Association Mapping of Flowering and Height Traits in Germplasm Enhancement of Maize Doubled Haploid (GEM-DH) Lines

Joint-GWAS, Linkage Mapping, and Transcriptome Analysis to Reveal the Genetic Basis of Plant Architecture-Related Traits in Maize

Plant architecture is one of the key factors affecting maize yield formation and can be divided into secondary traits, such as plant height (PH), ear height (EH), and leaf number (LN). It is a viable approach for exploiting genetic resources to improve plant density. In this study, one natural panel of 226 inbred lines and 150 family lines derived from the offspring of T32 crossed with Qi319 were genotyped by using the MaizeSNP50 chip and the genotyping by sequence (GBS) method and phenotyped under three different environments. Based on the results, a genome-wide association study (GWAS) and linkage mapping were analyzed by using the MLM and ICIM models, respectively. The results showed that 120 QTNs (quantitative trait nucleotides) and 32 QTL (quantitative trait loci) related to plant architecture were identified, including four QTL and 40 QTNs of PH, eight QTL and 41 QTNs of EH, and 20 QTL and 39 QTNs of LN. One dominant QTL, qLN7-2, was identified in the Zhangye environment. Six QTNs were commonly identified to be related to PH, EH, and LN in different environments. The candidate gene analysis revealed that Zm00001d021574 was involved in regulating plant architecture traits through the autophagy pathway, and Zm00001d044730 was predicted to interact with the male sterility-related gene ms26. These results provide abundant genetic resources for improving maize plant architecture traits by using approaches to biological breeding.

Genome-wide association analysis of plant architecture traits using doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic maize population

Selection in the Iowa Stiff Stalk Synthetic (BSSS) maize population for high yield, grain moisture, and root and stalk lodging has indirectly modified plant architecture traits that are important for adaptation to high plant density. In this study, we developed doubled haploid (DH) lines from the BSSS maize population in the earliest cycle of recurrent selection (BSSS), cycle 17 of reciprocal recurrent selection, [BSSS(R)17] and the cross between the two cycles [BSSS/BSSS(R)C17]. We aimed to determine the phenotypic variation and changes in agronomic traits that have occurred through the recurrent selection program in this population and to identify genes or regions in the genome associated with the plant architecture changes observed in the different cycles of selection. We conducted a per se evaluation of DH lines focusing on high heritability traits important for adaptation to high planting density and grain yield. Trends for reducing flowering time, anthesis-silking interval, ear height, and the number of primary tassel branches in BSSS(R)17 DH lines compared to BSSS and BSSS/BSSS(R)C17 DH lines were observed. Additionally, the BSSS(R)C17 DH lines showed more upright flag leaf angles. Using the entire panel of DH lines increased the number of SNP markers identified within candidate genes associated with plant architecture traits. The genomic regions identified for plant architecture traits in this study may help to elucidate the genetic basis of these traits and facilitate future work about marker-assisted selection or map-based cloning in maize breeding programs.

Genomic prediction of tocochromanols in exotic-derived maize

Tocochromanols (vitamin E) are an essential part of the human diet. Plant products, including maize (Zea mays L.) grain, are the major dietary source of tocochromanols; therefore, breeding maize with higher vitamin content (biofortification) could improve human nutrition. Incorporating exotic germplasm in maize breeding for trait improvement including biofortification is a promising approach and an important research topic. However, information about genomic prediction of exotic-derived lines using available training data from adapted germplasm is limited. In this study, genomic prediction was systematically investigated for nine tocochromanol traits within both an adapted (Ames Diversity Panel [AP]) and an exotic-derived (Backcrossed Germplasm Enhancement of Maize [BGEM]) maize population. Although prediction accuracies up to 0.79 were achieved using genomic best linear unbiased prediction (gBLUP) when predicting within each population, genomic prediction of BGEM based on an AP training set resulted in low prediction accuracies. Optimal training population (OTP) design methods fast and unique representative subset selection (FURS), maximization of connectedness and diversity (MaxCD), and partitioning around medoids (PAM) were adapted for inbreds and, along with the methods mean coefficient of determination (CDmean) and mean prediction error variance (PEVmean), often improved prediction accuracies compared with random training sets of the same size. When applied to the combined population, OTP designs enabled successful prediction of the rest of the exotic-derived population. Our findings highlight the importance of leveraging genotype data in training set design to efficiently incorporate new exotic germplasm into a plant breeding program.

