Association of SSR markers with functional traits from heat stress in diverse tall fescue accessions

Nitrate reduces copper toxicity by preventing oxidative stress and inhibiting copper translocation from roots to shoots in Liriodendron Chinense

Nitrogen forms can affect metal accumulation in plants and tolerance to metals, but a few published studies on the effects on Cu toxicity and Cu accumulation in plants are scarce. Thus, the objective of this study was to evaluate the responses of Liriodendron chinense to different nitrogen forms, by the oxidative stress, antioxidant enzymes system, GSH-AsA cycle, Cu uptake, translocation, and accumulation under Cu stress. We found that Cu-induced growth inhibiting was alleviated by added exclusive NO3--N. Adding N as NH4+-N with or without NO3--N was aggravated as evidenced by significantly elevated malonaldehyde (MDA) and hydrogen peroxide (H2O2) compared to N-Null. Cu exposure and adding NH4+-N inhibited superoxide dismutase activity, but remarkably stimulated the activities of catalase and peroxidase, the efficiency of glutathione-ascorbate (GSH-AsA) cycle, and the activity of glutathione reductase and nitrate reductase, with respect to the control. However, adding exclusive NO3--N progressively restored the alteration of antioxidant to prevent Cu-induced oxidative stress. Additionally, adding exclusive NO3--N significantly promoted the Cu uptake and accumulation in roots, but reduced Cu concentration in leaves, accompanied by the inhibited Cu translocation factor from roots to shoots by 36.7%, when compared with N-Null. Overall, adding NO3--N alleviated its Cu toxicity by preventing Cu-induced oxidative stress and inhibiting Cu translocation from roots to shoots, which provides an effective strategy for phytostabilization in Cu-contaminated lands.

Pigment Diversity in Leaves of Caladium × hortulanum Birdsey and Transcriptomic and Metabolic Comparisons between Red and White Leaves

Leaf color is a key ornamental characteristic of cultivated caladium (Caladium × hortulanum Birdsey), a plant with diverse leaf colors. However, the genetic improvement of leaf color in cultivated caladium is hindered by the limited understanding of leaf color diversity and regulation. In this study, the chlorophyll and anthocyanin content of 137 germplasm resources were measured to explore the diversity and mechanism of leaf color formation in cultivated caladium. Association analysis of EST-SSR markers and pigment traits was performed, as well as metabolomics and transcriptomics analysis of a red leaf variety and its white leaf mutant. We found significant differences in chlorophyll and anthocyanin content among different color groups of cultivated caladium, and identified three, eight, three, and seven EST-SSR loci significantly associated with chlorophyll-a, chlorophyll-b, total chlorophyll and total anthocyanins content, respectively. The results further revealed that the white leaf mutation was caused by the down-regulation of various anthocyanins (such as cyanidin-3-O-rutinoside, quercetin-3-O-glucoside, and others). This change in concentration is likely due to the down-regulation of key genes (four PAL, four CHS, six CHI, eight F3H, one F3'H, one FLS, one LAR, four DFR, one ANS and two UFGT) involved in anthocyanin biosynthesis. Concurrently, the up-regulation of certain genes (one FLS and one LAR) that divert the anthocyanin precursors to other pathways was noted. Additionally, a significant change in the expression of numerous transcription factors (12 NAC, 12 bZIP, 23 ERF, 23 bHLH, 19 MYB_related, etc.) was observed. These results revealed the genetic and metabolic basis of leaf color diversity and change in cultivated caladium, and provided valuable information for molecular marker-assisted selection and breeding of leaf color in this ornamental plant.

Phenotypic Variation in Flower Color and Morphology in the Gerbera (Gerbera hybrida) F1 Hybrid Population and Their Association with EST-SSR Markers

Gerbera (Gerbera hybrida) is a widely cultivated ornamental plant. However, its genetic improvement is limited by the lack of genetic analysis and molecular markers for traits. In this study, we analyzed the phenotypic and genotypic variation of 140 F1 progeny from two gerbera varieties with different flower types and colors. We evaluated the flower's morphology, color, and pigment content of the F1 population and performed cluster principal component analysis (PCA) and correlation analysis. The results showed that the main ornamental traits of the hybrid progeny varied greatly. The segregation ratios of single and double flowers and ligulate and split ray florets were both 1:1. The flower colors of the F1 progeny were mainly red and purple-red, similar to the male parent's color. Furthermore, we conducted a genetic analysis of the hybrid progeny using EST-SSR markers and performed association analysis with phenotypic traits. We identified 2, 2, 3, 1, and 2 loci to be associated with peduncle length (PL), ray floret length (RFL), and outer ray floret; the level of apex relative to the top of involucre (LAI); outer corolla lips (OCL); and the b* of ray floret color, respectively. Our results reveal the genetic patterns of important ornamental traits and provide a theoretical basis and practical tools for gerbera genetic breeding.

