Leaf Trait Relationships Research Articles

The third dimension of alpine plant leaf traits is related to cold-tolerance

Alpine plants possess unique traits to adapt alpine environments. Whether leaf trait relationships of alpine plants can be captured by the two trait dimensions of organ size and resource economics is unknown. We hypothesized that, beyond the trait dimensions of leaf size and resource economics, non-structured carbohydrates (NSC) would reflect a dimension of cold-tolerance in alpine plants. To test this hypothesis, we measured 12 leaf traits critical to leaf construction and growth in 143 species across 7 sites ranging from alpine steppes to alpine meadows along an environmental gradient on the Tibetan Plateau. Furthermore, a cold resistance experiment was conducted at one of these sites to estimate the lethal temperature causing 50% frost damage (LT50) of 11 alpine species. The majority of variations in 12 leaf traits of alpine plants were captured by three trait axes, in which leaf carbon (LCC) and NSC (including leaf starch; LSC and leaf soluble sugars; LSS) were clustered in a new dimension (PC3) beyond leaf size and structure, and resource economics. Although LCC, LSC and LSS all showed negative correlations with mean annual temperature, a significant negative correlation was only found between LSS and LT50. It indicated that PC3 was able to reflect the cold-tolerance of alpine plants to some extent, in which LSS was the most critical trait. The storage and transformation of NSC under stressful conditions could reflect a dimension of long-term metabolic adaptation and cold-tolerance, which is an extension of the resource-utilization strategy beyond construction cost and growth.

QTL mapping for branch- and leaf-related traits with a high-density SNP genetic map in litchi (Litchi chinensis Sonn.)

Litchi (Litchi chinensis Sonn.), an important fruit tree in tropical and subtropical regions, possesses substantial economic value. The branch- and leaf-related traits of litchi have a significant impact on litchi yield and quality. However, due to limitations such as the density of the genetic linkage map, there have been few studies on mapping QTLs of branch- and leaf-related traits. In this study, a high-density genetic map was constructed by next-generation sequencing (NGS) using an F1 population of 264 progenies, derived from the cross between the cultivars ‘Sanyuehong’ and ‘Ziniangxi’. A total of 2574 high-quality BINs (binomial intervals) were obtained, and a genetic linkage map was constructed with a total length of 1753.3 cM and an average marker distance of 0.68 cM. With the genetic map and the phenotyping of single leaf length (SLL), single leaf width (SLW), leaf shape index (LSI), weight of specific leaf (WSL), petiole length (PL) and compound leaf length (CLL) measured in three seasons, 11, 9, 9, 10, 9 and 12 QTLs were detected for SLL, SLW, WSL, LSI, PL and CLL traits, respectively. Among these QTLs, five QTLs were consistently detected in two seasons and 12 pleiotropic QTLs were identified for at least two traits. These findings will provide new insights for the gene cloning for branch- and leaf-related traits as well as marker-assisted selection (MAS).

Characterization of flag leaf morphology identifies a major genomic region controlling flag leaf angle in the US winter wheat (Triticum aestivum L.)

Key messageMulti-environmental characterization of flag leaf morphology traits in the US winter wheat revealed nine stable genomic regions for different flag leaf-related traits including a major region governing flag leaf angle.Flag leaf in wheat is the primary contributor to accumulating photosynthetic assimilates. Flag leaf morphology (FLM) traits determine the overall canopy structure and capacity to intercept the light, thus influencing photosynthetic efficiency. Hence, understanding the genetic control of these traits could be useful for breeding desirable ideotypes in wheat. We used a panel of 272 accessions from the hard winter wheat (HWW) region of the USA to investigate the genetic architecture of five FLM traits including flag leaf length (FLL), width (FLW), angle (FLANG), length–width ratio, and area using multilocation field experiments. Multi-environment GWAS using 14,537 single-nucleotide polymorphisms identified 36 marker-trait associations for different traits, with nine being stable across environments. A novel and major stable region for FLANG (qFLANG.1A) was identified on chromosome 1A accounting for 9–13% variation. Analysis of spatial distribution for qFLANG.1A in a set of 2354 breeding lines from the HWW region showed a higher frequency of allele associated with narrow leaf angle. A KASP assay was developed for allelic discrimination of qFLANG.1A and was used for its independent validation in a diverse set of spring wheat accessions. Furthermore, candidate gene analysis for two regions associated with FLANG identified seven putative genes of interest for each of the two regions. The present study enhances our understanding of the genetic control of FLM in wheat, particularly FLANG, and these results will be useful for dissecting the genes underlying canopy architecture in wheat facilitating the development of climate-resilient wheat varieties.