Phenotypic and genome-wide association analyses for nitrogen use efficiency related traits in maize (Zea mays L.) exotic introgression lines

Nitrogen (N) limits crop production, yet more than half of N fertilizer inputs are lost to the environment. Developing maize hybrids with improved N use efficiency can help minimize N losses and in turn reduce adverse ecological, economical, and health consequences. This study aimed to identify single nucleotide polymorphisms (SNPs) associated with agronomic traits (plant height, grain yield, and anthesis to silking interval) under high and low N conditions. A genome-wide association study (GWAS) was conducted using 181 doubled haploid (DH) lines derived from crosses between landraces from the Germplasm Enhancement of Maize (BGEM lines) project and two inbreds, PHB47 and PHZ51. These DH lines were genotyped using 62,077 SNP markers. The same lines from the per se trials were used as parental lines for the testcross field trials. Plant height, anthesis to silking interval, and grain yield were collected from high and low N conditions in three environments for both per se and testcross trials. We used three GWAS models, namely, general linear model (GLM), mixed linear model (MLM), and Fixed and Random model Circulating Probability Unification (FarmCPU) model. We observed significant genetic variation among the DH lines and their derived testcrosses. Interestingly, some testcrosses of exotic introgression lines were superior under high and low N conditions compared to the check hybrid, PHB47/PHZ51. We detected multiple SNPs associated with agronomic traits under high and low N, some of which co-localized with gene models associated with stress response and N metabolism. The BGEM panel is, thus, a promising source of allelic diversity for genes controlling agronomic traits under different N conditions.

Inhibition of ethylene involved in resistance to E. turcicum in an exotic-derived double haploid maize population

Northern corn leaf blight (NCLB) is an economically important disease of maize. While the genetic architecture of NCLB has been well characterized, the pathogen is known to overcome currently deployed resistance genes, and the role of hormones in resistance to NCLB is an area of active research. The objectives of the study were (i) to identify significant markers associated with resistance to NCLB, (ii) to identify metabolic pathways associated with NCLB resistance, and (iii) to examine role of ethylene in resistance to NCLB. We screened 252 lines from the exotic-derived double haploid BGEM maize population for resistance to NCLB in both field and greenhouse environments. We used a genome wide association study (GWAS) and stepwise regression to identify four markers associated with resistance, followed by a pathway association study tool (PAST) to identify important metabolic pathways associated with disease severity and incubation period. The ethylene synthesis pathway was significant for disease severity and incubation period. We conducted a greenhouse assay in which we inhibited ethylene to examine the role of ethylene in resistance to NCLB. We observed a significant increase in incubation period and a significant decrease in disease severity between plants treated with the ethylene inhibitor and mock-treated plants. Our study confirms the potential of the BGEM population as a source of novel alleles for resistance. We also confirm the role of ethylene in resistance to NCLB and contribute to the growing body of literature on ethylene and disease resistance in monocots.

Integration of GWAS, linkage analysis and transcriptome analysis to reveal the genetic basis of flowering time-related traits in maize

Maize (Zea mays) inbred lines vary greatly in flowering time, but the genetic basis of this variation is unknown. In this study, three maize flowering-related traits (DTT, days to tasselling; DTP, days to pollen shed; DTS, days to silking) were evaluated with an association panel consisting of 226 maize inbred lines and an F_2:3 population with 120 offspring from a cross between the T32 and Qi319 lines in different environments. A total of 82 significant single nucleotide polymorphisms (SNPs) and 117 candidate genes were identified by genome-wide association analysis. Twenty-one quantitative trait loci (QTLs) and 65 candidate genes were found for maize flowering time by linkage analysis with the constructed high-density genetic map. Transcriptome analysis was performed for Qi319, which is an early-maturing inbred line, and T32, which is a late-maturing inbred line, in two different environments. Compared with T32, Qi319 showed upregulation of 3815 genes and downregulation of 3906 genes. By integrating a genome-wide association study (GWAS), linkage analysis and transcriptome analysis, 25 important candidate genes for maize flowering time were identified. Together, our results provide an important resource and a foundation for an enhanced understanding of flowering time in maize.

