Pear (Pyrus spp.) is one of the most common fruit crops grown in temperate regions worldwide. Genetic enhancement of fruit quality is a fundamental goal of pear breeding programs. The genetic control of pear fruit quality traits is highly quantitative, and development of high-density genetic maps can facilitate fine-mapping of quantitative trait loci (QTLs) and gene identification. Bin-mapping is a powerful method of constructing high-resolution genetic maps from large-scale genotyping datasets. We performed whole-genome sequencing of pear cultivars ‘Niitaka’ and ‘Hongxiangsu’ and their 176 F₁ progeny to identify genome-wide single-nucleotide polymorphism (SNP) markers for constructing a high-density bin-map of pear. This analysis yielded a total of 1.93 million SNPs and a genetic bin-map of 3190 markers spanning 1358.5 cM, with an average adjacent interval of 0.43 cM. This bin-map, along with other high-density genetic maps in pear, improved the reference genome assembly from 75.5 to 83.7% by re-anchoring the scaffolds. A quantitative genetic analysis identified 148 QTLs for 18 fruit-related traits; among them, QTLs for stone cell content, several key monosaccharides, and fruit pulp acids were identified for the first time in pear. A gene expression analysis of six pear cultivars identified 399 candidates in the identified QTL regions, which showed expression specific to fruit developmental stages in pear. Finally, we confirmed the function of PbrtMT1, a tonoplast monosaccharide transporter-related gene responsible for the enhancement of fructose accumulation in pear fruit on linkage group 16, in a transient transformation experiment. This study provides genomic and genetic resources as well as potential candidate genes for fruit quality improvement in pear.

Harvest index (HI) is a complex and vital agronomic trait that is closely related to the economic benefits of rapeseed. In this study, we measured the HI and 13 HI-related agronomic traits of 104 core breeding lines of rapeseed during 3 years and sequenced the populations using the Bnapus50K array. The phenotypic analyses showed the complex connections among HI and other traits. A total of 212 significant SNPs related to the traits and 22 stable SNPs were identified. Four SNPs, A01_1783685 (PH and SYP), C06_26638717 (PH and NSS), C03_4731660 (MIL and MINS), and C09_36899682 (PH and BYP), were identified as potential pleiotropic loci. Compared to previous reports, 49 consensus loci were obtained that were related to PH, TSW, NSP, BAI, NSS, SL, BN, MINS, SYP, and BYP. Twelve stable SNPs were detected as promising novel loci related to BN (A05_19368584 and A05_19764389), SL (A06_23598999, A06_23608274, and C07_38735522), PH (C04_47349279, C04_47585236, and C09_36899680), MINS (C05_6251826), NSS (C06_22559430 and C06_22570315), and HI (C05_6554451). In addition, 39 putative genes were identified in the candidate intervals. This study provides novel insights into the genetic mechanisms of HI and HI-related traits, and lays a foundation for molecular marker development and casual gene cloning to improve the harvest index of rapeseed.

Polyembryonic maize, capable of producing multiple seedlings from a single kernel, holds great potential value in agricultural and industrial applications, but the seedling quality needs to be improved. In this study, seedlings of two waxy maize (Zea mays L. sinensis Kulesh) inbred lines, D35 (a polyembryonic line with twin shoots) and N6110 (single-shoot), exhibited similar relative growth rates during 1 to 5 days post-germination. UPLC-MS/MS profiling of 3- to 5-day-old seedling roots and shoots revealed that H2JA, MeSAG, and IAA-Val-Me were the common differentially accumulated metabolites (DAMs) of the 3-day-old vs. 5-day-old seedlings of D35 and N6110 in the same tissues, and MeSAG, tZ9G, cZROG, and DHZROG were identified in D35 vs. N6110 across the same tissues and the same periods. RNA-seq analyses showed various processes involved in seedling development, including DNA replication initiation, rhythmic processes, the cell cycle, secondary metabolic processes, and hormone biosynthetic regulation. The differentially expressed genes (DEGs) between D35 and N6110 were significantly enriched in organic hydroxy compound biosynthetic, alcohol biosynthetic, organic hydroxy compound metabolic, abscisic acid biosynthetic, and apocarotenoid biosynthetic processes. The KEGG-enriched pathways of DAMs and DEGs identified that AUX1, AHP, A-ARR, JAR1, SIMKK, ERF1, and GID2 might be conserved genes regulating seedling growth. The integrated analyses revealed that 98 TFs were potentially associated with multiple hormones, and 24 of them were identified to be core genes, including 11 AP2/ERFs, 4 Dofs, 2 bZIPs, 2 MADS-box genes, 2 MYBs, 1 GATA, 1 LOB, and 1 RWP-RK member. This study promotes a valuable understanding of the complex hormone interactions governing twin-shoot seedling growth and offers potential targets for improving crop establishment via seedling quality.

The leaf plastochron serves as an indicator of the rate of leaf appearance, biomass accumulation, and branch number, while also impacting plant architecture and seed yield. However, research on the leaf plastochron of crops remains limited. In this study, 2116C exhibited a rapid leaf plastochron compared to ZH18 during both rosette and bud periods. There were significant positive correlations among the leaf plastochron and primary branch number of the F₂ populations (r ranging from 0.395 to 0.635, p < 0.01). Genetic analyses over two years demonstrated that two equally dominant genes might govern the leaf plastochron. Through bulk segregant analysis sequencing (BSA-seq), three novel genomic intervals were identified on chromosomes A02 (9.04–9.48 Mb and 13.52–13.66 Mb) and A04 (19.84–20.14 Mb) of ZS11 and Darmor-bzh reference genomes. By gene functional annotations, single-nucleotide variation (SNV) analyses, transcriptome data from parents, genetic progeny, and natural accessions, we identified ten candidate genes within the intervals, including FLOWERING LOCUS T, RGL1, MYB-like, CYP96A8, BLH3, NIT2, ASK6, and three CLAVATA3/ESR (CLE)-related genes. These findings lay the molecular foundation for further exploration into the leaf plastochron and the implications in plastochron-related breeding in rapeseed.