Background: Carica papaya is a trioecious plant species with a genetic sex-determination system defined by sex chromosomes. Under unfavorable environmental conditions male and hermaphrodite exhibit sex-reversal. Previous genomic research revealed few candidate genes for sex differentiation in this species. Nevertheless, more analysis is still needed to identify the mechanism responsible for sex flower organ development in papaya.Results: The aim of this study was to identify differentially expressed genes among male, female and hermaphrodite flowers in papaya during early (pre-meiosis) and later (post-meiosis) stages of flower development. RNA-seq was used to evaluate the expression of differentially expressed genes and RT-qPCR was used to verify the results. Putative functions of these genes were analyzed based on their homology with orthologs in other plant species and their expression patterns. We identified a Male Sterility 1 gene (CpMS1) highly up-regulated in male and hermaphrodite flower buds compared to female flower buds, which expresses in small male flower buds (3–8 mm), and that might be playing an important role in male flower organ development due to its homology to MS1 genes previously identified in other plants. This is the first study in which the sex-biased expression of genes related to tapetum development in the anther developmental pathway is being reported in papaya. Besides important transcription factors related to flower organ development and flowering time regulation, we identified differential expression of genes that are known to participate in ABA, ROS and auxin signaling pathways (ABA-8-hydroxylases, AIL5, UPBEAT 1, VAN3-binding protein).Conclusions: CpMS1was expressed in papaya male and hermaphrodite flowers at early stages, suggesting that this gene might participate in male flower organ development processes, nevertheless, this gene cannot be considered a sex-determination gene. Due to its homology with other plant MS1 proteins and its expression pattern, we hypothesize that this gene participates in anther development processes, like tapetum and pollen development, downstream gender specification. Further gene functional characterization studies in papaya are required to confirm this hypothesis. The role of ABA and ROS signaling pathways in papaya flower development needs to be further explored as well.

Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 h to 8 days after treatment, 7961 genes were found to exhibit differential expression (DE) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up‐regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS‐like 3 (CO), a WUSCHEL gene, two APETALA1/FRUITFULL (AP1/FUL) genes, an epidermal patterning gene, and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up‐regulated within a day of treatment, their predicted targets being the up‐regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS‐like APETELAR (AP2), and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up‐regulated at the apex and not at the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads act directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP, and AP2. A model based on AP2/ERTF DE and predicted DE target genes was developed to give focus to future research. The identified candidate genes are potential targets for genetic manipulation to determine their molecular role in flower transition.

Genotyping‐by‐sequencing (GBS) is a widely used strategy for obtaining large numbers of genetic markers in model and non‐model organisms. In crop plants, GBS‐derived marker datasets are frequently used to perform quantitative trait locus (QTL) mapping. In some plant species, however, high heterozygosity and complex genome structure mean that researchers must use care in handling GBS data to conduct QTL mapping most effectively. Such outbred crops include most of the perennial grass and tree species used for bioenergy. To identify strategies for increasing accuracy and precision of QTL mapping using GBS data in outbred crops, we conducted an empirical study of SNP‐calling and genetic map‐building pipeline parameters in a Miscanthus sinensis population, and a complementary simulation study to estimate the relationship between genome‐wide error rate, read depth, and marker number. The bioenergy grass Miscanthus is an obligate outcrossing species with a recent (diploidized) whole‐genome duplication. For the study of empirical M. sinensis data, we compared two SNP‐calling methods (one non‐reference‐based and one reference‐based), a series of depth filters (12×, 20×, 30×, and 40×) and two map‐construction methods (i.e., marker ordering: linkage‐only and order‐corrected based on a reference genome). We found that correcting the order of markers on a linkage map by using a high‐quality reference genome improved QTL precision (shorter confidence intervals). For typical GBS datasets of between 1000 and 5000 markers to build a genetic map for biparental populations, a depth filter set at 30× to 40× applied to outbred populations provided a genome‐wide genotype‐calling error rate of less than 1%, improved accuracy of QTL point estimates and minimized type I errors for identifying QTL. Based on these results, we recommend using a reference genome to correct the marker order of genetic maps and a robust genotype depth filter to improve QTL mapping for outbred crops.

Introduction. The use of digital image analysis with the “Germinator” allows the automatic evaluation of seed germination. In addition to maximum germination, other parameters associated with seed germination vigor can be quantified simultaneously. Objective. To optimize the “Germinator” as a complement for the automatic analysis of seed germination quality in rice. Materials and methods. The experiments were conducted at the Centro para Investigaciones en Granos y Semillas (CIGRAS) from 2015 to 2018. The “Germinator” software package was optimized on the Palmar 18 variety, and then tested with a panel of 126 rice seed samples comprising fourteen varieties. The germination curves were quantified, the automatically acquired data were compared with manual counting based on radical protrusion and a standardized method. Besides, accelerated aging and controlled aging experiments were conducted to show the sensibility of the automatic method. Results. The relationship between germination quantified automatically and quantified manually was high (R2= 0.99). Maximum germination, quantified by image analysis, ranged from 69 % to 100 % in the panel of 126 samples. The correlation between germination assessed by digital images and the standard method was rho (spearman)= 0.34. The “Germinator” allowed the simultaneous quantification of other variables associated with seed vigor, such as the t50 parameter, which is the time the seed lot takes to reach 50 % of the germination. In addition, the automatic method revealed the differential effect of two seed aging protocols. Conclusions. The use of digital image analysis made it possible to evaluate automatically seed germination based on radicle protrusion and also made it possible to quantify other complementary variables associated with seed vigor (t50).

Winter survival remains a primary limitation to the deployment of Miscanthus biomass cultivars in temperate climates. To investigate the genetic architecture underlying this trait, we studied an F ₂ population ( n = 247) derived from a cross between the winter‐hardy M. sacchariflorus ‘Robustus’ and the non‐hardy M. sinensis ssp. condensatus ‘Cosmo Revert’. Phenotypic data on overwintering ability, hardiness score, and summer vigor were collected following the establishment year winter (2015–2016) and after an especially cold winter in 2018–2019, during which the soil temperature at 10 cm reached −4.2°C. Composite interval mapping (CIM) with a high‐density SNP linkage map identified 14 quantitative trait loci (QTL), and genome‐wide association studies (GWAS) incorporating both additive and dominant models detected an additional 23 loci, resulting in a total of 37 QTLs. Six QTL regions on five chromosomes were detected repeatedly across traits and/or analyses. In all cases, alleles inherited from the hardy M. sacchariflorus parent were associated with increased winter‐hardiness, whereas alleles from the non‐hardy M. sinensis parent were associated with decreased hardiness. We identified fourteen candidate genes within 10 kb of QTL peaks and that were orthologs of genes previously implicated in cold stress tolerance, including glycosyl and oxidoreductases, rare‐cold‐inducible (RCI) genes, peroxidase proteins, LRR sensors, cytochrome P450s, and stress‐responsive transcription factors. Largely non‐overlapping QTL sets for first‐year versus mature‐plant winter‐hardiness suggested distinct physiological mechanisms underlying differing strategies of overwintering. The consistently favorable effects of the hardy‐parent’s alleles, together with high heritability, suggest that marker‐assisted selection can accelerate the development of winter‐hardy Miscanthus .