Genetic Mapping for Leaf Shape and Leaf Size in Non-Heading Chinese Cabbage by a RIL Population

Leaves are the predominant photosynthetic and edible organs in non-heading Chinese cabbage (Brassica campestris ssp. chinensis, NHCC), contributing significantly to yield, appearance, and desirability to consumers. However, the genetic basis of leaf shape and size in non-heading Chinese cabbage remains unclear. In this study, we developed a RIL population using ‘Maertou’, with slender leaves and narrow petioles, and ‘Suzhouqing’, with oval leaves and wide petioles, to construct a genetic linkage map and detect QTLs. To obtain stable and reliable QTLs, the 11 leaf-related traits, including the leaf length, leaf width, and fresh weight of the lamina and petiole and the thickness of petiole was observed on two locations—while the leaf shape, petiole shape, index of lamina/petiole length, and index of petiole fresh weight were calculated based on 7 leaf-related traits. QTL mapping illustrated that a total of 27 QTLs for leaf-related traits were preliminarily detected. The candidate genes were annotated and several genes involved in leaf development and leaf shape appeared in the overlapping regions of multiple loci, such as KRP2, GRF4, ARGOS, and SAUR9. This study lays the foundation for further exploration of the genetic mechanisms and development of effective molecular markers for leaf shape and size in NHCC.

Genetic Characterization of Gardenia jasminoides Ellis Genotypes Derived from Seeds and Selection Based on Their Morphological Traits and Flower Aromatic Substances

Gardenia jasminoides Ellis is an evergreen shrub with white fragrant flowers, and it is cultivated for its ornamental, aromatic and medicinal value. The present study aimed to select desirable genotypes for potential commercial exploitation as pot plants or use in perfumery. Thus, 32 genotypes of G. jasminoides plants derived from seedlings, whose seeds were obtained from Australia and the USA, were evaluated for their genetic diversity in relation to four commercial cultivars (‘Pelion’, ‘Joy’, ‘Grandiflora’ and ‘Kimberly’, used as reference cultivars) using ISSR and SCoT markers. A cluster analysis separated the gardenia genotypes into the following three clusters: one cluster comprised the 16 genotypes originating from Australia, one included the 16 genotypes originating from the USA, and the third cluster contained the four reference cultivars. In other words, there was a clear demarcation of the genotypes investigated according to their geographical origin. In addition, the gardenia genotypes were evaluated for their morphological and chemical characteristics. Thus, flower- and leaf-related traits with ornamental value were measured, while the volatile compounds of flower extracts were identified with GC-MS analysis. Genotype 29-5 was selected for its acceptable morphological traits and genotype 51-8 for its rich volatile compounds. The major volatile compounds responsible for the floral aroma of the various gardenia genotypes examined were α-farnesene, benzyl tiglate, cis-3-hexenyltiglate, jasminelactone and linalool.

