Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa.
Mondi South Africa, Forests Operations, Research and Development Department, Trahar Technology Centre-TTC, PO Box 12, Hilton 3245, South Africa.
Plant Cell Physiol. 2020 Jul 1;61(7):1285-1296. doi: 10.1093/pcp/pcaa057.
The galling insect, Leptocybe invasa, causes significant losses in plantations of various Eucalyptus species and hybrids, threatening its economic viability. We applied a genome-wide association study (GWAS) to identify single-nucleotide polymorphism (SNP) markers associated with resistance to L. invasa. A total of 563 insect-challenged Eucalyptus grandis trees, from 61 half-sib families, were genotyped using the EUChip60K SNP chip, and we identified 15,445 informative SNP markers in the test population. Multi-locus mixed-model (MLMM) analysis identified 35 SNP markers putatively associated with resistance to L. invasa based on four discreet classes of insect damage scores: (0) not infested, (1) infested showing evidence of oviposition but no gall development, (2) infested with galls on leaves, midribs or petioles and (3) stunting and lethal gall formation. MLMM analysis identified three associated genomic regions on chromosomes 3, 7 and 8 jointly explaining 17.6% of the total phenotypic variation. SNP analysis of a validation population of 494 E. grandis trees confirmed seven SNP markers that were also detected in the initial association analysis. Based on transcriptome profiles of resistant and susceptible genotypes from an independent experiment, we identified several putative candidate genes in associated genomic loci including Nucleotide-binding ARC- domain (NB-ARC) and toll-interleukin-1-receptor-Nucleotide binding signal- Leucine rich repeat (TIR-NBS-LRR) genes. Our results suggest that Leptocybe resistance in E. grandis may be influenced by a few large-effect loci in combination with minor effect loci segregating in our test and validation populations.
令人烦恼的昆虫，Leptocybe invasa，对各种桉树物种和杂种的种植园造成了重大损失，威胁到其经济可行性。我们应用全基因组关联研究（GWAS）来鉴定与 L. invasa 抗性相关的单核苷酸多态性（SNP）标记。总共对来自 61 个半同胞家系的 563 棵受昆虫侵袭的巨桉进行了基因型分型，使用 EUChip60K SNP 芯片鉴定了测试群体中的 15445 个信息性 SNP 标记。多基因混合模型（MLMM）分析基于四个离散的昆虫损伤评分类别（0）未受侵袭、（1）受侵袭但未发现产卵迹象、（2）受侵袭但叶片、中脉或叶柄上有虫瘿、（3）生长受阻和致命的虫瘿形成，鉴定了与 L. invasa 抗性相关的 35 个 SNP 标记。MLMM 分析鉴定了三个位于染色体 3、7 和 8 上的共同解释总表型变异 17.6%的关联基因组区域。对 494 棵巨桉的验证群体的 SNP 分析证实了在初始关联分析中也检测到的七个 SNP 标记。基于来自独立实验的抗性和敏感基因型的转录组谱，我们在关联基因组位点中鉴定了几个可能的候选基因，包括核苷酸结合 ARC- 结构域（NB-ARC）和 Toll-白细胞介素-1-受体-核苷酸结合信号-亮氨酸丰富重复（TIR-NBS-LRR）基因。我们的结果表明，巨桉中的 Leptocybe 抗性可能受少数几个大效应位点与我们测试和验证群体中分离的小效应位点的共同影响。