Exploring genetic diversity and ascertaining genetic loci associated with important fruit quality traits in apple (Malus × domestica Borkh.)

Genetic diversity is the primary source of variability in any crop improvement program, and the diverse germplasm of any crop species represents an important genetic resource for gene or allele mining to meet future needs. Huge genetic and phenotypic diversity is present in the apple gene pool, even though, breeding programs have been mainly focused on a few traits of interests, which have resulted in the reduction of the diversity in the cultivated lines of apple. Therefore, the present study was carried out on 70 diverse apple genotypes with the objective of analyzing the genetic diversity and to identify the genetic loci associated with important fruit quality traits. A total of 140 SSR primers were used to characterize the 70 genotypes of apples, out of which only 88 SSRs were found to be polymorphic. The PIC values varied from 0.03 to 0.75. The value of MI, EMR, and RP varied from 0.03 to 3.5, 0.5 to 5.0, and 1.89 to 6.74, respectively. The dendrogram and structure analysis divided all the genotypes into two main groups. In addition to this, large phenotypic variability was observed for the fruit quality traits under study indicated the suitability of the genotypes for association studies. Altogether 71 novel MTAs were identified for 10 fruit quality traits, of which 15 for fruit length, 15 for fruit diameter, 12 for fruit weight, 2 for total sugar, 2 for TSS, 4 for reducing sugar, 5 for non-reducing sugar, 5 for fruit firmness, 5 for fruit acidity and 6 for anthocyanin, respectively. Consistent with the physicochemical evaluation of traits, there was a significant correlation coefficient among different fruit quality characters, and many common markers were found to be associated with these traits (fruit diameter, length, TSS, total sugar, acidity and anthocyanin, respectively) by using the different modeling techniques (GLM, MLM). The inferred genetic structure, diversity pattern and the identified MTAs will be serving as resourceful grounds for better predictions and understanding of apple genome towards efficient conservation and utilization of apple germplasm for facilitating genetic improvement of fruit quality traits. Furthermore, these findings also suggested that association mapping could be a viable alternative to the conventional QTL mapping approach in apple.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01382-w.

Root system architecture and genomic plasticity to salinity provide insights into salt-tolerant traits in tall fescue

Salinity is detrimental to soil health, plant growth, and crop productivity. Understanding salt tolerance mechanisms offers the potential to introduce superior crops, especially in coastal regions. Root system architecture (RSA) plasticity is vital for plant salt stress adaptation. Tall fescue is a promising forage grass in saline regions with scarce RSA studies. Here, we used the computer-integrated and -automated programs EZ-Rhizo II and ROOT-Vis II to analyze and identify natural RSA variations and adaptability to high salt stress at physiological and genetic levels in 17 global tall fescue accessions. Total root length rather than the number of lateral roots contribute more to water uptake and could be used to separate salt-tolerant (LS-11) and -sensitive accessions (PI531230). Comparative evaluation of LS-11 and PI531230 demonstrated that the lateral root length rather than the main root contributed more towards the total root length in LS-11. Also, high water uptake was associated with a larger lateral root vector and position while low water intake was associated with an insignificant correlation between root length, vector, and position. To examine candidate gene expression, we performed transcriptome and transcription analyses using high-throughput RNA sequencing and real-time quantitative PCR, respectively of the lateral and main roots. The main root displayed more differentially expressed genes than the lateral root. A Poisson comparison of LS-11 vs PI531230 demonstrated significant upregulation of PLASMA MEMBRANE AQUAPORIN 1 and AUXIN RESPONSE FACTOR 22 in both the main and lateral root, which are associated with transmembrane water transport and the auxin-activated signaling system, respectively. There is also an upregulation of BASIC HELIX-LOOP-HELIX 5 in the main root and a downregulation in the lateral root, which is ascribed to sodium ion transmembrane transport, as well as an upregulation of THE MEDIATOR COMPLEX 1 assigned to water transport in the lateral root and a downregulation in the main root. Gene-protein interaction analysis found that more genes interacting with aquaporins proteins were upregulated in the lateral root than in the main root. We inferred that deeper main roots with longer lateral roots emanating from the bottom of the main root were ideal for tall fescue water uptake and salt tolerance, rather than many shallow roots, and that, while both main lateral roots may play similar roles in salt sensing and water uptake, there are intrinsic genomic differences.

