到A09染色体上的稳定QTL cqSD-A9a，其可解释10.68%的表型变异。此外，通过DH群体的上位性QTL分析，共检测到4对上位性互作位点，表明SD不仅受加性效应调控，还受上位性效应影响，该效应在春性甘蓝型油菜中发挥重要作用，但受环境影响较小。针对cqSD-A9a，共开发得到18个紧密连锁的简单序列重复（Simple Sequence Repeat, SSR）标记，并将其定位至A09染色体的1.86Mb（7.80~9.66 Mb）区间内。通过RNA测序（RNA-seq）分析，在该候选区间内筛选得到13个差异表达基因（differentially expressed genes, DEGs），这些基因在两个亲本以及DH群体中极高低SD株系的两个混池的芽、叶与角果中均存在差异表达。13个DEGs中有3个为潜在的SD调控候选基因：BnaA09g14070D，编码胼胝质合酶，该酶在发育与胁迫响应过程中发挥重要作用；BnaA09g14800D，编码一种膜组分相关的植物突触蛋白；以及BnaA09g18250D，该基因参与DNA结合、转录调控与序列特异性DNA结合，并响应生长素刺激。综上，本研究结果为甘蓝型油菜SD性状的精细定位与基因克隆奠定了基础。