Identification of polymorphic markers for germplasm conservation of three precious Chinese palace goldfish using whole-genome sequencing

China was the first country in the world to breed goldfish and has generated many unique goldfish varieties, including the most aristocratic Chinese palace goldfish. Due to the lack of scientific research on Chinese palace goldfish, their selection and breeding are mainly carried out through traditional hybridization, leading to serious inbreeding and the degradation of germplasm resources. To this end, whole-genome resequencing was performed to understand the genetic variation among three different varieties (eggpompons, goosehead, and tigerhead) from nine core conserved populations in China. A total of 15 polymorphic SSRs were developed for population genetics, and all tested populations were considered moderately polymorphic with an average polymorphism information content value of 0.4943. Genetic diversity in different varieties showed that all conserved populations were well protected with the potential for continued exploitation. This study provides reliable molecular tools and a basis for designing conservation and management programs in Chinese palace goldfish.

Polyethylene Glycol Priming Enhances the Seed Germination and Seedling Growth of Scutellaria baicalensis Georgi under Salt Stress

Seed priming has become a practical pre-sowing strategy to deal with abiotic stresses. This study aims to explore the effects of polyethylene glycol (PEG) priming on seed germination and seedling growth of Scutellaria baicalensis Georgi under salt stress. Regardless of seed priming, salt stress significantly inhibited the seed germination and seedling growth of S. baicalensis. PEG priming significantly alleviates the inhibitory effects of salt stress on seed germination and seedling growth when compared to non-priming and water priming. Among all treatments, PEG priming exhibited the highest germination rate, germination potential, seed vigor index, fresh weight, dry weight, and plant length; the highest contents of proline, soluble sugar, and soluble protein; the highest K+/Na+ ratio and relative water content; the highest antioxidant activities and contents; but the lowest H2O2, malondialdehyde (MDA) content, and relative electrical conductivity in response to salt stress. In addition, PEG priming had the highest transcript levels of antioxidant-related genes among all treatments under NaCl stress. Taken together, the results demonstrated that seed priming with PEG could be recommended as an effective practice to enhance the germination and early seedling growth of S. baicalensis under saline conditions.

Optimized Pepper Target SNP-Seq Applied in Population Structure and Genetic Diversity Analysis of 496 Pepper (Capsicum spp.) Lines

Peppers are a major vegetable crop worldwide. With the completion of additional genome assemblies, a multitude of single-nucleotide polymorphisms (SNPs) can be utilized for population structure and genetic diversity analysis. In this study, we used target SNP-sequencing as a new high-throughput sequencing technology, screening out 425 perfect SNPs for analyzing the genetic diversity and population structure among 496 pepper lines from five pepper species in China and abroad. The perfect SNP panel exhibited commendable discriminative ability, as indicated by the average values of polymorphism information content, observed heterozygosity, minor allele frequency, and genetic diversity, which were 0.346, 0.011, 0.371, and 0.449, respectively. Based on phylogenetic, population structure, and principal component analyses, 484 C. annuum lines were divided into four subpopulations according to the shape of fruit: blocky fruit, wide-horn fruit, narrow-horn fruit, and linear fruit. These subpopulations displayed clear clustering with minimal or no overlap. Moreover, F statistic (Fst) analysis revealed considerable distinctions among these subpopulations. Additionally, we established a set of 47 core SNPs that could effectively differentiate among all pepper lines. This core SNP set could precisely classify the C. annuum lines into four distinct fruit-shape groups. The blocky and narrow-horn fruit subpopulations displayed the lowest and highest genetic diversity, respectively. This study highlights the importance of fruit shape as a crucial trait in pepper breeding. Moreover, this work indicates the immense potential of optimized target SNP technology in the addition of foreground markers of important traits to improve molecular breeding efficiency, and demonstrates its broad application prospects in the genetic analysis and variety identification of peppers.

CsMLO8/11 are required for full susceptibility of cucumber stem to powdery mildew and interact with CsCRK2 and CsRbohD

Powdery mildew (PM) is one of the most destructive diseases that threaten cucumber production globally. Efficient breeding of novel PM-resistant cultivars will require a robust understanding of the molecular mechanisms of cucumber resistance against PM. Using a genome-wide association study, we detected a locus significantly correlated with PM resistance in cucumber stem, pm-s5.1. A 1449-bp insertion in the CsMLO8 coding region at the pm-s5.1 locus resulted in enhanced stem PM resistance. Knockout mutants of CsMLO8 and CsMLO11 generated by CRISPR/Cas9 both showed improved PM resistance in the stem, hypocotyl, and leaves, and the double mutant mlo8mlo11 displayed even stronger resistance. We found that reactive oxygen species (ROS) accumulation was higher in the stem of these mutants. Protein interaction assays suggested that CsMLO8 and CsMLO11 could physically interact with CsRbohD and CsCRK2, respectively. Further, we showed that CsMLO8 and CsCRK2 competitively interact with the C-terminus of CsRbohD to affect CsCRK2-CsRbohD module-mediated ROS production during PM defense. These findings provide new insights into the understanding of CsMLO proteins during PM defense responses.