Association analysis revealed loci linked to post-drought recovery and traits related to persistence of smooth bromegrass (Bromus inermis)

Association analysis has been proven as a powerful tool for the genetic dissection of complex traits. This study was conducted to identify association of recovery, persistence, and summer dormancy with sequence related amplified polymorphism (SRAP) markers in 36 smooth bromegrass genotypes under two moisture conditions and find stable associations. In this study, a diverse panel of polycross-derived progenies of smooth bromegrass was phenotyped under normal and water deficit regimes for three consecutive years. Under water deficit, dry matter yield of cut 1 was approximately reduced by 36, 39, and 37% during 2013, 2014, and 2015, respectively, compared with the normal regime. For dry matter yield of cut 2, these reductions were approximately 38, 60, and 56% in the same three consecutive years relative to normal regime. Moreover, water deficit decreased the RY and PER of the genotypes by 35 and 28%, respectively. Thirty primer combinations were screened by polymerase chain reaction (PCR). From these, 541 polymorphic bands were developed and subjected to association analysis using the mixed linear model (MLM). Population structure analysis identified five main subpopulations possessing significant genetic differences. Association analysis identified 69 and 46 marker-trait associations under normal and water deficit regimes, respectively. Some of these markers were associated with more than one trait; which can be attributed to pleiotropic effects or tightly linked genes affecting several traits. In normal and water-deficit regimes, these markers could potentially be incorporated into marker-assisted selection and targeted trait introgression for the improvement of drought tolerance of smooth bromegrass.

Classification and Association Analysis of Gerbera (Gerbera hybrida) Flower Color Traits

Floral color plays a crucial role in plant life such as plant-pollinator interactions and modifying the abiotic environment of reproductive structures. In the current study, 123 gerbera accessions were divided into six color groups (white, yellow, orange, pink, red, and purple), based on Royal Horticultural Society Color Chart calibration and colorimeter measurement. Partial least squares discriminant analysis showed that the white group was mainly affected by L* value, a* value, C value, and total anthocyanin contents, while the yellow group was positively correlated with L* value, b* value, and total anthocyanin contents. Similarly, the orange group was mainly affected by b* value and total carotenoid contents, whereas the pink group was positively correlated with L* and h values. Furthermore, the red group was affected by L* value, a* value, C value, and total anthocyanin contents, whilst the purple group was mainly distributed by L* value, a* value, b* value, and total anthocyanin contents. Based on 'Jin Xiang' transcriptome data, 14,106 expressed sequence tag (EST)-SSR markers were identified and 48 pairs of primers (19 newly developed primers) were screened. Population genetic structure, neighbor-joining clustering, and principal coordinate analysis showed that 123 gerbera accessions could be divided into two groups. EST-SSR-based association analysis showed that 1, 1, 2, 1, 1, 2, and 1 significant loci were related to L*, a*, b*, C, and h, total carotenoid, and total anthocyanin contents, respectively. These results provide an important reference for flower color classification and genetic improvement of gerbera.

Overexpression of FaHSP17.8-CII improves cadmium accumulation and tolerance in tall fescue shoots by promoting chloroplast stability and photosynthetic electron transfer of PSII

Genetic improvement could play a significant role in enhancing the Cd accumulation, translocation and tolerance in plants. In this study, for the first time, we constructed transgenic tall fescue overexpressing a class II (CII) sHSP gene FaHSP17.8-CII, which enhanced Cd tolerance and the root-to-shoot Cd translocation. After exposed to 400 μM CdCl₂, two FaHSP17.8-CII overexpressing lines (OE#3 and OE#7) exhibited 30% and 40% more shoot fresh weight, respectively, relative to the wild-type (WT). Both transgenic lines showed higher tolerance to Cd, as evidenced by lower levels of electrolyte leakage and malondialdehyde compared to the WT plants under Cd stress. FaHSP17.8-CII overexpression increased shoot Cd contents 49-59% over the WT plants. The Cd translocation factor of root-to-shoot in OE grasses was 69-85% greater than WT under Cd stress. Furthermore, overexpression of FaHSP17.8-CII reduced Cd-induced damages of chloroplast ultra-structure and chlorophyll synthesis, and then improved photosystem II (PSII) function under Cd stress, which resulted in less reactive oxygen species (ROS) accumulation in OE grasses than that in WT exposed to Cd stress. The study suggests a novel FaHSP17.8-CII-PSII-ROS module to understand the mechanisms of Cd detoxification and tolerance, which provides a new strategy to improve phytoremediation efficiency in Cd-stressed grasses.

