A genome-wide association study (GWAS) and quantitative trait loci (QTL) analysis using two bi-parental (parental cultivars Smooth Cayenne and MD-2) pineapple seedling populations segregating for spiny and spiny-tip leaf margin and 12 wild and pre-Columbian domesticated genotypes were used to identify single nucleotide polymorphism (SNP) and silicoDArT markers associated with the spiny-tip leaf margin phenotype in pineapple. One QTL between the nucleotide positions 14,355,639 and 14,368,806 on linkage group six (LG06) was identified using SNP markers and one QTL between the nucleotide positions 14,330,844 and 14,346,378 using silicoDArT markers. GWAS and QTL analysis methods identified the same most significantly associated SNP and silicoDArT markers. The most significantly associated SNP and silicoDArT markers were positioned at 14,355,639 and 14,341,745 bp respectively, on or very near, a zeaxanthin epoxidase (ZEP) gene, a key gene in the abscisic acid (ABA) pathway. Other associated genes with a high significance by GWAS analysis using at least two algorithms include a detoxification 33-like (DTX) and a resistance gene analog (RGA2-like). It is proposed that a polymorphism in the putative ZEP gene is the main causal variant associated with the spiny-tip leaf margin in ‘Smooth Cayenne’ pineapple and its descendants including ‘MD-2’.

中文翻译：

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与菠萝刺叶边缘相关的DArTseq分子标记

全基因组关联研究（GWAS）和定量性状基因座（QTL）分析，使用两个双亲（亲本品种平滑卡宴和MD-2）菠萝幼苗种群进行刺棘和刺尖叶缘分离，以及12个野生和前叶哥伦比亚驯化的基因型用于鉴定与菠萝多刺叶缘表型相关的单核苷酸多态性（SNP）和silicoDArT标记。使用SNP标记鉴定了第六个连锁组（LG06）上核苷酸位置14,355,639和14,368,806之间的一个QTL，使用silicoDArT标记鉴定了核苷酸位置14,330,844和14,346,378之间的一个QTL。GWAS和QTL分析方法鉴定出了最相关的SNP和silicoDArT标记。与SNP和silicoDArT相关性最强的标记分别位于14,355,639和14 玉米黄质环氧化酶（ZEP）基因（脱落酸（ABA）途径中的关键基因）上或附近的341,745 bp。通过使用至少两种算法的GWAS分析，其他具有重要意义的相关基因包括排毒33样（DTX）和抗性基因类似物（RGA2样）。有人提出，假定的ZEP基因多态性是与“光滑卡宴”菠萝及其后代包括“ MD-2”的刺尖叶缘相关的主要因果变异。