scholarly journals Linkage Map Development by EST-SSR Markers and QTL Analysis for Inflorescence and Leaf Traits in Chrysanthemum (Chrysanthemum morifolium Ramat.)

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1342
Author(s):  
Min Fan ◽  
Yike Gao ◽  
Zhiping Wu ◽  
Qixiang Zhang
Keyword(s):  
Linkage Map ◽  
Ssr Markers ◽  
Genetic Map ◽  
Leaf Traits ◽  
Chrysanthemum Morifolium ◽  
Leaf Length ◽  
Integrated Map ◽  
Length Width ◽  
Ray Florets ◽  
Chrysanthemum Morifolium Ramat

Chrysanthemums (Chrysanthemum morifolium Ramat.) are famous ornamental crops with high medicinal and industrial values. The inflorescence and leaf traits are key factors that affect the yield and quality of chrysanthemum. However, the genetic improvement of those traits is slow within chrysanthemum because of its hexaploidy, high heterozygosity and enormous genome. To study the genetic control of the important traits and facilitate marker-assisted selection (MAS) in chrysanthemum, it is desirable to populate the genetic maps with an abundance of transferrable markers such as microsatellites (SSRs). A genetic map was constructed with expressed sequence tag–simple sequence repeat (EST-SSR) markers in an F1 progeny of 192 offspring. A total of 1000 alleles were generated from 223 EST-SSR primer pairs. The preliminary maternal and paternal maps consisted of 265 marker alleles arranged into 49 and 53 linkage groups (LGs), respectively. The recombined parental maps covered 906.3 and 970.1 cM of the genome, respectively. Finally, 264 polymorphic loci were allocated to nine LGs. The integrated map spanned 954.5 cM in length with an average genetic distance of 3.6 cM between two neighbouring loci. Quantitative trait loci (QTLs) analysis was performed using the integrated map for inflorescence diameter (ID), central disc flower diameter (CDFD), number of whorls of ray florets (NWRF), number of ray florets (NRF), number of disc florets (NDF), number of florets (NF), ray floret length (RFL), ray floret width (RFW), ray floret length/width (RFL/W), leaf length (LL), leaf width (LW) and leaf length/width (LL/W). Overall, 36 (21 major) QTLs were identified. The successful mapping of inflorescence and leaf traits QTL demonstrated the utility of the new integrated linkage map. This study is the first report of a genetic map based on EST-SSR markers in chrysanthemum. The EST-SSR markers, genetic map and QTLs reported here could be valuable resources in implementing MAS for chrysanthemums in breeding programs.

scholarly journals Dramatic Increase in Content of Diverse Flavonoids Accompanied with Down-Regulation of F-Box Genes in a Chrysanthemum (Chrysanthemum × morifolium (Ramat.) Hemsl.) Mutant Cultivar Producing Dark-Purple Ray Florets

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 865
Author(s):  
Yeong Deuk Jo ◽  
Jaihyunk Ryu ◽  
Ye-Sol Kim ◽  
Kyung-Yun Kang ◽  
Min Jeong Hong ◽  
...  
Keyword(s):  
Translational Regulation ◽  
High Performance ◽  
Flower Color ◽  
Chrysanthemum Morifolium ◽  
Ionization Mass ◽  
Photodiode Array Detection ◽  
Genes Encoding ◽  
Ray Florets ◽  
Chrysanthemum Morifolium Ramat ◽  
Flavonoid Accumulation

