Fine mapping and candidate gene analysis of flesh browning in pear (Pyrus L.)

Flesh browning significantly affects the quality of fresh pear and causes great waste and commercial losses of pear products. However, the inheritance of genetic factors controlling flesh browning in pear remains largely unknown. In this study, a mapping population from a cross between the browning cultivar 'Mantianhong' and the nonbrowning cultivar 'Hongxiangsu' was utilized. The browning degree of pear flesh was evaluated in successive years in 2020 and 2021, and the results fit a normal distribution. Using the QTL mapping approach, the major quantitative trait loci (QTL) associated with pear browning were identified on chromosome 2 (Chr 2), with a minor QTL on chromosome 17 (Chr 17). The QTL on Chr 2 showed a high confidence level (LOD > 10). In 2020, the interval length of the QTL was 48.301 cM, from 43.476 cM (LOD = 4.0) to 91.768 cM (LOD = 10.58), and contained 72 markers. The peak LOD value was 15.06, the percentage of total phenotypic variance explained was 49.98%, and the contribution rate was 65.6%. In 2021, the interval length of the QTL was 49.292 cM, from 43.476 cM (LOD = 4.68) to 92.768 cM (LOD = 6.32), and contained 76 markers. The peak LOD value was 13.77, the percentage of total phenotypic variance explained was 86.84%, and the contribution rate was 38.6%. To further delineate the QTL interval on Chr 2, 93 indel markers were designed for analysis, and 21 pairs showed polymorphism in the progeny. A total of 41 candidate genes were identified within the fine mapping QTL range on Chr 2. To further identify the candidate genes controlling flesh browning in pear, RNA-seq analysis was performed using three browning individuals and three nonbrowning individuals at three different times after cutting. The results showed that there were three candidate genes on Chr 2 and one candidate genes on Chr 17, and the expression levels of these four genes were analyzed. Gene expression analyses suggested that Pear_-GLEAN_10026026 (acyl-activating enzyme 1, peroxisomal) and Pear_GLEAN_10026027 (protein stritosidine synthase-like 5-like) may be involved in the regulation of pear flesh browning. Taken together, these findings will facilitate marker-assisted breeding for flesh browning in pear and provide a foundation for mining genes related to flesh browning.