QTL mapping for the flag leaf-related traits using RILs derived from Trititrigia germplasm line SN304 and wheat cultivar Yannong15 in multiple environments

BackgroundDeveloping and enriching genetic resources plays important role in the crop improvement. The flag leaf affects plant architecture and contributes to the grain yield of wheat (Triticum aestivum L.). The genetic improvement of flag leaf traits faces problems such as a limited genetic basis. Among the various genetic resources of wheat, Thinopyrum intermedium has been utilized as a valuable resource in genetic improvement due to its disease resistance, large spikes, large leaves, and multiple flowers. In this study, a recombinant inbred line (RIL) population was derived from common wheat Yannong15 and wheat-Th. intermedium introgression line SN304 was used to identify the quantitative trait loci (QTL) for flag leaf-related traits.ResultsQTL mapping was performed for flag leaf length (FLL), flag leaf width (FLW) and flag leaf area (FLA). A total of 77 QTLs were detected, and among these, 51 QTLs with positive alleles were contributed by SN304. Fourteen major QTLs for flag leaf traits were detected on chromosomes 2B, 3B, 4B, and 2D. Additionally, 28 QTLs and 8 QTLs for flag leaf-related traits were detected in low-phosphorus and drought environments, respectively. Based on major QTLs of positive alleles from SN304, we identified a pair of double-ended anchor primers mapped on chromosome 2B and amplified a specific band of Th. intermedium in SN304. Moreover, there was a major colocated QTL on chromosome 2B, called QFll/Flw/Fla-2B, which was delimited to a physical interval of approximately 2.9 Mb and contained 20 candidate genes. Through gene sequence and expression analysis, four candidate genes associated with flag leaf formation and growth in the QTL interval were identified.ConclusionThese results promote the fine mapping of QFll/Flw/Fla-2B, which have pleiotropic effects, and will facilitate the identification of candidate genes for flag leaf-related traits. Additionally, this work provides a theoretical basis for the application of Th. intermedium in wheat breeding.

Estimating leaf photosynthetic capacity using hyperspectral reflectance: Model variability and transferability

Leaf photosynthetic capacity is a crucial parameter for characterizing plant growth status and global nitrogen-carbon cycles. While leaf trait and reflectance models have been widely applied to assess leaf photosynthetic capacity across various plant species, the variability and transferability of these estimation models remain unclear. Thus, this study investigated the variability in estimating leaf maximum carboxylation rate of Rubisco (Vcmax, μmol m−2 s−1) using hyperspectral reflectance across seven plant species datasets. To improve model transferability, we proposed model updating by adding new samples and developed a stacking model to integrate multiple regression model results to reduce variability in the predictions. The PROSPECT model, coupled with spectral derivatives and similarity metrics, was used to retrieve leaf structural and biochemical traits. Our results showed that Vcmax was significantly correlated with the contents of leaf chlorophyll (Cab) and protein (Prot), and other traits such as leaf structure, carotenoid content, and water content also influenced Vcmax. However, the strength of these correlations varied among different datasets due to differences in vegetation types, growth periods, and the number of species. Leaf trait relationships also varied with datasets, with Cab proving to be a good proxy of photosynthesis across all datasets. Leaf traits were superior to leaf reflectance in characterizing the differences between datasets. While leaf reflectance performed well in estimating Vcmax for most datasets, leaf traits were more suitable for constructing transferable estimation models of Vcmax between different datasets. Model transferability was affected by differences in datasets, such as data range and plant species. Model updating by adding 10% new samples significantly improved the assessment of Vcmax, with leaf reflectance yielding better estimation results. Our data also revealed that different models produced inconsistent results, and a stacking model combining multiple models optimized the estimation of Vcmax using leaf traits and reflectance, with the cross-validation coefficient of determination and relative root mean square error of 0.88 and 19.92%, respectively. These findings offer new methods and ideas for assessing leaf photosynthetic capacity across different agro-ecosystems. Further recalibration of the proposed model with canopy radiative transfer models and datasets would enable monitoring of plant photosynthesis at large scales.

