Whole-Genome Re-Sequencing of Corylus heterophylla Blank-Nut Mutants Reveals Sequence Variations in Genes Associated With Embryo Abortion
Whole-Genome Re-Sequencing of Corylus heterophylla Blank-Nut Mutants Reveals Sequence Variations in Genes Associated With Embryo Abortion
复制标题
榛子空白坚果突变体的全基因组重测序揭示了与胚胎流产相关的基因的序列变异
DOI：
10.3389/fpls.2019.01465
复制
发表时间：
2019-11-13
影响因子：
5.6
通讯作者：
Liu, Jianfeng
中科院分区：
文献类型：
--
作者：
Cheng, Yunqing;Jiang, Siqi;Liu, Jianfeng
榛子（Corylus spp.）通过频繁形成毛坯螺母而发生。虽然这种情况与胚胎流产有关，但我们尚未确定涉及的调控基因。因此，本研究旨在确定榛子胚胎败育相关基因。我们对4株榛子突变体（Empty 1 ~ Empty 4、C. heterophylla）的种子和四个野生型树（Full 1至Full 4，C. heterophylla）。对Empty 1与Full 1、Empty 2与Full 2、Empty 3与Full 3、Empty 4与Full 4进行配对比较，沿着加上Empty 1与Empty 4的交叉点，共发现3 081个SNP。其中，外显子区域的215个同义SNP分布在178个候选基因中。杂合性分析表明，样本的平均纯合和杂合SNP比率分别为0.409和0.591。根据Gene Ontology的分类，候选基因主要集中在结合、催化、分子转导、转运和分子功能调节等方面。其中，178个基因中有18个在Empty 1 -4中具有纯合SNP。在淀粉合成酶4（SS 4）的启动子区的顺式元件含有RY元件，这意味着种子特异性表达。空1 -4子叶细胞中不存在淀粉颗粒，而在Full 1-Full 4子叶细胞中大量存在淀粉颗粒。空坚果表型具有较重的坚果壳。总的来说，我们得出结论，乙酰辅酶A羧化酶1（ACC 1），细胞内钠/氢交换器2（NHX 2），UDP-糖基转移酶74 E2（UGT 74 E2），分生组织沉默缺陷3（DMS 3），解毒43（FRD 3）和SS 4的单核苷酸变体可能诱导胚胎流产，导致空坚果形成。我们的研究结果将有利于未来的研究如何获得或丢失的候选基因影响种子发育。此外，我们的研究为无核品种的开发提供了新的前景。
Yield loss in the economically important hazelnut (Corylus spp.) occurs through the frequent formation of blank nuts. Although the condition is associated with embryo abortion, we have not yet identified the regulatory genes involved. Therefore, this study aimed to determine the genes related to embryo abortion in hazel. We performed whole-genome re-sequencing and single-nucleotide polymorphism (SNP) analysis on four mutant hazelnut trees (Empty1 to Empty4, C. heterophylla) bearing blank nuts and four wild-type trees (Full1 to Full4, C. heterophylla). A paired comparison of Empty1 vs. Full1, Empty2 vs. Full2, Empty3 vs. Full3, and Empty4 vs. Full4, along with the intersection of Empty1 to Empty4, revealed 3 081 common SNPs in the four blank-nut mutants. Of these, 215 synonymous SNPs in exonic regions were distributed across 178 candidate genes. Heterozygosity analysis showed that average homozygous and heterozygous SNP ratios were respectively 0.409 and 0.591 in the samples. According to Gene Ontology classification, candidate genes were enriched in the categories of binding, catalysis, molecular transducer, transporter, and molecular function regulator. Among these, 18 of 178 genes had homozygous SNPs in Empty1–4. Cis elements in the promoter region of starch synthase 4 (SS4) contain the RY-element, implying seed-specific expression. Starch granules were absent from Empty1–4 cotyledon cells, but abundantly present in Full1–Full4 cotyledon cells. The blank-nut phenotype has heavier nut shells. Overall, we conclude that single-nucleotide variants of Acetyl-CoA carboxylase 1 (ACC1), intracellular sodium/hydrogen exchanger 2 (NHX2), UDP-glycosyltransferase 74E2 (UGT74E2), DEFECTIVE IN MERISTEM SILENCING 3 (DMS3), DETOXIFICATION 43 (FRD3), and SS4 may induce embryo abortion, leading to blank-nut formation. Our results will benefit future research on how the gain or loss of candidate genes influences seed development. Moreover, our study provides novel prospects for seedless cultivar development.