Intricate genetic variation networks control the adventitious root growth angle in apple

Identification and characterization of CmPP2C31 playing a positive role in the abiotic stress resistance of Chinese chestnut via an integrated strategy

Chinese chestnut (Castanea mollissima Blume) is an important economic forest tree species and mainly cultivated in mountainous areas and wastelands, subjecting it to various abiotic stresses. The protein phosphatase 2C (PP2C) genes contributes largely to stress responses in plants. However, the characteristics and functions of PP2C genes in C. mollissima remain unknown. This study provides comprehensive analyses (including phylogenetic, synteny, RNA-seq, transgenic and yeast one-hybrid methods) revealing the characteristics of CmPP2C gene, which plays an important role in response to abiotic stress. Here, we identified 68 CmPP2Cs in the Chinese chestnut genome, and analyzed their characteristics and phylogenetic relationships. Furthermore, synteny analysis revealed that segmental and tandem duplication drove the expansion of the CmPP2C family to adapt to natural environmental pressures. RNA sequencing and co-expression analyses indicated that four hub CmPP2Cs in two key modules probably play important roles in the resistance to abiotic stress in chestnut. Among them, CmPP2C31 was significantly down-regulated under drought stress. Transgenic experiments via pollen magnetofection revealed that CmPP2C31 could positively and significantly regulate the drought resistance of Chinese chestnut seedlings. Subcellular localization showed that CmPP2C31 was a nuclear protein. Yeast one-hybrid assays suggested that EVM0007407 could regulate CmPP2C31 expression by binding to its promoter, thereby participating in abiotic stress resistance. These findings in our study provided detailed information on the CmPP2C family genes and laid a foundation for further elucidating the molecular mechanism of resistance to abiotic stress chestnut.

Genetic variations in MdSAUR36 participate in the negative regulation of mesocarp cell division and fruit size in Malus species

Final fruit size of apple (Malus domestica) cultivars is related to both mesocarp cell division and cell expansion during fruit growth, but it is unclear whether the cell division and/or cell enlargement determine most of the differences in fruit size between Malus species. In this study, by using an interspecific hybrid population between Malus asiatica "Zisai Pearl" and Malus domestica cultivar "Red Fuji," we found that the mesocarp cell number was the main causal factor of diversity in fruit size between Malus species. Rapid increase in mesocarp cell number occurred prior to 28 days after anthesis (DAA), while cell size increased gradually after 28 DAA until fruit ripening. Six candidate genes related to auxin signaling or cell cycle were predicted by combining the RNA-seq data and previous QTL data for fruit weight. Two InDels and 10 SNPs in the promoter of a small auxin upregulated RNA gene MdSAUR36 in Zisai Pearl led to a lower promoter activity than that of Red Fuji. One non-synonymous SNP G/T at 379 bp downstream of the ATG codon of MdSAUR36, which was heterozygous in Zisai Pearl, exerted significant genotype effects on fruit weight, length, and width. Transgenic apple calli by over-expressing or RNAi MdSAUR36 confirmed that MdSAUR36 participated in the negative regulation of mesocarp cell division and thus apple fruit size. These results could provide new insights in the molecular mechanism of small fruit size in Malus accession and be potentially used in molecular assisted breeding via interspecific hybridization.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01441-4.

A single QTL harboring multiple genetic variations leads to complicated phenotypic segregation in apple flesh firmness and crispness

Within a QTL, the genetic recombination and interactions among five and two functional variations at MdbHLH25 and MdWDR5A caused much complicated phenotype segregation in apple FFR and FCR. The storability of climacteric fruit like apple is a quantitative trait. We previously identified 62 quantitative trait loci (QTLs) associating flesh firmness retainability (FFR) and flesh crispness retainability (FCR), but only a few functional genetic variations were identified and validated. The genetic variation network controlling fruit storability is far to be understood and diagnostic markers are needed for molecular breeding. We previously identified overlapped QTLs F16.1/H16.2 for FFR and FCR using an F1 population derived from 'Zisai Pearl' × 'Red Fuji'. In this study, five and two single-nucleotide polymorphisms (SNPs) were identified on the candidate genes MdbHLH25 and MdWDR5A within the QTL region. The SNP1 A allele at MdbHLH25 promoter reduced the expression and SNP2 T allele and/or SNP4/5 GT alleles at the exons attenuated the function of MdbHLH25 by downregulating the expression of the target genes MdACS1, which in turn led to a reduction in ethylene production and maintenance of higher flesh crispness. The SNPs did not alter the protein-protein interaction between MdbHLH25 and MdWDR5A. The joint effect of SNP genotype combinations by the SNPs on MdbHLH25 (SNP1, SNP2, and SNP4) and MdWDR5A (SNPi and SNPii) led to a much broad spectrum of phenotypic segregation in FFR and FCR. Together, the dissection of these genetic variations contributes to understanding the complicated effects of a QTL and provides good potential for marker development in molecular breeding.

MdWOX4-2 modulated MdLBD41 functioning in adventitious shoot of apple (Malus domestica)

Apple (Malus domestica Borkh.) is not only an important fruit crop distributed worldwide, but also a common model plant. However, the lack of efficient genetic transformation procedures for apples limits the in-depth studies of their gene functions. Although leaf-regenerated adventitious shoots (LRAS) are a prerequisite for successful genetic transformation of apple, little is known about the underlying molecular mechanism of LRAS. Here, we identified the WUSCHEL-related homeobox (WOX) transcription factor in apple, MdWOX4-2, which was a transcriptional activator. Gene expression as well as morphological and histological observations revealed that MdWOX4-2 is involved in the development of LRAS. Overexpression of MdWOX4-2 conferred higher regenerative capacity in transgenic tobacco (Nicotiana tabacum) as compared to the wild type (WT). The combined results of the yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA), dual luciferase assays, and transient transactivation assay, revealed that MdWOX4-2 directly bound to and activated the MdLBD41 promoter. Moreover, transgenic experiments further demonstrated that MdLBD41 could significantly enhance the formation of adventitious shoot in transgenic tobacco. Collectively, our findings demonstrate that MdWOX4-2 is important for regulating the LRAS development by activating MdLBD41.

A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple

INTRODUCTION

Genomic heterozygosity, self-incompatibility, and rich-in somatic mutations hinder the molecular breeding efficiency of outcrossing plants.

OBJECTIVES

We attempted to develop an efficient integrated strategy to identify quantitative trait loci (QTLs) and trait-associated genes, to develop gene markers, and to construct genomics-assisted prediction (GAP) modes.

METHODS

A novel protocol, bulked segregant analysis tool for out-crossing species (BSATOS), is presented here, which is characterized by taking full advantage of all segregation patterns (including AB × AB markers) and haplotype information. To verify the effectiveness of the protocol in dealing with the complex traits of outbreeding species, three apple cross populations with 9,654 individuals were adopted.

RESULTS

By using BSATOS, 90, 60, and 77 significant QTLs were identified successfully and candidate genes were predicted for apple fruit weight (FW), fruit ripening date (FRD), and fruit soluble solid content (SSC), respectively. The gene-based markers were developed and genotyped for 1,396 individuals in a training population, including 145 Malus accessions and 1,251 F1 plants of the three full-sib families. GAP models were trained using marker genotype effect estimates of the training population. The prediction accuracy was 0.7658, 0.6455, and 0.3758 for FW, FRD, and SSC, respectively.

CONCLUSION

The BSATOS and GAP models provided a convenient and efficient methodology for candidate gene mining and molecular breeding in out-crossing plant species. The BSATOS pipeline can be freely downloaded from: https://github.com/maypoleflyn/BSATOS.