Variation in shoot architecture traits and their relationship to canopy coverage and light interception in soybean (Glycine max)

BackgroundIn soybeans, faster canopy coverage (CC) is a highly desirable trait but a fully covered canopy is unfavorable to light interception at lower levels in the canopy with most of the incident radiation intercepted at the top of the canopy. Shoot architecture that influences CC is well studied in crops such as maize and wheat, and altering architectural traits has resulted in enhanced yield. However, in soybeans the study of shoot architecture has not been as extensive.ResultsThis study revealed significant differences in CC among the selected soybean accessions. The rate of CC was found to decrease at the beginning of the reproductive stage (R1) followed by an increase during the R2-R3 stages. Most of the accessions in the study achieved maximum rate of CC between R2-R3 stages. We measured Light interception (LI), defined here as the ratio of Photosynthetically Active Radiation (PAR) transmitted through the canopy to the incoming PAR or the radiation above the canopy. LI was found to be significantly correlated with CC parameters, highlighting the relationship between canopy structure and light interception. The study also explored the impact of plant shape on LI and CO2 assimilation. Plant shape was characterized into distinct quantifiable parameters and by modeling the impact of plant shape on LI and CO2 assimilation, we found that plants with broad and flat shapes at the top maybe more photosynthetically efficient at low light levels, while conical shapes were likely more advantageous when light was abundant. Shoot architecture of plants in this study was described in terms of whole plant, branching and leaf-related traits. There was significant variation for the shoot architecture traits between different accessions, displaying high reliability. We found that that several shoot architecture traits such as plant height, and leaf and internode-related traits strongly influenced CC and LI.ConclusionIn conclusion, this study provides insight into the relationship between soybean shoot architecture, canopy coverage, and light interception. It demonstrates that novel shoot architecture traits we have defined here are genetically variable, impact CC and LI and contribute to our understanding of soybean morphology. Correlations between different architecture traits, CC and LI suggest that it is possible to optimize soybean growth without compromising on light transmission within the soybean canopy. In addition, the study underscores the utility of integrating low-cost 2D phenotyping as a practical and cost-effective alternative to more time-intensive 3D or high-tech low-throughput methods. This approach offers a feasible means of studying basic shoot architecture traits at the field level, facilitating a broader and efficient assessment of plant morphology.

Prohexadione-Calcium Mitigates the Overgrowth of Corn Seedlings

In the temperate climate of South Korea, specific corn varieties are cultivated using plug trays. The cultivation process is initiated from February to March within greenhouse facilities, maintaining a temperature below 10 degrees Celsius. Following this, in April, seedlings are transplanted to enable an exceptionally early harvest for increased profitability. However, the subsequent elevation in indoor temperatures leads to seedling overgrowth. This study explores the effectiveness of three plant growth regulators—paclobutrazol, prohexadione-calcium, and diniconazole–on super sweet corn seedlings. Significantly, the application of prohexadione-calcium at 2 ppm during the first leaf stage substantially reduces seedling height and impedes the growth of both the first and second internodes. This impact extends to leaf-related traits, manifesting reductions in the area, length, and width of the third leaf. Furthermore, prohexadione-calcium induces a significant decrease in both fresh and dried shoot weight, while simultaneously augmenting root weight. This alteration results in a noteworthy shift in the root–shoot ratio, particularly at 2 ppm. Subsequent experiments have identified the optimal concentration of prohexadione-calcium at 15 ppm, effectively mitigating overgrowth in both hybrid and inbred corn varieties. These findings provide essential insights for practitioners seeking to efficiently manage corn seedling overgrowth. The study contributes to understanding the retardant effect of prohexadione-calcium on various morphological traits, offering practical applications for optimizing plant growth regulator concentrations in corn cultivation strategies.

Leaf trait relationships with species ecological optimum and sustainability across wetland plants