QTL Analysis Reveals Conserved and Differential Genetic Regulation of Maize Lateral Angles above the Ear

Improving the density tolerance and planting density has great importance for increasing maize production. The key to promoting high density planting is breeding maize with a compact canopy architecture, which is mainly influenced by the angles of the leaves and tassel branches above the ear. It is still unclear whether the leaf angles of different stem nodes and tassel branches are controlled by similar genetic regulatory mechanisms, which limits the ability to breed for density-tolerant maize. Here, we developed a population with 571 double haploid lines derived from inbred lines, PHBA6 and Chang7-2, showing significant differences in canopy architecture. Phenotypic and QTL analyses revealed that the genetic regulation mechanism was largely similar for closely adjacent leaves above the ears. In contrast, the regulation mechanisms specifying the angles of distant leaves and the angles of leaves vs. tassel branches are largely different. The liguless1 gene was identified as a candidate gene for QTLs co-regulating the angles of different leaves and the tassel branch, consistent with its known roles in regulating plant architecture. Our findings can be used to develop strategies for the improvement of leaf and tassel architecture through the introduction of trait-specific or pleiotropic genes, thus benefiting the breeding of maize with increased density tolerance in the future.

Combining datasets for maize root seedling traits increases the power of GWAS and genomic prediction accuracies

The identification of genomic regions associated with root traits and the genomic prediction of untested genotypes can increase the rate of genetic gain in maize breeding programs targeting roots traits. Here, we combined two maize association panels with different genetic backgrounds to identify single nucleotide polymorphisms (SNPs) associated with root traits, and used a genome-wide association study (GWAS) and to assess the potential of genomic prediction for these traits in maize. For this, we evaluated 377 lines from the Ames panel and 302 from the Backcrossed Germplasm Enhancement of Maize (BGEM) panel in a combined panel of 679 lines. The lines were genotyped with 232 460 SNPs, and four root traits were collected from 14-day-old seedlings. We identified 30 SNPs significantly associated with root traits in the combined panel, whereas only two and six SNPs were detected in the Ames and BGEM panels, respectively. Those 38 SNPs were in linkage disequilibrium with 35 candidate genes. In addition, we found higher prediction accuracy in the combined panel than in the Ames or BGEM panel. We conclude that combining association panels appears to be a useful strategy to identify candidate genes associated with root traits in maize and improve the efficiency of genomic prediction.

Genome-Wide Association Study Reveals the Genetic Basis of Kernel and Cob Moisture Changes in Maize at Physiological Maturity Stage

Low moisture content (MC) and high dehydration rate (DR) at physiological maturity affect grain mechanical harvest, transport, and storage. In this study, we used an association panel composed of 241 maize inbred lines to analyze ear moisture changes at physiological maturity stage. A genome-wide association study revealed nine significant SNPs and 91 candidate genes. One SNP (SYN38588) was repeatedly detected for two traits, and 15 candidate genes were scanned in the linkage disequilibrium regions of this SNP. Of these, genes Zm00001d020615 and Zm00001d020623 were individually annotated as a polygalacturonase (PG) and a copper transporter 5.1 (COPT5.1), respectively. Candidate gene association analysis showed that three SNPs located in the exons of Zm00001d020615 were significantly associated with the dehydration rate, and AATTAA was determined as the superior haplotype. All these findings suggested that Zm00001d020615 was a key gene affecting moisture changes of maize at the physiological maturity stage. These results have demonstrated the genetic basis of ear moisture changes in maize and indicated a superior haplotype for cultivating maize varieties with low moisture content and high dehydration rates.

Integrating Genomic and Phenomic Approaches to Support Plant Genetic Resources Conservation and Use

Plant genebanks provide genetic resources for breeding and research programs worldwide. These programs benefit from having access to high-quality, standardized phenotypic and genotypic data. Technological advances have made it possible to collect phenomic and genomic data for genebank collections, which, with the appropriate analytical tools, can directly inform breeding programs. We discuss the importance of considering genebank accession homogeneity and heterogeneity in data collection and documentation. Citing specific examples, we describe how well-documented genomic and phenomic data have met or could meet the needs of plant genetic resource managers and users. We explore future opportunities that may emerge from improved documentation and data integration among plant genetic resource information systems.

