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Main conclusion
High-quality and dense genetic maps were constructed, and leaf shape variation was dissected by QTL mapping in poplar.
Species in the genus Populus, also known as poplars, are important woody species and considered model plants for perennial trees. High-density genetic maps are valuable genomic resources for population genetics. Her...
Citations
... Leaf morphology regulation is controlled by both environmental factors and genetic regulators [14]. Several genes and pathways have been reported to be involved in leaf morphology regulation in many plants [15], and mutations in these genes frequently result in atypical leaf morphology in model plants. For example, a change in the SERRATE gene (SE) would lead to abnormal leaf morphology in Arabidopsis. ...
... GLYCINE MAX DWARF CRINKLED LEAF 1 (GmDCL1) is a promising gene involved in the morphogenesis of the crinkled leaf trait of the soybean [10]. These studies demonstrate that leaf morphology is a complex trait involved in many genetic pathways such as hormone signals, transcription factors and the interactions between them [15]. In sorghum, BY1 influences both biomass and grain yield. ...
Biomass yield is one of the important traits of sorghum, which is greatly affected by leaf morphology. In this study, a lobed-leaf mutant (sblob) was screened and identified, and its F2 inbred segregating line was constructed. Subsequently, MutMap and whole-genome sequencing were employed to identify the candidate gene (sblob1), the locus of which is Sobic.003G010300. Pfam and homologous analysis indicated that sblob1 encodes a Cytochrome P450 protein and plays a crucial role in the plant serotonin/melatonin biosynthesis pathway. Structural and functional changes in the sblob1 protein were elucidated. Hormone measurements revealed that sblob1 regulates both leaf morphology and sorghum biomass through regulation of the melatonin metabolic pathway. These findings provide valuable insights for further research and the enhancement of breeding programs, emphasizing the potential to optimize biomass yield in sorghum cultivation.
... Quantitative trait locus (QTL) mapping is a well-established technique for studying complex traits and identifying functional genes with those traits [7]. It has been widely applied in various plant species, including Zea mays [7], Oryza sativa [8], Populus [9], Cunninghamia lanceolate [10], and Eucommia ulmoides [11]. Genome-wide association studies GWASs) have indeed emerged as a powerful tool for dissecting QTLs and identifying genes associated with complex traits. ...
... In correlation analysis, when comparing DBH and height, it is observed that height is more influenced by environmental factors. It can be predicted that the heritability of height may be lower compared to DBH, which is similar to previous studies [9]. By fitting growth curves to all individuals, it has been determined that the Richard function best describes the potential growth trajectories of poplar clones. ...
As an important timber genus with high economic and ecological values, Populus is a model for dissecting the genetic architecture of growth traits in perennial forest trees. However, the genetic mechanisms of longitudinal growth traits in poplar remain incompletely understood. In this study, we conducted longitudinal genetic analysis of height and diameter at breast height (DBH) in eleven-year poplar clones using ultra-deep sequencing datasets. We compared four S-shaped growth models, including asymptotic, Gompertz, logistic, and Richard, on eleven-year height and DBH records in terms of five metrics. We constructed the best-fitting growth model (Richard) and determined poplar ontogenetic stages by virtue of growth curve fitting and likelihood ratio testing. This study provides some scientific clues for temporal variation of longitudinal growth traits in Populus species.
... Quantitative trait locus (QTL) mapping can locate QTLs or genes related to complex quantitative traits on chromosome, which is always the interest of biogenetics and has been successfully applied to many breeding projects (Tang et al., 2010;Wei et al., 2012;Sonah et al., 2015;Fu et al., 2016;Xia et al., 2018). However, traditional QTL mapping mainly focuses on phenotypic data of one trait at one time point, ignoring that plant growth is a dynamic and continuous process. ...
Introduction
The cooperative strategy of phenotypic traits during the growth of plants reflects how plants allocate photosynthesis products, which is the most favorable decision for them to optimize growth, survival, and reproduction response to changing environment. Up to now, we still know little about why plants make such decision from the perspective of biological genetic mechanisms.