Structural and functional parameters of leaves were studied in 19 dominant and abundant species growing in shallows and wet riversides at the mouth of the Maksimikha River (Barguzinsky district, Republic of Buryatia). To evaluate the species ecological optimum Tsyganov’ scales were used (Tsyganov, 1983). To assess the resistance, the potential ecological valence of the species on the illumination scale, as well as the climatic and soil tolerance indices of the species were applied (Zhukova et al., 2010). It was shown that the index of climatic tolerance of the species was negatively correlated with the leaf mass per area (LMA) (r = -0,68) and positively with the chlorophyll photosynthetic activity of (r = 0,51). A tendency was revealed to decrease in LMA and leaf dry matter content (LDMC) and increase in the chlorophyll photosynthetic activity in more thermophilic wetland plants. Leaf area positively correlated with the scores of the species optimum on the soil moisture and acidity scales (r = 0,59 and r = 0,72, respectively). LMA, the content and photosynthetic activity of chlorophyll correlated with the optimum scores on the soil nitrogen supply scale (r = -0,53, r = -0,50 and r = 0,72, respectively). The tolerance index of the species to soil factors was associated only with the content of chlorophylls (r = 0,68) and carotenoids (r = 0,55) per unit leaf area. The potential ecological valence of the species to illumination was positively correlated with leaf density and LDMC (r = 0,58 and r = 0,57, respectively). It was concluded that the thermoclimatic optimum of species of wetland plants, as well as their climate sustainability, are associated with changes in the LMA and chlorophyll photosynthetic activity. Edaphic factors had a greater influence on the structural and functional parameters of leaves than climatic ones, which manifested in a large number of relationships between soil scales and leaf traits. Wetland plant tolerance to a wider range of edaphic conditions was associated with a high content of chlorophylls and carotenoids.

Divergences in stem and leaf traits between lianas and coexisting trees in a subtropical montane forest

Abstract Patterns in functional trait variation associated with the ecological strategies of lianas and trees in subtropical montane forests remain poorly understood due to lack of trait comparisons. Here, we filled this gap by investigating trait divergence between lianas and trees with different leaf habits for 13 traits of 33 species (7 deciduous and 4 evergreen liana species, and 10 deciduous and 12 evergreen tree species) in a subtropical montane forest in southwestern China. We found that lianas had significantly larger stem xylem vessel diameter, higher theoretical hydraulic conductivity, specific leaf area, leaf nitrogen, and phosphorus concentrations, but lower leaf dry-matter content and N/P ratio than sympatric trees, indicating that lianas employ an acquisitive ecological strategy, with a more efficient stem hydraulic system and more productive leaves. In contrast to trees, lianas exhibited a larger variation in vessel diameter, with a few wide and many narrow vessels in the xylem, indicating a greater vessel dimorphism. Growth form explained 48.7% of the total trait variation, while leaf habit only explained 3.8% of trait variation, without significant interaction between growth form and leaf habit. In addition, significant stem–leaf trait relationships were only found in trees, but not in lianas, indicating decoupling of stem hydraulic function and leaf traits in subtropical lianas. These results suggest that subtropical montane lianas and trees differ strikingly in stem and leaf functional traits. Further studies are warranted to strengthen our understanding of the mechanisms underlying the strong divergence in ecological strategies between lianas and trees in subtropical forest ecosystems.

Genome-Wide Association Analysis of Rice Leaf Traits

Yield-related traits have always been a research hotspot in rice breeding, and functional leaves directly affect the photosynthetic efficiency and yield of rice. Therefore, it is of great significance to explore the genes related to rice leaf size and shape to improve rice leaf morphology, photosynthesis efficiency, and yield. This study detected the quantitative trait loci (QTLs) for the length, width, length–width ratio, and area of rice flag leaf and second leaf in 393 accessions from the 3000 Rice Genome Project (3KRGP) by high-density single-nucleotide polymorphism genotyping. As a result, 91 QTLs were detected, among which 5 candidate genes (LOC_Os03g29170, LOC_Os06g17285, LOC_Os04g35060, LOC_Os03g27450, and LOC_Os09g16280) were identified. In addition, the epistatic interactions affecting leaf-related traits were also investigated, resulting in the identification of 134 significant QQIs (QTL by QTL interactions) pairs. The results of this study provide an important genetic basis for mining genes associated with rice leaf shape and valuable genetic information for rice breeding.