Dissecting the Genetic Basis of Flowering Time and Height Related-Traits Using Two Doubled Haploid Populations in Maize

In the field, maize flowering time and height traits are closely linked with yield, planting density, lodging resistance, and grain fill. To explore the genetic basis of flowering time and height traits in maize, we investigated six related traits, namely, days to anthesis (AD), days to silking (SD), the anthesis-silking interval (ASI), plant height (PH), ear height (EH), and the EH/PH ratio (ER) in two locations for two years based on two doubled haploid (DH) populations. Based on the two high-density genetic linkage maps, 12 and 22 quantitative trait loci (QTL) were identified, respectively, for flowering time and height-related traits. Of these, ten QTLs had overlapping confidence intervals between the two populations and were integrated into three consensus QTLs (qFT_YZ1a, qHT_YZ5a, and qHT_YZ7a). Of these, qFT_YZ1a, conferring flowering time, is located at 221.1-277.0 Mb on chromosome 1 and explained 10.0-12.5% of the AD and SD variation, and qHT_YZ5a, conferring height traits, is located at 147.4-217.3 Mb on chromosome 5 and explained 11.6-15.3% of the PH and EH variation. These consensus QTLs, in addition to the other repeatedly detected QTLs, provide useful information for further genetic studies and variety improvements in flowering time and height-related traits.

Transcriptome and metabolome profiling provide insights into molecular mechanism of pseudostem elongation in banana

BACKGROUND

Banana plant height is an important trait for horticultural practices and semi-dwarf cultivars show better resistance to damages by wind and rain. However, the molecular mechanisms controlling the pseudostem height remain poorly understood. Herein, we studied the molecular changes in the pseudostem of a semi-dwarf banana mutant Aifen No. 1 (Musa spp. Pisang Awak sub-group ABB) as compared to its wild-type dwarf cultivar using a combined transcriptome and metabolome approach.

RESULTS

A total of 127 differentially expressed genes and 48 differentially accumulated metabolites were detected between the mutant and its wild type. Metabolites belonging to amino acid and its derivatives, flavonoids, lignans, coumarins, organic acids, and phenolic acids were up-regulated in the mutant. The transcriptome analysis showed the differential regulation of genes related to the gibberellin pathway, auxin transport, cell elongation, and cell wall modification. Based on the regulation of gibberellin and associated pathway-related genes, we discussed the involvement of gibberellins in pseudostem elongation in the mutant banana. Genes and metabolites associated with cell wall were explored and their involvement in cell extension is discussed.

CONCLUSIONS

The results suggest that gibberellins and associated pathways are possibly developing the observed semi-dwarf pseudostem phenotype together with cell elongation and cell wall modification. The findings increase the understanding of the mechanisms underlying banana stem height and provide new clues for further dissection of specific gene functions.

Multivariate linear mixed model enhanced the power of identifying genome-wide association to poplar tree heights in a randomized complete block design

With the advances in high-throughput sequencing technologies, it is not difficult to extract tens of thousands of single-nucleotide polymorphisms (SNPs) across many individuals in a fast and cheap way, making it possible to perform genome-wide association studies (GWAS) of quantitative traits in outbred forest trees. It is very valuable to apply traditional breeding experiments in GWAS for identifying genome variants associated with ecologically and economically important traits in Populus. Here, we reported a GWAS of tree height measured at multiple time points from a randomized complete block design (RCBD), which was established with clones from an F₁ hybrid population of Populus deltoides and Populus simonii. A total of 22,670 SNPs across 172 clones in the RCBD were obtained with restriction site-associated DNA sequencing (RADseq) technology. The multivariate mixed linear model was applied by incorporating the pedigree relationship matrix of individuals to test the association of each SNP to the tree heights over 8 time points. Consequently, 41 SNPs were identified significantly associated with the tree height under the P-value threshold determined by Bonferroni correction at the significant level of 0.01. These SNPs were distributed on all but two chromosomes (Chr02 and Chr18) and explained the phenotypic variance ranged from 0.26% to 2.64%, amounting to 63.68% in total. Comparison with previous mapping studies for poplar height as well as the candidate genes of these detected SNPs were also investigated. We therefore showed that the application of multivariate linear mixed model to the longitudinal phenotypic data from the traditional breeding experimental design facilitated to identify far more genome-wide variants for tree height in poplar. The significant SNPs identified in this study would enhance understanding of molecular mechanism for growth traits and would accelerate marker-assisted breeding programs in Populus.

