Gene-centromere mapping in meiotic gynogenetic European seabass

Fully isogenic lines in fish can be developed using "mitotic" gynogenesis (suppression of first zygotic mitosis following inactivation of the sperm genome). However, genome-wide verification of the steps in this process has seldom been applied. We used ddRADseq to generate SNP markers in a meiotic gynogenetic family of European seabass (Dicentrarchus labrax): (i) to verify the lack of paternal contribution in a meiotic gynogenetic family; (ii) to generate a gene-centromere map from this family; (iii) to identify telomeric markers that could distinguish mitotic gynogenetics from meiotic gynogenetics, which sometimes arise spontaneously in mitotic gynogenetic families. From a single meiotic gynogenetic family consisting of 79 progeny, 42 million sequencing reads (Illumina, trimmed to 148 bases) resolved 6866 unique RAD-tags. The 340 male-informative SNP markers that were identified confirmed the lack of paternal contribution. A gene-centromere map was constructed based on 804 female-informative SNPs in 24 linkage groups (2n = 48) with a total length of 1251.02 cM (initial LG assignment was based on the seabass genome assembly, dicLab v1). Chromosome arm structure could be clearly discerned from the pattern of heterozygosity in each linkage group in 18 out of 24 LGs: the other six showed anomalies that appeared to be related to issues in the genome assembly. Genome-wide screening enabled substantive verification of the production of the gynogenetic family used in this study. The large number of telomeric and subtelomeric markers with high heterozygosity values in the meiotic gynogenetic family indicate that such markers could be used to clearly distinguish between meiotic and mitotic gynogenetics.

鱼类的完全同源纯合系（isogenic lines）可通过有丝分裂雌核发育（mitotic gynogenesis）构建，该技术指在精子基因组灭活后抑制合子的首次有丝分裂（zygotic mitosis）。然而，目前鲜有针对该过程各环节的全基因组水平验证研究。本研究以欧洲海鲈（Dicentrarchus labrax）的一个减数分裂雌核发育（meiotic gynogenesis）家系为材料，采用双酶切限制性位点关联DNA测序（ddRADseq）开发单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，旨在达成三个目标：（1）验证该减数分裂雌核发育家系不存在父本遗传贡献；（2）基于该家系构建基因-着丝粒图谱（gene-centromere map）；（3）筛选可区分有丝分裂雌核发育个体与减数分裂雌核发育个体的端粒标记（telomeric markers）——后者有时会在有丝分裂雌核发育家系中自发产生。
本研究的实验材料为包含79个子代个体的单个减数分裂雌核发育家系，经Illumina测序并截短至148bp的4200万条测序读段，共解析得到6866个唯一的RAD标签（RAD-tags）。所鉴定出的340个父本信息性SNP标记，证实该家系确实不存在父本遗传贡献。基于24个连锁群（linkage group, LG；2n=48）中的804个母本信息性SNP标记，本研究构建了总长度为1251.02 cM的基因-着丝粒图谱——初始连锁群分组基于欧洲海鲈基因组组装版本dicLab v1完成。在24个连锁群中，有18个可通过各连锁群的杂合性（heterozygosity）模式清晰辨识出染色体臂结构；剩余6个连锁群则存在异常，该异常疑似与基因组组装过程中的问题相关。
全基因组水平的筛选，为本研究中所用雌核发育家系的构建提供了充分的验证依据。
该减数分裂雌核发育家系中存在大量具有高杂合度的端粒及亚端粒标记，这表明此类标记可用于清晰区分减数分裂雌核发育个体与有丝分裂雌核发育个体。