A Genome-Wide Association Study Reveals the Genetic Mechanisms of Nutrient Accumulation in Spinach

Spinach is a significant source of vitamins, minerals, and antioxidants. These nutrients make it delicious and beneficial for human health. However, the genetic mechanism underlying the accumulation of nutrients in spinach remains unclear. In this study, we analyzed the content of chlorophyll a, chlorophyll b, oxalate, nitrate, crude fiber, soluble sugars, manganese, copper, and iron in 62 different spinach accessions. Additionally, 3,356,182 high-quality, single-nucleotide polymorphisms were found using resequencing and used in a genome-wide association study. A total of 2077 loci were discovered that significantly correlated with the concentrations of the nutritional elements. Data mining identified key genes in these intervals for four traits: chlorophyll, oxalate, soluble sugar, and Fe. Our study provides insights into the genetic architecture of nutrient variation and facilitates spinach breeding for good nutrition.

polyGBLUP: a modified genomic best linear unbiased prediction improved the genomic prediction efficiency for autopolyploid species

Given the universality of autopolyploid species in nature, it is crucial to develop genomic selection methods that consider different allele dosages for autopolyploid breeding. However, no method has been developed to deal with autopolyploid data regardless of the ploidy level. In this study, we developed a modified genomic best linear unbiased prediction (GBLUP) model (polyGBLUP) through constructing additive and dominant genomic relationship matrices based on different allele dosages. polyGBLUP could carry out genomic prediction for autopolyploid species regardless of the ploidy level. Through comprehensive simulations and analysis of real data of autotetraploid blueberry and guinea grass and autohexaploid sweet potato, the results showed that polyGBLUP achieved higher prediction accuracy than GBLUP and its superiority was more obvious when the ploidy level of autopolyploids is high. Furthermore, when the dominant effect was added to polyGBLUP (polyGDBLUP), the greater the dominance degree, the more obvious the advantages of polyGDBLUP over the diploid models in terms of prediction accuracy, bias, mean squared error and mean absolute error. For real data, the superiority of polyGBLUP over GBLUP appeared in blueberry and sweet potato populations and a part of the traits in guinea grass population due to the high correlation coefficients between diploid and polyploidy genomic relationship matrices. In addition, polyGDBLUP did not produce higher prediction accuracy than polyGBLUP for most traits of real data as dominant genetic variance was not captured for these traits. Our study will be a significant promising method for genomic prediction of autopolyploid species.

Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Bolting Periods in Spinacia oleracea

Bolting is a symbol of the transition from vegetative to reproductive growth in plants. Late bolting can effectively prolong the commercial value of spinach and is of great importance for spinach breeding. Bolting has complex regulatory networks, and current research on spinach bolting is relatively weak, with specific regulatory pathways and genes unclear. To clarify the regulatory characteristics and key genes related to bolting in spinach, we conducted a comparative transcriptome analysis. In this study, 18 samples from three periods of bolting-tolerant spinach material 12S3 and bolting-susceptible material 12S4 were analyzed using RNA-seq on, resulting in 10,693 differentially expressed genes (DEGs). Functional enrichment and co-expression trend analysis indicated that most DEGs were enriched in the photoperiod pathway, the hormone signaling pathway, and the cutin, suberin, and wax biosynthetic pathways. According to the weighted gene co-expression network analysis (WGCNA), SpFT (SOV4g003400), SOV4g040250, and SpGASA1 (SOV6g017600) were likely to regulate bolting through the gibberellin and photoperiod pathways, and SpELF4 (SOV1g028600) and SpPAT1 (SOV4g058860) caused differences in early and late bolting among different cultivars. These results provide important insights into the genetic control of bolting in spinach and will help elucidate the molecular mechanisms of bolting in leafy vegetables.

Natural variation in STAYGREEN contributes to low-temperature tolerance in cucumber

Low-temperature (LT) stress threatens cucumber production globally; however, the molecular mechanisms underlying LT tolerance in cucumber remain largely unknown. Here, using a genome-wide association study (GWAS), we found a naturally occurring single nucleotide polymorphism (SNP) in the STAYGREEN (CsSGR) coding region at the gLTT5.1 locus associated with LT tolerance. Knockout mutants of CsSGR generated by clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 exhibit enhanced LT tolerance, in particularly, increased chlorophyll (Chl) content and reduced reactive oxygen species (ROS) accumulation in response to LT. Moreover, the C-repeat Binding Factor 1 (CsCBF1) transcription factor can directly activate the expression of CsSGR. We demonstrate that the LT-sensitive haplotype CsSGRHapA , but not the LT-tolerant haplotype CsSGRHapG could interact with NON-YELLOW COLORING 1 (CsNYC1) to mediate Chl degradation. Geographic distribution of the CsSGR haplotypes indicated that the CsSGRHapG was selected in cucumber accessions from high latitudes, potentially contributing to LT tolerance during cucumber cold-adaptation in these regions. CsSGR mutants also showed enhanced tolerance to salinity, water deficit, and Pseudoperonospora cubensis, thus CsSGR is an elite target gene for breeding cucumber varieties with broad-spectrum stress tolerance. Collectively, our findings provide new insights into LT tolerance and will ultimately facilitate cucumber molecular breeding.