Dissection of Allelic Variation Underlying Floral and Fruit Traits in Flare Tree Peony (Paeonia rockii) Using Association Mapping

Allelic variation in floral quantitative traits, including the elements of flowers and fruits, is caused by extremely complex regulatory processes. In the genetic improvement of flare tree peony (Paeonia rockii), a unique ornamental and edible oil woody species in the genus Paeonia, a better understanding of the genetic composition of these complex traits related to flowers and fruits is needed. Therefore, we investigated the genetic diversity and population structure of 160 P. rockii accessions and conducted single-marker association analysis for 19 quantitative flower and fruit traits using 81 EST-SSR markers. The results showed that the population had a high phenotypic diversity (coefficients of variation, 11.87-110.64%) and a high level of genetic diversity (mean number of alleles, N _A = 6.09). These accessions were divided into three subgroups by STRUCTURE analysis and a neighbor-joining tree. Furthermore, we also found a low level of linkage disequilibrium between these EST-SSRs and, by single-marker association analysis, identified 134 significant associations, including four flower traits with 11 EST-SSRs and 10 fruit traits with 32 EST-SSRs. Finally, based on the sequence alignment of the associated markers, P280, PS2, PS12, PS27, PS118, PS131, and PS145 may be considered potential loci to increase the yield of flare tree peony. These results laid the foundation for further analysis of the genetic structure of some key traits in P. rockii and had an obvious potential application value in marker-assisted selection breeding.

Marker-trait association analysis for drought tolerance in smooth bromegrass

BACKGROUND

Little information is available on the application of marker-trait association (MTA) analysis for traits related to drought tolerance in smooth bromegrass. The objectives of this study were to identify marker loci associated with important agronomic traits and drought tolerance indices as well as fining stable associations in a diverse panel of polycross derived genotypes of smooth bromegrass. Phenotypic evaluations were performed at two irrigation regimes (normal and deficit irrigation) during 2 years; and association analysis was done with 626 SRAP markers.

RESULTS

The results of population structure analysis identified three main subpopulations possessing significant genetic differences. Under normal irrigation, 68 and 57 marker-trait associations were identified using general linear model (GLM) and mixed linear mode1 (MLM), respectively. While under deficit irrigation, 61 and 54 markers were associated with the genes controlling the studied traits, based on these two models, respectively. Some of the markers were associated with more than one trait. It was revealed that markers Me1/Em5-11, Me1/Em3-15, and Me5/Em4-7 were consistently linked with drought-tolerance indices.

CONCLUSION

Following marker validation, the MTAs reported in this panel could be useful tools to initiate marker-assisted selection (MAS) and targeted trait introgression of smooth bromegrass under normal and deficit irrigation regimes, and possibly fine mapping and cloning of the underlying genes and QTLs.

Development and validation of heat-responsive candidate gene and miRNA gene based SSR markers to analysis genetic diversity in wheat for heat tolerance breeding

Being a major staple food crop of the world, wheat provides nutritional food security to the global populations. Heat stress is a major abiotic stress that adversely affects wheat production throughout the world including Indo-Gangatic Plains (IGP) where four wheat growing countries viz., India, Bangladesh, Nepal and Pakistan produce 42% of the total wheat production. Therefore, identification of heat stress responsive molecular markers is imperative to marker assisted breeding programs. Information about trait specific gene based SSRs is available but there is lack of information on SSRs from non-coding regions. In the present study, we developed 177 heat-responsive gene-based SSRs (cg-SSR) and MIR gene-based SSR (miRNA-SSR) markers from wheat genome for assessing genetic diversity analysis of thirty- six contrasting wheat genotypes for heat tolerance. Of the 177 SSR loci, 144 yielded unambiguous and repeatable amplicons, however, thirty-seven were found polymorphic among the 36 wheat genotypes. The polymorphism information content (PIC) of primers used in this study ranged from 0.03-0.73, with a mean of 0.35. Number of alleles produced per primer varied from 2 to 6, with a mean of 2.58. The UPGMA dendrogram analysis grouped all wheat genotypes into four clusters. The markers developed in this study has potential application in the MAS based breeding programs for developing heat tolerant wheat cultivars and genetic diversity analysis of wheat germplasm. Identification of noncoding region based SSRs will be fruitful for identification of trait specific wheat germplasm.

High temperature damage to fatty acids and carbohydrate metabolism in tall fescue by coupling deep transcriptome and metabolome analysis

High temperature damage impairs the growth of tall fescue by inhibiting secondary metabolites. Little is known about the regulation pattern of the fatty acids and carbohydrate metabolism at the whole-transcriptome level in tall fescue under high temperature stress. Here, two tall fescue genotypes, heat tolerant PI578718 and heat sensitive PI234881 were subjected to high temperature stress for 36 h. PI 578718 showed higher SPAD chloroplast value, lower EL and leaf injury than PI 234881 during the first 36 h high-temperature stress. Furthermore, by transcriptomic analysis, 121 genes were found to be induced during the second energy production phase in tall fescue exposed to high-temperature conditions, indicating that there may be one energy-sensing system in cool-season turfgrass to adapt high-temperature conditions. PI 578718 showed higher differentially expressed unigenes involved in fatty acids and carbohydrate metabolism compared with PI 234881 for 36 h heat stress. Interestingly, a metabolomic analysis using GC-MS uncovered that the sugars and sugar alcohol accounted for more than 65.06% of the total 41 metabolites content and high-temperature elevated the rate to 82.89-91.16% in PI 578718. High-temperature damage decreased the rate of fatty acid in the total 41 metabolites content and PI 578718 showed lower content than in PI 234881, which might be attributed to the down-regulated genes in fatty acid biosynthesis pathway in tall fescue. The integration of deep transcriptome and metabolome analyses provides systems-wide datasets to facilitate the identification of crucial regulation factors in cool-season turfgrass in response to high-temperature damage.

