Data_Sheet_1_A High-Density Genetic Map of an Allohexaploid Brassica Doubled Haploid Population Reveals Quantitative Trait Loci for Pollen Viability and Fertility.PDF

A doubled haploid (DH) mapping population was obtained from microspore culture of an allohexaploid F1 from the cross between two recently-synthesized allohexaploid Brassica lines. We used single nucleotide polymorphism (SNP) genetic variation based on restriction-site associated DNA (RAD) sequencing to construct a high density genetic linkage map of the population. RAD libraries were constructed from the genomic DNA of both parents and 146 DH progenies. A total of 2.87 G reads with an average sequencing depth of 2.59 × were obtained in the parents and of 1.41 × in the progeny. A total of 290,422 SNPs were identified from clustering of RAD reads, from which we developed 7,950 high quality SNP markers that segregated normally (1:1) in the population. The linkage map contained all 27 chromosomes from the parental A, B and C genomes with a total genetic distance of 5725.19 cM and an average of 0.75 cM between adjacent markers. Genetic distance on non-integrated linkage groups was 1534.23 cM, or 21% of total genetic distance. Out of 146 DH progenies, 91 had a complete set of 27 chromosomes as expected of a hexaploid species, and 21 out of 27 chromosomes showed high collinearity between the physical and linkage maps. The loss of chromosome(s) or chromosome segment(s) in the DH population was associated with a reduction in pollen viability. Twenty-five additive QTL were associated with pollen viability and fertility-related traits (seed number, seed yield, pod length, plant height, 1000-seed weight). In addition, 44 intra-genomic and 18 inter-genomic epistatic QTL pairs were detected for 4 phenotypic traits. This provides confidence that the DH population may be selected for improved pollen viability and fertility in a future allohexaploid Brassica species.

本研究构建的双单倍体（doubled haploid, DH）作图群体，源自两个新近合成的异源六倍体芸薹属（Brassica）品系杂交获得的异源六倍体F1的小孢子培养。我们基于限制性酶切位点相关DNA（restriction-site associated DNA, RAD）测序得到的单核苷酸多态性（single nucleotide polymorphism, SNP）遗传变异，构建了该群体的高密度遗传连锁图谱。分别以双亲本及146个DH后代个体的基因组DNA构建RAD测序文库。双亲本测序共获取2.87 G读段，平均测序深度为2.59×；后代个体的平均测序深度为1.41×。通过对RAD读段进行聚类分析，共鉴定得到290,422个SNP位点，据此开发出7,950个在群体中呈1:1正常分离的高质量SNP标记。该遗传连锁图谱覆盖亲本A、B、C基因组的全部27条染色体，总遗传距离达5725.19 cM，相邻标记间的平均遗传距离为0.75 cM。未整合连锁群的遗传距离为1534.23 cM，占总遗传距离的21%。在146个DH后代个体中，有91个个体携带异源六倍体物种预期的完整27条染色体；27条染色体中有21条在物理图谱与连锁图谱间呈现高度共线性。DH群体中出现的染色体或染色体片段丢失现象，与花粉活力降低显著相关。共检测到25个与花粉活力及育性相关性状（种子数、种子产量、荚果长度、株高、千粒重）相关的加性数量性状位点（quantitative trait locus, QTL）。此外，针对4个表型性状，共检测到44个基因组内及18个基因组间的上位性QTL位点对。上述研究结果为利用该DH作图群体开展后续异源六倍体芸薹属物种的花粉活力与育性改良选育工作提供了可靠依据。