Characterization of the Molecular Events Underlying the Establishment of Axillary Meristem Region in Pepper

Plant architecture is a major motif of plant diversity, and shoot branching patterns primarily determine the aerial architecture of plants. In this study, we identified an inbred pepper line with fewer lateral branches, 20C1734, which was free of lateral branches at the middle and upper nodes of the main stem with smooth and flat leaf axils. Successive leaf axil sections confirmed that in normal pepper plants, for either node n, Pn (Primordium n) < 1 cm and Pn+1 < 1 cm were the critical periods between the identification of axillary meristems and the establishment of the region, whereas Pn+3 < 1 cm was fully developed and formed a completely new organ. In 20C1734, the normal axillary meristematic tissue region establishment and meristematic cell identity confirmation could not be performed on the axils without axillary buds. Comparative transcriptome analysis revealed that "auxin-activated signaling pathway", "response to auxin", "response to abscisic acid", "auxin biosynthetic process", and the biosynthesis of the terms/pathways, such as "secondary metabolites", were differentially enriched in different types of leaf axils at critical periods of axillary meristem development. The accuracy of RNA-seq was verified using RT-PCR for some genes in the pathway. Several differentially expressed genes (DEGs) related to endogenous phytohormones were targeted, including several genes of the PINs family. The endogenous hormone assay showed extremely high levels of IAA and ABA in leaf axils without axillary buds. ABA content in particular was unusually high. At the same time, there is no regular change in IAA level in this type of leaf axils (normal leaf axils will be accompanied by AM formation and IAA content will be low). Based on this, we speculated that the contents of endogenous hormones IAA and ABA in 20C1734 plant increased sharply, which led to the abnormal expression of genes in related pathways, which affected the formation of Ams in leaf axils in the middle and late vegetative growth period, and finally, nodes without axillary buds and side branches appeared.

Effects of the quantitative trait locus qPss3 on inhibition of photoperiod sensitivity and resistance to stalk rot disease in maize

KEY MESSAGE

We identified a quantitative trait locus, qPss3, and fine-mapped the causal locus to a 120-kb interval in maize. This locus inhibits the photoperiod sensitivity caused by ZmCCT9 and ZmCCT10, resulting in earlier flowering by 2 ~ 4 days without reduction in stalk-rot resistance in certain genotypes. Photoperiod sensitivity is a key factor affecting the adaptation of maize (Zea mays L.) to high-latitude growing areas. Although many genes associated with flowering time have been identified in maize, no gene that inhibits photoperiod sensitivity has been reported. In our previous study, we detected large differences in photoperiod sensitivity among maize inbred lines with the same photoperiod-sensitive allele at the ZmCCT10 locus. Here, we used two segregating populations with the same genetic backgrounds but different ZmCCT10 alleles to perform quantitative trait locus (QTL) analysis. We identified a unique QTL, qPss3, on chromosome 3 in the population carrying the sensitive ZmCCT10 allele. After sequential fine-mapping, we eventually delimited qPss3 to an interval of ~ 120 kb. qPss3 behaved as a dominant locus and caused earlier flowering by 2-4 days via inhibiting ZmCCT10-induced photoperiod sensitivity under long-day conditions. qPss3 also inhibited the photoperiod sensitivity induced by another flowering-related gene, ZmCCT9. For application in agriculture, an F₁ hybrid heterozygous at both qPss3 and ZmCCT10 loci constitutes an optimal allele combination, showing high resistance to stalk rot without a significant delay in flowering time. Moreover, qPss3 is of great value in regulating the flowering time of tropical maize grown at high-latitude regions.

Tomato MED25 regulates fruit ripening by interacting with EIN3-like transcription factors

Fruit ripening relies on the precise spatiotemporal control of RNA polymerase II (Pol II)-dependent gene transcription, and the evolutionarily conserved Mediator (MED) coactivator complex plays an essential role in this process. In tomato (Solanum lycopersicum), a model climacteric fruit, ripening is tightly coordinated by ethylene and several key transcription factors. However, the mechanism underlying the transmission of context-specific regulatory signals from these ripening-related transcription factors to the Pol II transcription machinery remains unknown. Here, we report the mechanistic function of MED25, a subunit of the plant Mediator transcriptional coactivator complex, in controlling the ethylene-mediated transcriptional program during fruit ripening. Multiple lines of evidence indicate that MED25 physically interacts with the master transcription factors of the ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE (EIL) family, thereby playing an essential role in pre-initiation complex formation during ethylene-induced gene transcription. We also show that MED25 forms a transcriptional module with EIL1 to regulate the expression of ripening-related regulatory as well as structural genes through promoter binding. Furthermore, the EIL1-MED25 module orchestrates both positive and negative feedback transcriptional circuits, along with its downstream regulators, to fine-tune ethylene homeostasis during fruit ripening.