Effects of long‐term mowing on leaf‐ and root‐associated bacterial community structures are linked to functional traits in 11 plant species from a temperate steppe

Abstract Long‐term mowing can cause morphological stuntedness of plants, thus reducing grassland productivity and exacerbating grassland degradation. Although plant microbiomes can enhance plant resistance against disturbance, considerable uncertainty exists regarding how mowing and mowing‐induced plant trait plasticity affect plant microbiomes in natural grasslands. Here we examined the responses of leaf/root‐associated bacterial (LAB/RAB) communities of 11 dominant herbaceous perennials (six replicates per species) to a 17‐year mowing treatment in a temperate grassland. We also measured leaf/root physiological and morphological traits, and analysed the relationships among mowing practice, bacterial community structures and leaf/root trait parameters. We found that both leaf and root functional traits showed interspecific variations (variations across different plant species), while only the leaf traits exhibited intraspecific variation (treatment‐induced variations within plant species) between the treatments. Similarly, the LAB community structure was more sensitive to mowing but less influenced by host species identity, compared to the RAB community. The RAB community structure was primarily shaped by host species identity, while mowing was a secondary influencing factor. The different patterns of LAB and RAB communities in response to mowing could be specifically explained by the inter/intraspecific variations of the related leaf and root traits. The LAB community was strongly correlated with the leaf traits which exhibited mowing‐induced plasticity (intraspecific variation), with the correlations with nitrogen resorption efficiency and above‐ground dry weight being the greatest. The root traits were important indicators of bacterial community structure in the root compartment across the hosts, rather than between the treatments. Root tissue density showed the strongest interspecific variation, and was identified as an overwhelming driver of the RAB community. The shifts in LAB/RAB communities under mowing were largely attributed to the increased proportions of Actinobacteria. The high mowing sensitivity of the LAB community was associated with the enrichment of soil‐derived Actinobacteria in leaves under mowing. Actinobacteria were also the main keystone taxa in the bacterial community networks under mowing. Our results demonstrate that the magnitude of plant‐associated microbial community response to long‐term mowing is plant compartment and trait variation dependent, and advance our understanding of the leaf/root microbiome‐trait relationships in complex plant communities. Read the free Plain Language Summary for this article on the Journal blog.

Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing

BackgroundStudying the genetic characteristics of tea plant (Camellia spp.) leaf traits is essential for improving yield and quality through breeding and selection. Guizhou Plateau, an important part of the original center of tea plants, has rich genetic resources. However, few studies have explored the associations between tea plant leaf traits and single nucleotide polymorphism (SNP) markers in Guizhou.ResultsIn this study, we used the genotyping-by-sequencing (GBS) method to identify 100,829 SNP markers from 338 accessions of tea germplasm in Guizhou Plateau, a region with rich genetic resources. We assessed population structure based on high-quality SNPs, constructed phylogenetic relationships, and performed genome-wide association studies (GWASs). Four inferred pure groups (G-I, G-II, G-III, and G-IV) and one inferred admixture group (G-V), were identified by a population structure analysis, and verified by principal component analyses and phylogenetic analyses. Through GWAS, we identified six candidate genes associated with four leaf traits, including mature leaf size, texture, color and shape. Specifically, two candidate genes, located on chromosomes 1 and 9, were significantly associated with mature leaf size, while two genes, located on chromosomes 8 and 11, were significantly associated with mature leaf texture. Additionally, two candidate genes, located on chromosomes 1 and 2 were identified as being associated with mature leaf color and mature leaf shape, respectively. We verified the expression level of two candidate genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and designed a derived cleaved amplified polymorphism (dCAPS) marker that co-segregated with mature leaf size, which could be used for marker-assisted selection (MAS) breeding in Camellia sinensis.ConclusionsIn the present study, by using GWAS approaches with the 338 tea accessions population in Guizhou, we revealed a list of SNPs markers and candidate genes that were significantly associated with four leaf traits. This work provides theoretical and practical basis for the genetic breeding of related traits in tea plant leaves.

Individual and combined effects of arbuscular mycorrhizal fungi and phytohormones on the growth and physiobiochemical characteristics of tea cutting seedlings.