Methods
In this study, we construct an analytical mapping framework to explore the genetic mechanism regulating the interaction of two complex traits. The framework describes the dynamic growth of two traits and their interaction as Differential Interaction Regulatory Equations (DIRE), then DIRE is embedded into QTL mapping model to identify the key quantitative trait loci (QTLs) that regulate this interaction and clarify the genetic effect, genetic contribution and genetic network structure of these key QTLs. Computer simulation experiment proves the reliability and practicability of our framework.
Results
In order to verify that our framework is universal and flexible, we applied it to two sets of data from Populus euphratica, namely, aboveground stem length - underground taproot length, underground root number - underground root length, which represent relationships of phenotypic traits in two spatial dimensions of plant architecture. The analytical result shows that our model is well applicable to datasets of two dimensions.
Discussion
Our model helps to better illustrate the cooperation-competition patterns between phenotypic traits, and understand the decisions that plants make in a specific environment that are most conducive to their growth from the genetic perspective.
... For example, Zhang et al. (2015) identified seven QTLs, each of which explained up to 10% of the variance for the leaf length-width ratio in rice [38]. In poplar, nine leaf-shape traits were controlled by QTLs with small to moderate effects [39]. The small-to-moderate effect size of the leaf shape QTLs in these studies is also consistent with our research. ...
Exploring the genetic basis of adaptive divergence at fine spatial scales can broaden our basic understanding of evolution and how organisms may adapt to changing environments in the future. Cave-associated microhabitats provide a unique opportunity to gain insight into microgeographic adaptation. We studied the genetic architecture of microhabitat-related divergence in flower phenology and leaf traits between two sister species of Primulina, P. depressa and P. danxiaensis, which live in sympatry but occupy contrasting microhabitats. We identified 40 significant quantitative trait loci (QTLs) associated with the interspecific differences in these microhabitat adaptation traits. Flowering time was controlled by one major-effect and six minor-effect QTLs, while leaf traits were influenced by 9–12 QTLs of small to moderate effect. The genetic architecture of the flowering time and the specific leaf area was genetically independent of other traits. Our results suggest that microhabitat adaptation in sympatric populations of Primulina differs according to different traits, with leaf traits diverging with the accumulation of many small changes and flowering phenology being driven by major effect variance.
... Moreover, the cost of SNP genotyping continues to fall, with the development of highthroughput technology such as genotyping by sequencing (GBS) (Elshire et al., 2011). Recently, GBS technology has been widely applied to the genotyping of perennial woody plants, such as Eucalyptus (Brenton et al., 2019;Klaṕsťěet al., 2021), Populus (Carletti et al., 2016;Xia et al., 2018), Cinnamomum (Gong et al., 2021) and Pinus (Hirao et al., 2022), accelerating the molecular breeding progress in these species. The publication of the E. grandis reference genome (Myburg et al., 2014) has also significantly aided QTL mapping efforts, with high synteny between E. grandis and other common commercial eucalypts. ...
... Generally, the density of maps constructed here also compare favourably with recent GBS-or restriction site-associated sequencing (RAD-seq) maps for other forest species. For example, the density of our maps was close to that for Pinus (Hirao et al., 2022) and significantly superior to the Populus maps (Carletti et al., 2016;Xia et al., 2018;Tong et al., 2020). ...
... Some of the differences in resolution of the genetic maps may be explained by the size of the mapping population (Yang et al., 2018b). For example, 1025 F1 progenies were employed in the previous E. urophylla map (Bartholoméet al., 2015), compared with 320 F1 progenies in ours and 130 F1 offspring in Pinus map (Hirao et al., 2022), and 131 to 300 F1 progenies in Populus maps (Carletti et al., 2016;Xia et al., 2018;Tong et al., 2020). Although preserving large mapping populations is difficult and rarely implemented in forest trees, it may contribute to the accuracy and reliability of genetic linkage mapping and subsequent QTL mapping. ...