Development of EST-SSR markers and association mapping with floral traits in Syringa oblata

BACKGROUND

Lilac (Syringa oblata) is an important woody plant with high ornamental value. However, very limited genetic marker resources are currently available, and little is known about the genetic architecture of important ornamental traits for S. oblata, which is hindering its genetic studies. Therefore, it is of great significance to develop effective molecular markers and understand the genetic architecture of complex floral traits for the genetic research of S. oblata.

RESULTS

In this study, a total of 10,988 SSRs were obtained from 9864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3611). A set of 2042 primer pairs were validated, out of which 932 (45.7%) exhibited successful amplifications, and 248 (12.1%) were polymorphic in eight S. oblata individuals. In addition, 30 polymorphic EST-SSR markers were further used to assess the genetic diversity and the population structure of 192 cultivated S. oblata individuals. Two hundred thirty-four alleles were detected, and the PIC values ranged from 0.23 to 0.88 with an average of 0.51, indicating a high level of genetic diversity within this cultivated population. The analysis of population structure showed two major subgroups in the association population. Finally, 20 significant associations were identified involving 17 markers with nine floral traits using the mixed linear model. Moreover, marker SO104, SO695 and SO790 had significant relationship with more than one trait.

CONCLUSION

The results showed newly developed markers were valuable resource and provided powerful tools for genetic breeding of lilac. Beyond that, our study could serve an efficient foundation for further facilitate genetic improvement of floral traits for lilac.

Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome

BACKGROUND

Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS).

RESULTS

The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%).

CONCLUSIONS

Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.

The transferability of microsatellite loci from a homoploid to a polyploid hybrid complex: an example from fine-leaved Festuca species (Poaceae)

Background

Microsatellite loci, or single sequence repeats (SSR), are widely used as powerful markers in population genetics. They represent an attractive tool for studying plants such as grasses, whose evolution is driven by hybridisation and polyploidization. However, the development of microsatellite markers has been challenging and time-consuming, especially for non-model organisms lacking available genome-wide sequence data. One straightforward and low-cost approach is to transfer the SSR loci developed for one species, or complex, to another closely-related one. This work evaluates the transferability of microsatellite loci from homoploid to allopolyploid complexes of fine-leaved Festuca species and to assess their use in two new species. The studied complex (F. amethystina-F. tatrae) is a useful model for research on the local adaptability of grasses with different ploidy levels. Since both species can be considered as rare or threatened (F. tatrae-as a mountain and narrow endemic species and F. amethystina-a mountain species with relict lowland populations), any tool enabling studies on genetic diversity and population genetics, such as SSR markers, could also be very useful in a conservation context.

Methods

The ploidy level within populations was estimated using flow cytometry. One diploid and one tetraploid population of F. amethystina and a diploid population of F. tatrae were chosen to test the transferability of SSR loci. Because our work describes the transfer of SSR nuclear markers designed originally for F. gautieri, a phylogenetic tree was prepared based on the ITS marker to assess the genetic distance between the studied complexes. The PCR products were separated on a high-resolution agarose gel, intended for SSR marker analysis. Appropriate solutions for the allotetraploid population and whole mixed-ploidy complex were implemented.

Results

Flow cytometry confirmed earlier data regarding DNA content in the investigated species and cytotypes. The phylogenetic ITS tree indicated a small genetic distance between F. gautieri complexes and the studied species. Ten microsatellite markers were successfully transferred. All markers were polymorphic. In total, 163 different alleles were scored from the 10 SSR loci. PCoA of accessions revealed well-separated groups corresponding to studied populations. Over 60% of the total variance is explained by differentiation within populations and one third among them.

Conclusions

The transferred markers are valid tools for the study of population genetics and inheritance relationships within cytotypes and species and between them. The presented markers can be used to study inbreeding depression in the Festuca species, and variations in the degrees of genetic diversity between different cytotypes in mountain and lowland areas. Our findings can also be applied to study conservation strategies for ensuring biodiversity at the genetic level in polyploid complexes.