Using single-plant-omics in the field to link maize genes to functions and phenotypes

Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.

Mapping of QTL for Grain Yield Components Based on a DH Population in Maize

The elite maize hybrid Zhengdan 958 (ZD958), which has high and stable yield and extensive adaptability, is widely grown in China. To elucidate the genetic basis of yield and its related traits in this elite hybrid, a set of doubled haploid (DH) lines derived from ZD958 were evaluated in four different environments at two locations over two years, and a total of 49 quantitative trait loci (QTL) and 24 pairs of epistatic interactions related to yield and yield components were detected. Furthermore, 21 QTL for six investigated phenotypic traits were detected across two different sites. Combining the results of these QTL in each environment and across both sites, three main QTL hotspots were found in chromosomal bins 2.02, 2.05–2.06, and 6.05 between the simple sequence repeat (SSR) markers umc1165-bnlg1017, umc1065-umc1637, and nc012-bnlg345, respectively. The existence of three QTL hotspots associated with various traits across multiple environments could be explained by pleiotropic QTL or multiple tightly linked QTL. These genetic regions could provide targets for genetic improvement, fine mapping, and marker-assisted selection in future studies.

Mapping of QTL and identification of candidate genes conferring spontaneous haploid genome doubling in maize (Zea mays L.)

In vivo doubled haploid (DH) technology is widely used in commercial maize (Zea mays L.) breeding. Haploid genome doubling is a critical step in DH breeding. In this study, inbred lines GF1 (0.65), GF3(0.29), and GF5 (0) with high, moderate, and poor spontaneous haploid genome doubling (SHGD), respectively, were selected to develop mapping populations for SHGD. Three QTL, qshgd1, qshgd2, and qshgd3, related to SHGD were identified by selective genotyping. With the exception of qshgd3, the source of haploid genome doubling alleles were derived from GF1. Furthermore, RNA-Seq was conducted to identify putative candidate genes between GF1 and GF5 within the qshgd1 region. A differentially expressed formin-like protein 5 transcript was identified within the qshgd1 region.

Doubled haploid technology for line development in maize: technical advances and prospects

KEY MESSAGE

Increased efficiencies achieved in different steps of DH line production offer greater benefits to maize breeding programs. Doubled haploid (DH) technology has become an integral part of many commercial maize breeding programs as DH lines offer several economic, logistic and genetic benefits over conventional inbred lines. Further, new advances in DH technology continue to improve the efficiency of DH line development and fuel its increased adoption in breeding programs worldwide. The established method for maize DH production covered in this review involves in vivo induction of maternal haploids by a male haploid inducer genotype, identification of haploids from diploids at the seed or seedling stage, chromosome doubling of haploid (D0) seedlings and finally, selfing of fertile D0 plants. Development of haploid inducers with high haploid induction rates and adaptation to different target environments have facilitated increased adoption of DH technology in the tropics. New marker systems for haploid identification, such as the red root marker and high oil marker, are being increasingly integrated into new haploid inducers and have the potential to make DH technology accessible in germplasm such as some Flint, landrace, or tropical material, where the standard R1-nj marker is inhibited. Automation holds great promise to further reduce the cost and time in haploid identification. Increasing success rates in chromosome doubling protocols and/or reducing environmental and human toxicity of chromosome doubling protocols, including research on genetic improvement in spontaneous chromosome doubling, have the potential to greatly reduce the production costs per DH line.

Overexpression of zmm28 increases maize grain yield in the field

Increasing maize grain yield has been a major focus of both plant breeding and genetic engineering to meet the global demand for food, feed, and industrial uses. We report that increasing and extending expression of a maize MADS-box transcription factor gene, zmm28, under the control of a moderate-constitutive maize promoter, results in maize plants with increased plant growth, photosynthesis capacity, and nitrogen utilization. Molecular and biochemical characterization of zmm28 transgenic plants demonstrated that their enhanced agronomic traits are associated with elevated plant carbon assimilation, nitrogen utilization, and plant growth. Overall, these positive attributes are associated with a significant increase in grain yield relative to wild-type controls that is consistent across years, environments, and elite germplasm backgrounds.