Introduction
Eucalyptus urophylla, E. tereticornis and their hybrids are the most important commercial forest tree species in South China where they are grown for pulpwood and solid wood production. Construction of a fine-scale genetic linkage map and detecting quantitative trait loci (QTL) for economically important traits linked to these end-uses will facilitate identification of the main candidate genes and elucidate the regulatory mechanisms.
Method
A high-density consensus map (a total of 2754 SNPs with 1359.18 cM) was constructed using genotyping by sequencing (GBS) on clonal progenies of E. urophylla × tereticornis hybrids. QTL mapping of growth and wood property traits were conducted in three common garden experiments, resulting in a total of 108 QTLs. A total of 1052 candidate genes were screened by the efficient combination of QTL mapping and transcriptome analysis.
Results
Only ten QTLs were found to be stable across two environments, and only one (qSG10Stable mapped on chromosome 10, and associated with lignin syringyl-to-guaiacyl ratio) was stable across all three environments. Compared to other QTLs, qSG10Stable explained a very high level of phenotypic variation (18.4–23.6%), perhaps suggesting that QTLs with strong effects may be more stably inherited across multiple environments. Screened candidate genes were associated with some transcription factor families, such as TALE, which play an important role in the secondary growth of plant cell walls and the regulation of wood formation.
Discussion
While QTLs such as qSG10Stable, found to be stable across three sites, appear to be comparatively uncommon, their identification is likely to be a key to practical QTL-based breeding. Further research involving clonally-replicated populations, deployed across multiple target planting sites, will be required to further elucidate QTL-by-environment interactions.
... QTLs associated with plant resistance have also been detected in poplar, including those related to cadmium tolerance (Induri et al. 2012), woolly poplar aphid (Phloeomyzus passerinii L.) resistance and cold-resistant dormancy (Carletti et al. 2016;Howe et al. 2015). Genes related to physiological traits, such as poplar height, bark characteristics, and leaf traits, have also been localized by QTL analysis (Zhigunov et al. 2017a, b;Bdeir et al. 2017;Drost et al. 2015;Xia et al. 2018). These studies have proved that QTL mapping has the potential to characterize the complex architecture of poplar traits. ...
Branching angle is a critical factor that determines the morphological establishment and is a typical quantitative trait controlled by multiple genes. In this study, we used SLAF-seq to construct a high-density genetic map, to investigate the genetic architecture of branching angle in poplar (Populus leucopyramidalis). A total of 240,672 SLAF tags were obtained, including 103,691 polymorphic SLAF tags. After filtering, 53,407 polymorphic markers were sorted into eight segregation types, and 11,162 of them were used to construct the genetic map. 8447 were on the female parent map, 8532 were on the male parent map, and 11,162 were on the integrated map. The marker coverage was 4820.84 and 5044.80 cM for the female and male maps, and 3142.61 cM for the integrated map. The average intervals between two adjacent mapped markers were 0.55, 0.59, and 0.28 cM for the three maps, respectively. Two quantitative trait loci (QTLs) were detected. Seven markers that exceeded the threshold in these two regions were considered as being associated with branching angle and the phenotypic variance explained by each of these marker was 10.64–11.66%. After functional annotation, we identified 15 candidate genes and analyzed the expression of candidate genes in narrow and wide crown progenies by qRT-PCR. These results show that the combination of QTL and SLAF-seq will contribute to future breeding plans in poplar breeding, especially in narrow crown poplar breeding.
... Compared with previous studies for poplar leaf shape, we found that there were a few overlapping regions (<5 Mb) containing significant SNPs or QTLs. S11 Table lists those significant SNPs or QTLs associated with leaf shape in the current study and in four recent studies [17,18,26,61], excluding those previous QTL studies in which no physical QTL position information was available [11,25,27,28]. The results in the previous studies for single leaf traits such leaf length and width were not considered because we thought that the leaf shape could not be described by a single leaf parameter. ...
... The results in the previous studies for single leaf traits such leaf length and width were not considered because we thought that the leaf shape could not be described by a single leaf parameter. We found that there were 7 significant SNPs detected in our study very close (<5 Mb) to one or more SNPs identified in previous studies, of which 5 were consistent with Xia et al. [61], 4 with Chhetri et al. [17], 1 with McKown et al. [26], and 1 with Chhetri et al. [18]. In contrast, 5 overlapping regions were found between the four previous studies. ...