Effect of simulated warming on leaf functional traits of urban greening plants

BACKGROUND

Response and adaptation strategies of plants to the environment have always been the core issues in ecological research. So far, relatively little study exists on its functional traits responses to warming, especially in an urban environment. This information is the key to help understand plant responses and trade-off strategy to urban warming.

RESULTS

We chose the common greening trees of mature age in Beijing (Fraxinus pennsylvanica, Koelreuteria paniculata, and Sophora japonica) as the research subjects, and used infrared heaters to simulate warming for three gradients of natural temperature (CK), moderate warming (T1) and severe warming (T2). Results showed that:(1) Leaf dry matter content (LDMC), chlorophyll content (CHL), leaf tissue density (LTD), and stomatal density (SD) all increased with temperature warming. Specific leaf area (SLA), stomatal size (SS), and stomatal aperture (SA) decreased with simulated warming. (2) SLA was extremely significantly negatively correlated with CHL, LDMC, LTD and SD (P < 0.01), and was extremely significantly positively correlated with SS (P < 0.01). SA was extremely negatively correlated with SD (P < 0.01), and was extremely significantly positively correlated with SS (P < 0.01). There was a significant positive correlation between LDMC and LTD (P < 0.01). This showed that urban greening trees adapted to the environment by coordinating adjustment among leaf functional traits. (3) Under the T1 treatment, the R2 and slope among the leaf traits were higher than CK, and the significance was also enhanced. The correlation between leaf traits was strengthened in this warming environment. Conversely, it will weaken the correlation between leaf traits under the T2 treatment.

CONCLUSION

Our study demonstrated that there was a strong trade-off between leaf functional traits in the urban warming environment. Plants in the warming environment have adopted relatively consistent trade-offs and adaptation strategies. Moderate warming was more conducive to strengthening their trade-off potential. It is further verified that the global leaf economics spectrum also exists in urban ecosystems, which is generally tend to a quick-investment return type with the characteristics of thick leaves, strong photosynthetic capacity, low transpiration efficiency and long life in urban environments.

Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora

The insufficient number of available simple sequence repeats (SSRs) inhibits genetic research on and molecular breeding of Paeonia lactiflora, a flowering crop with great economic value. The objective of this study was to develop SSRs for P. lactiflora with Illumina RNA sequencing and assess the role of SSRs in gene regulation. The results showed that dinucleotides with AG/CT repeats were the most abundant type of repeat motif in P. lactiflora and were preferentially distributed in untranslated regions. Significant differences in SSR size were observed among motif types and locations. A large number of unigenes containing SSRs participated in catalytic activity, metabolic processes and cellular processes, and 28.16% of all transcription factors and 21.74% of hub genes for inflorescence stem straightness were found to contain SSRs. Successful amplification was achieved with 89.05% of 960 pairs of SSR primers, 55.83% of which were polymorphic, and most of the 46 tested primers had a high level of transferability to the genus Paeonia. Principal component and cluster dendrogram analyses produced results consistent with known genealogical relationships. This study provides a set of SSRs with abundant information for future accession identification, marker-trait association and molecular assisted breeding in P. lactiflora.

Genetic dissection of grain iron and zinc concentrations in lentil (Lens culinaris Medik.)

Iron (Fe) and zinc (Zn) deficiencies are wide spread in South Asia and Africa. Biofortification of food crops is a viable means of addressing micronutrient deficiencies. Lentil is an important pulse crop that provides affordable source of proteins, minerals, fibre and carbohydrates for micronutrient deficient countries. An association mapping (AM) panel of 96 diverse lentil genotypes from India and Mediterranean region was evaluated for three seasons and genotyped using 80 polymorphic simple-sequence repeat (SSR) markers for identification of the markers associated with grain Fe and Zn concentrations. A Bayesian model based clustering identified five subpopulations, adequately explaining the genetic structure of the AM panel. The linkage disequilibrium (LD) analysis using mixed linear model (MLM) identified two SSR markers, GLLC106 and GLLC108, associated with grain Fe concentration explaining 17% and 6% phenotypic variation, respectively and three SSR markers (PBALC 364, PBALC 92 and GLLC592) associated with grain Zn concentration, explaining 6%, 8% and 13% phenotypic variation, respectively. The identified SSRs exhibited consistent performance across three seasons and have potential for utilization in lentil molecular breeding programme.

Comprehensive Transcriptome Profiling and Identification of Potential Genes Responsible for Salt Tolerance in Tall Fescue Leaves under Salinity Stress

Soil salinity is a serious threat to plant growth and crop productivity. Tall fescue utilization in saline areas is limited by its inferior salt tolerance. Thus, a transcriptome study is a prerequisite for future research aimed at providing deeper insights into the molecular mechanisms of tall fescue salt tolerance as well as molecular breeding. Recent advances in sequencing technology offer a platform to achieve this. Here, Illumina RNA sequencing of tall fescue leaves generated a total of 144,339 raw reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to various databases. Further structural analyses revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. In total, 1862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs. 24 h salt treatment. Protein interaction analysis revealed a high interaction of chaperonins and Rubisco proteins in 48 h vs. 24 h salt treatment. The gene expressions were finally validated using quantitative polymerase chain reaction (qPCR), which was coherent with sequencing results.