Genome-Wide Association Analysis of Plant Height Using the Maize F1 Population

Drastic changes in plant height (PH) are observed when maize adapt to a higher plant density. Most importantly, PH is an important factor affecting maize yield. Although the genetic basis of PH has been extensively studied using different populations during the past decades, genetic basis remains unclear in the F1 population, which was a widely used population in production. In this study, a genome-wide association study (GWAS) was conducted using an F1 population consisting of 300 maize hybrids with 17,652 single nucleotide polymorphisms (SNPs) makers to identify candidate genes for controlling PH. A total of nine significant SNPs makers and two candidate genes were identified for PH. The candidate genes, Zm00001d018617 and Zm00001d023659, were the genes most probable to be involved in the development of PH. Our results provide new insights into the genetic basis of PH in maize.

Technological advances in maize breeding: past, present and future

Maize has for many decades been both one of the most important crops worldwide and one of the primary genetic model organisms. More recently, maize breeding has been impacted by rapid technological advances in sequencing and genotyping technology, transformation including genome editing, doubled haploid technology, parallelled by progress in data sciences and the development of novel breeding approaches utilizing genomic information. Herein, we report on past, current and future developments relevant for maize breeding with regard to (1) genome analysis, (2) germplasm diversity characterization and utilization, (3) manipulation of genetic diversity by transformation and genome editing, (4) inbred line development and hybrid seed production, (5) understanding and prediction of hybrid performance, (6) breeding methodology and (7) synthesis of opportunities and challenges for future maize breeding.

Stability Analysis of Kernel Quality Traits in Exotic-Derived Doubled Haploid Maize Lines

Variation in kernel composition across maize ( L.) germplasm is affected by a combination of the plant's genotype, the environment in which it is grown, and the interaction between these two elements. Adapting exotic germplasm to the US Corn Belt is highly dependent on the plant's genotype, the environment where it is grown, and the interaction between these components. Phenotypic plasticity is ill-defined when specific exotic germplasm is moved over large latitudinal distances and for the adapted variants being created. Reduced plasticity (or stability) is desired for the adapted variants, as it allows for a more rapid implementation into breeding programs throughout the Corn Belt. Here, doubled haploid lines derived from exotic maize and adapted through backcrossing exotic germplasm to elite adapted lines were used in conjunction with genome-wide association studies to explore stability in four kernel composition traits. Genotypes demonstrated a response to environments that paralleled the mean response of all genotypes used across all traits, with protein content and kernel density exhibiting the highest levels of Type II stability. Genes such as , , and were identified as potential candidates within quantitative trait locus regions. The findings within this study aid in validating previously identified genomic regions and identified novel genomic regions affecting kernel quality traits.

The Complex Interactions Between Flowering Behavior and Fiber Quality in Hemp

Hemp, Cannabis sativa L., is a sustainable multipurpose fiber crop with high nutrient and water use efficiency and with biomass of excellent quality for textile fibers and construction materials. The yield and quality of hemp biomass are largely determined by the genetic background of the hemp cultivar but are also strongly affected by environmental factors, such as temperature and photoperiod. Hemp is a facultative short-day plant, characterized by a strong adaptation to photoperiod and a great influence of environmental factors on important agronomic traits such as "flowering-time" and "sex determination." This sensitivity of hemp can cause a considerable degree of heterogeneity, leading to unforeseen yield reductions. Fiber quality for instance is influenced by the developmental stage of hemp at harvest. Also, male and female plants differ in stature and produce fibers with different properties and quality. Next to these causes, there is evidence for specific genotypic variation in fiber quality among hemp accessions. Before improved hemp cultivars can be developed, with specific flowering-times and fiber qualities, and adapted to different geographical regions, a better understanding of the molecular mechanisms controlling important phenological traits such as "flowering-time" and "sex determination" in relation to fiber quality in hemp is required. It is well known that genetic factors play a major role in the outcome of both phenological traits, but the major molecular factors involved in this mechanism are not characterized in hemp. Genome sequences and transcriptome data are available but their analysis mainly focused on the cannabinoid pathway for medical purposes. Herein, we review the current knowledge of phenotypic and genetic data available for "flowering-time," "sex determination," and "fiber quality" in short-day and dioecious crops, respectively, and compare them with the situation in hemp. A picture emerges for several controlling key genes, for which natural genetic variation may lead to desired flowering behavior, including examples of pleiotropic effects on yield quality and on carbon partitioning. Finally, we discuss the prospects for using this knowledge for the molecular breeding of this sustainable crop via a candidate gene approach.