Leaf morphology exhibits tremendous diversity between and within species, and is likely related to adaptation to environmental factors. Most poplar species are of great economic and ecological values and their leaf morphology can be a good predictor for wood productivity and environment adaptation. It is important to understand the genetic mechanism behind variation in leaf shape. Although some initial efforts have been made to identify quantitative trait loci (QTLs) for poplar leaf traits, more effort needs to be expended to unravel the polygenic architecture of the complex traits of leaf shape. Here, we performed a genome-wide association analysis (GWAS) of poplar leaf shape traits in a randomized complete block design with clones from F 1 hybrids of Populus deltoides and Populus simonii . A total of 35 SNPs were identified as significantly associated with the multiple traits of a moderate number of regular polar radii between the leaf centroid and its edge points, which could represent the leaf shape, based on a multivariate linear mixed model. In contrast, the univariate linear mixed model was applied as single leaf traits for GWAS, leading to genomic inflation; thus, no significant SNPs were detected for leaf length, measures of leaf width, leaf area, or the ratio of leaf length to leaf width under genomic control. Investigation of the candidate genes showed that most flanking regions of the significant leaf shape-associated SNPs harbored genes that were related to leaf growth and development and to the regulation of leaf morphology. The combined use of the traditional experimental design and the multivariate linear mixed model could greatly improve the power in GWAS because the multiple trait data from a large number of individuals with replicates of clones were incorporated into the statistical model. The results of this study will enhance the understanding of the genetic mechanism of leaf shape variation in Populus . In addition, a moderate number of regular leaf polar radii can largely represent the leaf shape and can be used for GWAS of such a complicated trait in Populus , instead of the higher-dimensional regular radius data that were previously considered to well represent leaf shape.
... Leaf morphologies observed on currently available soybean varieties can be mainly classi ed into two categories: ovate and lanceolate (Jun et al. 2014;Xia et al. 2018;Baldocchi et al. 1985;Wang et al. 2019). Soybean with lanceolate leaves tend to produce more seeds per pod (SPP) than those with ovate leaves, which are more likely to generate bigger and heavier seeds than soybeans with lanceolate leaves (Domingo et al. 1945;Mandl et al. 1981). ...
Leaf morphology, as a critical measure of plant architecture, has been associated with soybean yield and quality. As yet, conclusive investigations into the genetic basis and biological significance of heteroblasty in soybean remain sparse. To identify and biologically characterize the quantitative trait loci (QTLs) influencing heteroblasty in soybean, 11 traits associated with leaf morphology, seed quality, and grain yield were observed for two recombinant inbred line (RIL) populations grown in two environments. Values of broad-sense heritability ( H 2 ) for leaf traits in two RIL populations varied from 0.62 to 0.99. These high heritabilities, taken together with the Kurtosis and Skewness values indicate that the phenotypic variation in leaf morphology observed for both RIL populations are mainly controlled by quantitative traits. The three observed leaf morphology traits exhibited significant correlations (P < 0.05) with more than half of the grain yield and seed quality traits, with correlation coefficients varying from − 0.40 to 0.43, which suggests that leaf morphology can significantly influence soybean yield and quality. A total of 11 QTLs were detected for leaf morphology, with logarithm of odds (LOD) values ranging from 3.40 to 89.6, which accounted for 1.38 ~ 74.53% of genetic variation. Eight of these loci for leaf morphology co-located with those for seed quality and grain yield, which coincided large and extensive leaf morphologies that contributed to seed quality and grain yield formation. Overall, these results provide important information for breeding high yielding crop varieties with improved quality traits produced through optimization of leaf morphology.
