Background: Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh.Results: We generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lignocellulose formation in the stone cells of pear fruits. Our data with a total of 35,897 expressed genes and 974,404 SNPs support the identification of seven stone cell formation modules and the detection of 139,515 eQTLs for 3229 genes in these modules. Focusing on regulatory factors and using a co-expression network comprising 39 structural genes, we identify PbrNSC as a candidate regulator of stone cell formation. We then verify the function ofPbrNSCin regulating lignocellulose formation using both pear fruit andArabidopsisplants and further show that PbrNSC can transcriptionally activate multiple target genes involved in secondary cell wall formation.Conclusions: This study generates a large resource for studying stone cell formation and provides insights into gene regulatory networks controlling the formation of stone cell and lignocellulose.

Fruit crops cultivated in almost all countries and regions around the world serve as important agricultural commodities of significant economic value because they contribute to overall food security by providing a diverse food and nutrient supply to sustain human life and human health. Recent advances in high-throughput sequencing technologies offer unprecedented opportunities for pursuing genomic and genetic studies of fruit crops. Here, we will review major advances in fruit crop genome sequencing efforts undertaken over the past 15 years that have contributed to significant accumulation of publicly available genomic resources. We will highlight the expanding pool of genomic data that offer unprecedented opportunities to better unravel the genetic origin and domestication of fruit trees, as well as in deciphering the genetics of important horticultural traits of these fruit trees. Furthermore, we will explore how utilization of these genetic features of fruit trees along with new genomic-assisted tools, including genomic selection and gene editing, are informing and guiding plant geneticists and breeders in moving forward in their fruit crop breeding efforts. Finally, we will outline future prospects and unresolved questions that remain in both genomic research and genetic improvement of fruit crops.

Anthocyanins are important specialized fruit metabolites and major pigments, whose abundance depends on co-regulation of activators and repressors, primarily transcription factors (TFs) of the MYB family. Herein, a KANADI-like TF PuKAN4 was characterized in pear. This TF could be transcriptionally up-regulated by the anthocyanin-related R2R3-MYBs PuMYB10/PuMYB114 and exhibited high expression within red-skinned pears. Interestingly, PuKAN4 repressed anthocyanin biosynthesis in transiently overexpressed pear fruit, and stable transformation in pear calli and tobacco plants. The PuKAN4 had a conserved EAR repression domain in C-terminal, while the repression function of PuKAN4 could be offset by a transcription activation domain VP64. The dual luciferase analysis proved that PuMYB114/PuMYB10 up-regulated expression of PuKAN4. Furthermore, the PuKAN4 could physically interact with PuMYB10/PuMYB114 and did not affect the combination of MYB10/MYB114-bHLH3, as demonstrated by Y2H, pull-down and firefly luciferase complementation. Thus, the PuKAN4 should play the role of active repressor, the formation of PuKAN4-PuMYB10/PuMYB114-PubHLH3 complex inhibited pear anthocyanin biosynthesis. Our findings unveiled an activator-and-repressor feedback loop between PuMYB114/PuMYB10 and PuKAN4, which possibly balance biosynthesis activity and prevents over-accumulation of phenylpropanoids.

Lignified stone cells are a unique feature of pear fruit, significantly affecting fruit texture. Even though some research efforts have already been made, the stone cell formation mechanism is complex, with many aspects yet to be elucidated. Here, through a genome‐wide association analysis of stone cell traits, we identified PbrMADS1 , a member of the SEPALLATA3 (SEP3) subfamily, as a candidate gene specifically expressed in stone cells during early fruit development. Functional studies confirmed that PbrMADS1 promotes stone cell formation; however, it does not directly activate lignin‐related genes. Instead, PbrMADS1 interacts with PbrMYB169, enhancing PbrMYB169's binding to AC elements and amplifying downstream gene activation. Notably, homologous MADS1 and MYB169 proteins from closely related species such as apple and loquat do not form a similar complex. Sequence analysis revealed that the protein sequence of PbrMADS1 contains methionine (M) at the 63 ^rd amino acid position, while apple and loquat homologs carry threonine (T) at the same site. Substituting M with T (PbrMADS1 ^M63T ) weakened its interaction with PbrMYB169 and impaired its function in regulating stone cell formation. This study offers new insights into MADS gene‐mediated stone cell formation and highlights functional divergence within the SEP3 subfamily among apple tribe species of the Rosaceae family.