Two apple rootstock genotypes G.935 and B.9 were recently demonstrated to exhibit distinct resistance responses following infection by Pythium ultimum. As part of an effort to elucidate the genetic regulation of apple root resistance to soilborne pathogens, preinoculation transcriptome variations in roots of these two apple rootstock genotypes are hypothesized to contribute to the observed disease resistance phenotypes. Results from current comparative transcriptome analysis demonstrated elevated transcript abundance for many genes which function in a system-wide defense response in the root tissue of the resistant genotype of G.935 in comparison with susceptible B.9. Based on the functional annotation, these differentially expressed genes encode proteins that function in several tiers of defense responses, such as pattern recognition receptors for pathogen detection and subsequent signal transduction, defense hormone biosynthesis and signaling, transcription factors with known roles in defense activation, enzymes of secondary metabolism, and various classes of resistance proteins. The data set suggested a more poised status, which is ready to defend pathogen infection, in the root tissues of resistant genotype of G.935, compared to the susceptible B.9. The significance of preformed defense in the absence of a pathogen toward overall resistance phenotypes in apple root and the potential fitness cost due to the overactivated defense system were discussed.

Apple replant disease (ARD) is a worldwide problem that threatens the industry. However, the genetic mechanism underlying plant disease resistance against ARD remains unclear. In this study, a negative regulatory microRNA in Malus domestica, mdm-miR397b \, and its direct target MdLAC7b (Laccase) was selected for examination based on our previous small RNA and degradome sequencing results. Overexpressing the mdm-miR397b-MdLAC7b module altered the lignin deposition and JA contents in apple roots, which also led to increased resistance to Fusarium solani. Additionally, Y1H library screening using mdm-miR397b promoter recombinants identified a transcription factor, MdERF61, that represses mdm-miR397b transcriptional activity by directly binding to two GCC-boxes in the mdm-miR397b promoter. In summary, our results suggest that the MdERF61-mdm-miR397b-MdLAC7b module plays a crucial role in apple resistance to F. solani and offers insights for enhancing plant resistance to soilborne diseases in apple.

Plant resistance responses against invading pathogens require a coordinated set of cellular processes to optimize the effective defense output. Previous transcriptome analyses have identified a multi-phase and multi-layered defense strategy in apple root towards infection from a necrotrophic oomycete pathogen Pythium ultimum. Among the identified apple genes, members of the laccase gene family represent an actively regulated group at both transcriptional and posttranscriptional levels. In this study, several apple laccase genes were selected for further analyses on their sequence features and potential roles during defense activation in apple roots. Their bioinformatic specifics, genotype-specific induction, and lignin deposition patterns during pathogen infection were examined between two apple rootstock genotypes, a resistant O3R5-#161 and a susceptible O3R5-#132. The sequences these laccase genes contain the conserved cu-oxidase domains and the characteristic gene structures with MdLAC7a as an exception. While MdLAC3 and MdLAC5 showed a partial induction to P. ultimum infection, both MdLAC7a and MdLAC7b genes demonstrated consistent and high-level inducibility. Moreover, MdLAC7b exhibited a differential expression pattern, with a higher expression in the resistant O3R5-#161. Lignin deposition appeared to be stronger in the infected root of the resistant genotype compared to that of the susceptible one. The efficient lignin biosynthesis and deposition at the initial stage of infection is crucial for impeding the progression of this fast-growing necrotrophic pathogen. Future study regarding the role of MdLAC7b, including the transgenic manipulation and biochemical analysis, should provide more definitive evidence for its contribution to resistance to P. ultimum infection.

Apple is a major fruit crop grown worldwide and provides humans with an essential diet and health benefits. One of the health benefits is related to the accumulation of fruit anthocyanin, which also provides fruit with an attractive red colour. It is known that an MdMYB10 allele containing a transposable element (TE) insertion in its promoter (termed Red-TE allele) underlies anthocyanin accumulation and red colouration in the fruit skin of cultivated apples. However, the distribution of this Red-TE allele in wider Malus germplasm accessions is not clear. In this study, we showed that MdMYB10 RNA in fruit skin was specifically expressed from the Red-TE allele by using allele-specific expression analysis of transcriptome data. Apple cultivars and hybrids with homozygous Red-TE alleles showed stronger red colour than those with heterozygous alleles after analysing 65 cultivars and 337 hybrids. Furthermore, both hetero- and homozygous plants growing in the same high-temperature conditions had different colourations. However, the Red-TE allele was not detected in 16 wild apple accessions showing red skin, indicating that the red skin colour of these wild apples was not conferred by the Red-TE allele. These findings provide guidance for selecting cultivars able to develop consistent red colouration under high growth temperature conditions and open the opportunity for identifying novel genetic variants underpinning fruit red colouration in wild apple species.