Wildtype fruit of cultivated strawberry (Fragaria × ananassa) are typically soft and highly perishable when fully ripe. The development of firm-fruited cultivars by phenotypic selection has greatly increased shelf life, decreased post-harvest perishability, and driven the expansion of strawberry production worldwide. Hypotheses for the firm-fruited phenotype include mutations affecting the expression of genes encoding polygalacturonases that soften fruit by degrading cell wall pectins. Here we show that loss-of-function mutations in the fruit softening gene POLYGALACTURONASE1 (FaPG1; PG1-6A1) double fruit firmness in strawberry. PG1-6A1 was one of three tandemly duplicated polygalacturonase genes found to be in linkage disequilibrium with a quantitative trait locus affecting fruit firmness on chromosome 6A. PG1-6A1 was strongly expressed in soft-fruited (wildtype) homozygotes and weakly expressed in firm-fruited (mutant) homozygotes. Genome-wide association, quantitative trait transcript, DNA sequence, and expression-QTL analyses identified genetic variants in linkage disequilibrium with PG1-6A1 that were positively correlated with fruit firmness and negatively correlated with PG1-6A1 expression. An Enhancer/Suppressor-mutator (En/Spm) transposable element insertion was discovered upstream of PG1-6A1 in mutant homozygotes that we hypothesize transcriptionally downegulates the expression of PG1-6A1. The PG1-6A1 locus was incompletely dominant and explained 26-76% of the genetic variance for fruit firmness among phenotypically diverse individuals. Additional loci are hypothesized to underlie the missing heritability. Highly accurate codominant genotyping assays were developed for modifying fruit firmness by marker-assisted selection of the En/Spm insertion and SNPs associated with the PG1-6A1 locus.

中文翻译：

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草莓果实软化基因功能丧失突变POLYGALACTURONASE1果实硬度增加一倍


栽培草莓 （Fragaria × ananassa） 的野生型果实在完全成熟时通常很软且极易腐烂。通过表型选择开发结实果实的栽培品种大大延长了保质期，降低了收获后易腐烂性，并推动了全球草莓生产的扩张。硬果表型的假说包括影响编码多半乳糖醛酸酶的基因表达的突变，这些基因通过降解细胞壁果胶来软化果实。在这里，我们表明水果软化基因的功能丧失突变POLYGALACTURONASE1 （FaPG1;PG1-6A1） 草莓中的双果实硬度。PG1-6A1 是发现的三个串联重复的多半乳糖醛酸酶基因之一，与影响 6A 染色体上果实硬度的数量性状基因座处于连锁不平衡状态。PG1-6A1 在软果（野生型）纯合子中强表达，在硬果（突变）纯合子中弱表达。全基因组关联、数量性状转录本、DNA 序列和表达 QTL 分析确定了与 PG1-6A1 连锁不平衡的遗传变异，这些变异与果实硬度呈正相关，与 PG1-6A1 表达呈负相关。在突变纯合子中发现增强子/抑制因子突变体 （En/Spm） 转座因子插入 PG1-6A1 的上游，我们假设转录下调 PG1-6A1 的表达。PG1-6A1 位点不完全显性，解释了表型不同个体中果实硬度遗传变异的 26-76%。假设额外的基因座是缺失遗传力的基础。 开发了高度准确的共显性基因分型分析，用于通过标记辅助选择与 PG1-6A1 基因座相关的 En/Spm 插入和 SNP 来修饰果实硬度。