... For example, researchers have employed a restriction site-associated DNA sequencing (RAD-seq) approach to develop an integrated Catalpa bungei genetic map, containing 9,593 pleiotropic markers across 20 linkage groups, identifying 20 QTLs associated with seven leaf traits and13 QTLs associated with plant height, in addition to predicting that cyclin genes are key determinants of leaf development (Lu et al., 2019). In Ziziphus jujuba Mill, a map spanning 2,167.5 cM and containing 3,792 markers across 12 linkage groups was constructed via a genotyping-by-sequencing strategy, leading to the identification of 27 leaf trait-related QTLs (Wang et al., 2019b); in Populus, a next-generation sequencing (NGS) strategy was used to generate male and female genetic maps, containing 889 and 1,650 SNPs, respectively, that were associated with 42 QTLs linked to nine leaf shape parameters (Xia et al., 2018). In Citrullus lanatus L., genome-wide RNA-seq and BSA were combined to identify 5,966 SNPs and indels associated with the lobed leaf trait, enabling the researchers to identify two candidate leaf shape-related genes . ...
Chinese bayberry (Myrica rubra) is an economically important fruit tree that is grown in southern China. Owing to its over 10-year seedling period, the crossbreeding of bayberry is challenging. The characteristics of plant leaves are among the primary factors that control plant architecture and potential yields, making the analysis of leaf trait-related genetic factors crucial to the hybrid breeding of any plant. In the present study, molecular markers associated with leaf traits were identified via a whole-genome re-sequencing approach, and a genetic map was thereby constructed. In total, this effort yielded 902.11 Gb of raw data that led to the identification of 2,242,353 single nucleotide polymorphisms (SNPs) in 140 F1 individuals and parents (Myrica rubra cv. Biqizhong × Myrica rubra cv. 2012LXRM). The final genetic map ultimately incorporated 31,431 SNPs in eight linkage groups, spanning 1,351.85 cM. This map was then used to assemble and update previous scaffold genomic data at the chromosomal level. The genome size of M. rubra was thereby established to be 275.37 Mb, with 94.98% of sequences being assembled into eight pseudo-chromosomes. Additionally, 18 quantitative trait loci (QTLs) associated with nine leaf and growth-related traits were identified. Two QTL clusters were detected (the LG3 and LG5 clusters). Functional annotations further suggested two chlorophyll content-related candidate genes being identified in the LG5 cluster. Overall, this is the first study on the QTL mapping and identification of loci responsible for the regulation of leaf traits in M. rubra, offering an invaluable scientific for future marker-assisted selection breeding and candidate gene analyses.
... As to the genetic regulators, the leaf shape-regulating network is complex, which involves many pathways and genes (Zhao et al., 2016;Xia et al., 2018). Change of some key genes would lead to abnormal leaf morphology: The SERRATE gene (SE) encodes a zinc-finger protein in Arabidopsis, and the se mutant displayed fewer leaves in rosettes and all the leaves were serrated (Prigge, 2001). ...
Leaf is an important organ for higher plants, and the shape of it is one of the crucial traits of crops. In this study, we investigated a unique aberrant leaf morphology trait in a mutational rapeseed material, which displayed ectopic blade-like outgrowths on the adaxial side of leaf. The abnormal line 132000B-3 was crossed with the normal line 827-3. Based on the F2:3 family, we constructed two DNA pools (normal pool and abnormal pool) by the bulked segregant analysis (BSA) method and performed whole genome re-sequencing (WGR), obtaining the single-nucleotide polymorphism (SNP) and insertion/deletion (InDel) data. The SNP-index method was used to calculate the Δ(SNP/InDel-index), and then an association region was identified on chromosome A10 with a length of 5.5 Mbp, harboring 1048 genes totally. Subsequently, the fine mapping was conducted by using the penta-primer amplification refractory mutation system (PARMS), and the associated region was narrowed down to a 35.1-kbp segment, containing only seven genes. These seven genes were then analyzed according to their annotations and finally, BnA10g0422620 and BnA10g0422610, orthologs of LATE MERISTEM IDENTITY1 (LMI1) gene from Arabidopsis and REDUCED COMPLEXITY (RCO) gene from its relative Cardamine hirsuta, respectively, were identified as the candidate genes responding to this blade-like outgrowth trait in rapeseed. This study provides a novel perspective into the leaf formation in Brassica plants.