Ascorbic Acid Alleviates Damage from Heat Stress in the Photosystem II of Tall Fescue in Both the Photochemical and Thermal Phases

L-Ascorbate (Asc) plays important roles in plant development, hormone signaling, the cell cycle and cellular redox system, etc. The higher content of Asc in plant chloroplasts indicates its important role in the photosystem. The objective of this study was to study the roles of Asc in tall fescue leaves against heat stress. After a heat stress treatment, we observed a lower value of the maximum quantum yield for primary photochemistry (φPo), which reflects the inhibited activity of the photochemical phase of photosystem II (PSII). Moreover, we observed a higher value of efficiency of electron transfer from QB to photosystem I acceptors (δR0), which reflects elevated activity of the thermal phase of the photosystem of the tall fescue. The addition of Asc facilitate the behavior of the photochemical phase of the PSII by lowering the ROS content as well as that of the alternative electron donor to provide electron to the tyrosine residue of the D1 protein. Additionally, exogenous Asc reduces the activity of the thermal phase of the photosystem, which could contribute to the limitation of energy input into the photosystem in tall fescue against heat stress. Synthesis of the Asc increased under heat stress treatment. However, under heat stress this regulation does not occur at the transcription level and requires further study.

Identification of genetic loci associated with crude protein and mineral concentrations in alfalfa (Medicago sativa) using association mapping

BACKGROUND

Alfalfa (Medicago sativa) is one of the most important legume forage species in China and many other countries of the world. It provides a quality source of proteins and minerals to animals. Genetic underpinnings for these important traits, however, are elusive. An alfalfa (M. sativa) association mapping study for six traits, namely crude protein (CP), rumen undegraded protein (RUP), and four mineral elements (Ca, K, Mg and P), was conducted in three consecutive years using a large collection encompassing 336 genotypes genotyped with 85 simple sequence repeat (SSR) markers.

RESULTS

All the traits were significantly influenced by genotype, environment, and genotype × environment interaction. Eight-five significant associations (P < 0.005) were identified. Among these, five associations with Ca were repeatedly observed and six co-localized associations were identified.

CONCLUSIONS

The identified marker alleles significantly associated with the traits provided important information for understanding genetic controls of alfalfa quality. The markers could be used in assisting selection for the individual traits in breeding populations for developing new alfalfa cultivars.

Gaps in the capacity of modern forage crops to adapt to the changing climate in northern Europe

The within-species diversity in response to weather and the gaps in the response diversity in the modern set of forage crop cultivars were determined using an approach that assessed the adaptive capacity under global climate change. The annual dry matter (DM) yields were recorded in multi-location MTT (Maa- ja elintarviketalouden tutkimuskeskus) Agrifood Research Official Variety Trials in Finland for modern forage crop cultivars from 2000 to 2012, as a response to agroclimatic variables critical to yield based on the year-round weather data. The effect and interaction of cultivars and agroclimatic variables were analysed using mixed model. The relatively low adaptive capacity of timothy (Phleum pratense L.) and meadow fescue (Festuca pratensis Huds.) indicates that diversification of the breeding material is warranted, particularly for resistance to high temperatures during primary growth and to high temperature sum 7 days after the first cut. All red clover cultivars (Trifolium pratense L.) suffered from both low and high accumulation of warm winter temperatures. Except for the red clover cultivars, cold stress during winter and lack of warm winter temperatures consistently reduced the yields of all species and cultivars. All tall fescue (Festuca arundinacea Schreb.) cultivars suffered from low precipitation during the fall hardening period. Although the set of festulolium (Festulolium pabulare) cultivars was also sensitive to low precipitation during the fall, festulolium was a good example of enhanced capacity to adapt to climate change with high response diversity because the cultivar germplasm base was diversified. Foreign origin in a cultivar pool was apparently not sufficient or necessary to ensure added value for a diversity of responses to climate change. Similar analyses to those used in this study, applied as practical tools for breeders, farmers and public actors, are important to secure the adaptive capacity of crops worldwide under global climate change.