Both arbuscular mycorrhizal fungi (AMF) and phytohormones collectively regulate plant growth and root development, but their individual and combined effects on tea [Camellia sinensis (L.) O. Kuntze] cutting seedings remain unclear. This study examined the individual and combined effects of two species of AMF (Rhizophagus intraradices, RI and Funneliformis mosseae, FM) and two types of palnt hormones (strigolactones, SLs; polyamines, PAs) on tea cutting seedings, by evaluating the growth and physiobiochemical characteristics of plants treated with the AMFs and/or hormones. The results showed that inoculation with either AMF individually or hormones treatment alone could significantly enhanced mycorrhizal colonization, growth target and physiobiochemical characteristics of tea cutting seedlings. Interestingly, the addition of a combination of AMFs and hormones showed superior effects, while SL and RI exhibited the most improvements to the colonization rate, plant growth, root-morphological traits, root DHA activity, photosynthesis, chlorophyll content, soluble sugar content in leaves, and the activities of antioxidant enzymes (SOD, POD, and CAT), compared to other treatment combinations (SL + FM, PA + RI, and PA + FM). Correlation analyses revealed a significantly (p < 0.05) positive correlation of root AMF colonization with root-related traits (e.g., DHA, root total length, surface area, and volume) and leaf-related traits (e.g., leaf area, shoot biomass, total chlorophyll, and antioxidant enzyme activities). This study demonstrated that while the apllication of individual AMF or plant hormones had a certain good effects on most growth and physiobiochemical characteristics parameters of tea cutting seedings, the additive effect was from specific combined of AMF and plant hormones. These results highlight the possibility for combined of AMF and plant hormones to improve the asexual reproduction of tea plants via cuttings.

QTL Mapping of Leaf-Related Traits Using a High-Density Bin Map in Brassica rapa

The species Brassica rapa includes enormous leafy vegetables with extreme leaf morphological diversity. Leaf traits such as size, shape, weight, and ratio of the leaf blade to the petiole contribute to yield, appearance, and desirability to consumers. These leaf-related traits are controlled by quantitative trait loci (QTLs). The construction of high-density bin maps using low-coverage sequencing is a powerful method for QTL fine-mapping and gene identification. In this study, we performed whole-genome re-sequencing of Wutacai ‘Zhongbaye’ and Chinese cabbage ‘HN53’ and 150 F2 individuals to construct a high-density bin map for QTL mapping of 11 leaf-related traits. The parental lines and F2 population were re-sequenced at 10x and 1x coverage, respectively. A map containing 565 bin markers was constructed based on parental single-nucleotide polymorphisms and a modified sliding window approach. The total map length was 944.6 cM and the average distance of the bins was 1.65 cM. In total, 60 significant QTLs controlling 11 leaf-related traits were detected. We further identified candidate genes responsible for these complex leaf-related traits. These findings suggest that this cost-effective bin-mapping approach is capable of rapid identification of QTLs and candidate genes, and will thus facilitate the dissection of the underlying molecular basis of leaf morphological variations and accelerate the improvement of B. rapa vegetable breeding.

Characteristics of plant trait network and its influencing factors in impounded lakes and channel rivers of South-to-North Water Transfer Project, China.

Trait-based approaches have been widely used to evaluate the effects of variable environments on submerged macrophytes communities. However, little research focused on the response of submerged macrophytes to variable environmental factors in impounded lakes and channel rivers of water transfer project, especially from a whole plant trait network (PTN) perspective. Here, we conducted a field survey designed to clarify the characteristic of PTN topology among impounded lakes and channel rivers of the East Route of South-to-North Water Transfer Project (ERSNWTP) and to unravel the effects of determining factors on the PTN topology structure. Overall, our results showed that leaf-related traits and organ mass allocation traits were the hub traits of PTNs in impounded lakes and channel rivers of the ERSNWTP, which traits with high variability were more likely to be the hub traits. Moreover, PTNs showed different structures among impounded lakes and channel rivers, and PTNs topologies were related to the mean functional variation coefficients of lakes and channel rivers. Specially, higher mean functional variation coefficients represented tight PTN, and lower mean functional variation coefficients indicated loose PTN. The PTN structure was significantly affected by water total phosphorus and dissolved oxygen. Edge density increased, while average path length decreased with increasing total phosphorus. Edge density and average clustering coefficient showed significant decreases with increasing dissolved oxygen, while average path length and modularity exhibited significant increases with increasing dissolved oxygen. This study explores the changing patterns and determinants of trait networks along environmental gradients to improve our understanding of ecological rules regulating trait correlations.

