A metabolic perspective of selection for fruit quality related to apple domestication and improvement

Abstract

Background Apple is an economically important fruit crop. Changes in metabolism accompanying human-guided evolution can be revealed using a multiomics approach. We perform genome-wide metabolic analysis of apple fruits collected from 292 wild and cultivated accessions representing various consumption types. Results We find decreased amounts of certain metabolites, including tannins, organic acids, phenolic acids, and flavonoids as the wild accessions transition to cultivated apples, while lysolipids increase in the “Golden Delicious” to “Ralls Janet” pedigree, suggesting better storage. We identify a total of 222,877 significant single-nucleotide polymorphisms that are associated with 2205 apple metabolites. Investigation of a region from 2.84 to 5.01 Mb on chromosome 16 containing co-mapping regions for tannins, organic acids, phenolic acids, and flavonoids indicates the importance of these metabolites for fruit quality and nutrition during breeding. The tannin and acidity-related genes Myb9-like and PH4 are mapped closely to fruit weight locus fw1 from 3.41 to 3.76 Mb on chromosome 15, a region under selection during domestication. Lysophosphatidylethanolamine (LPE) 18:1, which is suppressed by fatty acid desaturase-2 (FAD2), is positively correlated to fruit firmness. We find the fruit weight is negatively correlated with salicylic acid and abscisic acid levels. Further functional assays demonstrate regulation of these hormone levels by NAC-like activated by Apetala3/Pistillata (NAP) and ATP binding cassette G25 (ABCG25), respectively. Conclusions This study provides a metabolic perspective for selection on fruit quality during domestication and improvement, which is a valuable resource for investigating mechanisms controlling apple metabolite content and quality.

High red/far-red ratio promotes root colonization ofSerratia plymuthicaA21-4 in tomato by root exudates-stimulated chemotaxis and biofilm formation

“…Tomato plants with or without A21-4 inoculation were grown on half Hoagland's nutrient solution under low or high R/FR ratio conditions for 1 day,and then the nutrient solutions were were collected,lyophilized and stored at -80 °C.Each treatment contained five replicates and each replicate included four plants.For sample preparation and extraction,the samples were thawed from the refrigerator at -80 °C and mixed with vortex for 10 s.23 mL of the sample was taken after mixing,placed in 50mL of the centrifuge tube, then immersed in liquid nitrogen as a whole and put into the lyophilizer until the samples were completely frozen.After that the samples were dissolved with 0.5 ml 70% methanol internal standard extract,scrolled for 3 min and then centrifuged (12000 r/min, 4 °C) for 10 min.The supernatant was filtered with a microporous filter membrane (0.22 μm) and stored in a sample flask for ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) test.The primary metabolome of tomato root exudates was performed using the non-targeted metabolome method at Metware Biotechnology Co., Ltd. (Wuhan, Hubei, China) as recently reported (Lin et al, 2023).…”

Comparative Analysis of Metabolic Variation in Eggplant Fruit of Different Varieties Reveals Metabolites Important for Quality Traits

“…Changes in fatty acyl chains that result in more rapid lysophospholipid accumulation are associated with date fruit ripening and softness [27], and glycerophospholipid metabolism was shown to be closely associated with the softening of pears at both the transcriptomic and metabolic level [27]. In apple, LPE18:1 was reported to be positively correlated to fruit firmness [29]. In addition, lipids are the main precursors of flavor substances and volatile organic compounds in fruit [23].…”

Metabolomics to understand metabolic regulation underpinning fruit ripening, development, and quality

“…Much of this work has also been carried out in tomato with particularly notable studies being those of the Klee group, defining the genetics that underlie the taste of tomato fruit ( Tieman et al , 2017 ; Klee and Tieman, 2018 ), and those of the Martin group, evaluating nutritionally important components of tomato ( Zhang et al , 2015 ; Martin and Li, 2017 ; Butelli et al , 2019 ; Li et al , 2022 ). However, work has extended well beyond this species, with studies recently focusing on the change of crop chemical composition during the domestication of a wide range of species ( Alseekh et al , 2021b ) including the fruit species tomato ( Zhu et al , 2018 ), melon ( Ren et al , 2021 ; Yuan et al , 2023 ), jejube ( Zhang et al , 2022 ), peach ( Cao et al , 2022 ), pummelo ( Zheng et al , 2023 ), apple ( Lin et al , 2023 ), citrus ( Wang et al , 2017 ), and watermelon ( Yuan et al , 2023 ). These changes, whilst very much species-specific, were general in that they frequently reduced the accumulation of bitter-tasting substances ( Alseekh et al , 2021b ).…”