Association mapping for floral traits in cultivated Paeonia rockii based on SSR markers

Tree peony (Paeonia Sect. Moutan) is an economically important ornamental plant, but little is known about the genetic architecture of important ornamental traits. To effectively improve ornamental value, we require a better understanding of genetic architecture in the complex traits of the tree peony. Association mapping is a powerful tool for detection of variation associated with traits. Thus, we examined the genetic diversity and the population structure of 462 unrelated cultivated P. rockii individuals, then performed association mapping to identify simple sequence repeat (SSR) markers associated with 12 floral traits. We observed a moderate level of genetic diversity (PIC = 0.459) and low linkage disequilibrium (LD) between markers, demonstrating that the potential value of an LD approach in elucidating the molecular basis of the quantitative variation in this species. An analysis of population structure revealed three subgroups in the association population. Subsequent single-marker association analysis identified 46 significant associations, involving the 11 traits with 37 SSRs. These loci explained a small proportion of the phenotypic variance, ranging from 2.68 to 23.97% (mean 5.50%). We also validated 15 of the 46 associations in a linkage mapping population of 159 individuals. Finally, five associations were further confirmed in the linkage mapping population, involving the four traits with four SSRs. These results can serve as a foundation for further analyses of the genetic architecture of floral traits, and the SSRs associated in this work have potential applications in marker-assisted breeding in tree peony.

Comparative study of diversity based on heat tolerant-related morpho-physiological traits and molecular markers in tall fescue accessions

Heat stress is a critical challenge to tall fescue (Festuca arundinacea Schreb.) in many areas of the globe and variations in genetic structure and functional traits is for the efficient breeding programs on developing heat tolerant cultivars. Tolerant-related morpho-physiological traits and simple sequence repeat (SSR) markers were employed to survey genetic diversity in greenhouse and growth chamber trials. 100 tall fescue accessions, including 8 commercial cultivars and 92 natural genotypes, showed a high variation in phenotypic performance under heat stress. Based on standardized heat tolerant-related morpho-physiological data, all tall fescue accessions were clustered into five groups. The accessions with similar heat tolerance were likely to be clustered in the same group. The highest genetic diversity was obtained for accessions from Africa judged by Nei’s gene diversity (0.2640) and PIC (0.2112). All grass accessions could be divided into three major groups based on SSR markers, which was partially congruous to the geographical regions and history of introduction. A low correlation was found between morpho-physiological traits and SSR markers by Mantel test. The patterns in morpho-physiological trait variations and genetic diversity associated with heat tolerance were useful to design breeding programs for developing heat stress resistance in tall fescue.

Association Analysis of Simple Sequence Repeat (SSR) Markers with Agronomic Traits in Tall Fescue (Festuca arundinacea Schreb.)

Tall fescue is widely used in temperate regions throughout the world as a dominant forage grass as well as a turfgrass, in pastoral and turf industry. However, the utilization of tall fescue was limited because of its leaf roughness, poor regeneration ability and poor stress resistance. New cultivars were desirable in modern pastoral industries exceed the potential of existing cultivars. Therefore, well understanding the agronomic traits and describing germplasms would help to overcome these constraints, and morphological evaluation of tall fescue germplasm is the key component in selecting rational parents for hybridization breeding. However, describing the morphological traits of tall fescue germplasm is costly and time-consuming. Fortunately, biotechnology approaches can supplement conventional breeding efforts for tall fescue improvement. Association mapping, as a powerful approach to identify association between agronomic traits and molecular markers has been widely used for enhancing the utilization, conservation and management of the tall fescue germplasms. Therefore, in the present research, 115 tall fescue accessions from different origins (25 accessions are cultivars; 31 accessions from America; 32 accessions from European; 7 accessions from Africa; 20 accessions from Asia), were evaluated for agronomic traits and genetic diversity with 90 simple sequence repeat (SSR) markers. The panel displayed significant variation in spike count per plant (SCP) and spike weight (SW). However, BCS performed the lowest CV among all the observed agronomic traits. Three subpopulations were identified within the collections but no obvious relative kinship (K) was found. The GLM model was used to describe the association between SSR and agronomic traits. Fifty-one SSR markers associated with agronomic traits were observed. Twelve single-associated markers were associated with PH; six single-associated markers were associated with BCS; eight single-associated markers were associated with SW; five single-associated markers were associated with SC; seven single-associated markers were associated with SCP; three single-associated markers were associated with SL. Especially, we observed that the genetic variation of SW was explained 11.6 % by M37 marker. It is interesting to observe that nine markers (M1, M2, M35, M54 marker was associated with both BCS and SC; M3, M4 markers were associated with BCS, SW, and SC; M19 marker was associated with both pH and PD, M40 marker was associated with both SCP and SW; and M193 marker was associated with both PH and SL) were associated with more than two agronomic traits. Notably, Branch count per spike (BCS) was explained by four markers (M1, M2, M3, and M4) exceeding 10 %. These identified marker alleles associated with agronomic traits could provide important information and markers for molecular-assisted breeding that facilitate the breeding process in tall fescue.