A Wheat 660K SNP array-based high-density genetic map facilitates QTL mapping of flag leaf-related traits in wheat.

A high-density genetic map containing122,620 SNP markers was constructed, which facilitated the identification of eight major flag leaf-related QTL in relatively narrow intervals. The flag leaf plays an important role in photosynthetic capacity and yield potential in wheat. In this study, we used a recombinant inbred line population containing 188 lines derived from a cross between 'Lankao86' (LK86) and 'Ermangmai' to construct a genetic map using the Wheat 660K single-nucleotide polymorphism (SNP) array. The high-density genetic map contains 122,620 SNP markers spanning 5185.06cM. It shows good collinearity with the physical map of Chinese Spring and anchors multiple sequences of previously unplaced scaffolds onto chromosomes. Based on the high-density genetic map, we identified seven, twelve, and eight quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), and area (FLA) across eight environments, respectively. Among them, three, one, and four QTL for FLL, FLW, and FLA are major and stably express in more than four environments. The physical distance between the flanking markers for QFll.igdb-3B/QFlw.igdb-3B/QFla.igdb-3B is only 444kb containing eight high confidence genes. These results suggested that we could directly map the candidate genes in a relatively small region by the high-density genetic map constructed with the Wheat 660K array. Furthermore, the identification of environmentally stable QTL for flag leaf morphology laid a foundation for the following gene cloning and flag leaf morphology improvement.

Combined linkage mapping and association analysis uncovers candidate genes for 25 leaf-related traits across three environments in maize.

Combined linkage and association analysis revealed five co-localized genetic loci across multiple environments. The key gene Zm00001d026491 was further verified to influence leaf length by candidate gene association analysis. Leaf morphology and number determine the canopy structure and thus affect crop yield. Herein, the genetic basis and key genes for 25 leaf-related traits, including leaf lengths (LL), leaf widths (LW), and leaf areas (LA) of eight continuous leaves under the tassel, and the number of leaves above the primary ear (LAE), were dissected by using an association panel and a biparental population. Using an intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, 290 quantitative trait loci (QTL) controlling these traits were detected across different locations, among which 115 QTL were individually repeatedly identified in at least two environments. Using the association panel, 165 unique significant single-nucleotide polymorphisms (SNPs) were associated with target traits (P < 2.15E-06), of which 35 were separately detected across multiple environments. In total, 42 pleiotropic QTL/SNPs (pQTL/SNPs) were responsible for at least two of the LL, LW, LA, and LAE traits across multiple environments. Combining the QTL mapping and association study, five unique SNPs were located within the confidence intervals of seven QTL, and 77 genes were identified based on the linkage disequilibrium regions of co-localized SNP loci. Gene-based association studies verified that the intragenic variants in the candidate gene Zm00001d026491 influenced LL of the third leaf counted from the top node. These findings will provide vital information to understanding the genetic basis of leaf-related traits and help to cultivate maize varieties with ideal plant architecture.

Predicting ecosystem productivity based on plant community traits.

With the rapid accumulation of plant trait data, major opportunities have arisen for the integration of these data into predicting ecosystem primary productivity across a range of spatial extents. Traditionally, traits have been used to explain physiological productivity at cell, organ, or plant scales, but scaling up to the ecosystem scale has remained challenging. Here, we show the need to combine measures of community-level traits and environmental factors to predict ecosystem productivity at landscape or biogeographic scales. We show how theory can extend the production ecology equation to enormous potential for integrating traits into ecological models that estimate productivity-related ecosystem functions across ecological scales and to anticipate the response of terrestrial ecosystems to global change.