Anthocyanins (a subclass of flavonoids) and flavonoids are crucial determinants of flower color and substances of pharmacological efficacy, respectively, in chrysanthemum. However, metabolic and transcriptomic profiling regarding flavonoid accumulation has not been performed simultaneously, thus the understanding of mechanisms gained has been limited. We performed HPLC-DAD-ESI-MS (high-performance liquid chromatography coupled with photodiode array detection and electrospray ionization mass spectrometry) and transcriptome analyses using “ARTI-Dark Chocolate” (AD), which is a chrysanthemum mutant cultivar producing dark-purple ray florets, and the parental cultivar “Noble Wine” for metabolic characterization and elucidation of the genetic mechanism determining flavonoid content. Among 26 phenolic compounds identified, three cyanidins and eight other flavonoids were detected only in AD. The total amounts of diverse flavonoids were 8.0 to 10.3 times higher in AD. Transcriptome analysis showed that genes in the flavonoid biosynthetic pathway were not up-regulated in AD at the early flower stage, implying that the transcriptional regulation of the pathway did not cause flavonoid accumulation. However, genes encoding post-translational regulation-related proteins, especially F-box genes in the mutated gene, were enriched among down-regulated genes in AD. From the combination of metabolic and transcriptomic data, we suggest that the suppression of post-translational regulation is a possible mechanism for flavonoid accumulation in AD. These results will contribute to research on the regulation and manipulation of flavonoid biosynthesis in chrysanthemum.

scholarly journals Genetic analysis of water loss of excised leaves associated with drought tolerance in wheat

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5063 ◽  
Author(s):  
Ilona Mieczysława Czyczyło-Mysza ◽  
Izabela Marcińska ◽  
Edyta Skrzypek ◽  
Jan Bocianowski ◽  
Kinga Dziurka ◽  
...  
Keyword(s):  
Cross Sections ◽  
Water Loss ◽  
Unit Area ◽  
Doubled Haploids ◽  
Leaf Size ◽  
Leaf Traits ◽  
Leaf Length ◽  
Detached Leaf ◽  
Length Width ◽  
Leaf Water Loss

Background Wheat is widely affected by drought. Low excised-leaf water loss (ELWL) has frequently been associated with improved grain yield under drought. This study dissected the genetic control of ELWL in wheat, associated physiological, morphological and anatomical leaf traits, and compared these with yield QTLs. Methods Ninety-four hexaploid wheat (Triticum aestivum L.) doubled haploids, mapped with over 700 markers, were tested for three years for ELWL from detached leaf 4 of glasshouse-grown plants. In one experiment, stomata per unit area and leaf thickness parameters from leaf cross-sections were measured. QTLs were identified using QTLCartographer. Results ELWL was significantly negatively correlated with leaf length, width, area and thickness. Major QTLs for ELWL during 0–3 h and 3–6 h were coincident across trials on 3A, 3B, 4B, 5B, 5D, 6B, 7A, 7B, 7D and frequently coincident (inversely) with leaf size QTLs. Yield in other trials was sometimes associated with ELWL and leaf size phenotypically and genotypically, but more frequently under non-droughted than droughted conditions. QTL coincidence showed only ELWL to be associated with drought/control yield ratio. Discussion Our results demonstrated that measures of ELWL and leaf size were equally effective predictors of yield, and both were more useful for selecting under favourable than stressed conditions.

scholarly journals QTL Mapping of Kernel Traits and Validation of a Major QTL for Kernel Length-Width Ratio Using SNP and Bulked Segregant Analysis in Wheat

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Fang Xin ◽  
Ting Zhu ◽  
Shuwei Wei ◽  
Yucui Han ◽  
Yue Zhao ◽  
...  
Keyword(s):  
Linkage Map ◽  
Ssr Markers ◽  
Shaanxi Province ◽  
Width Ratio ◽  
Significant Qtls ◽  
Chip Technology ◽  
Kernel Length ◽  
Length Width ◽  
Kernel Traits ◽  
Major Qtl

AbstractOne RIL population derived from the cross between Dalibao and BYL8 was used to examine the phenotypes of kernel-related traits in four different environments. Six important kernel traits, kernel length (KL), kernel width (KW), kernel perimeter (KP), kernel area (KA), kernel length/width ratio (KLW), and thousand-kernel weight (TKW) were evaluated in Yangling, Shaanxi Province, China (2016 and 2017), Nanyang, Henan Province, China (2017) and Suqian, Jiangsu Province, China (2017). A genetic linkage map was constructed using 205 SSR markers, and a total of 21 significant QTLs for KL, KW, KP, KA, KLW and TKW were located on 10 of the 21 wheat chromosomes, including 1A, 1B, 2A, 2B, 2D, 3D, 4D, 5A, 5B, and 7D, with a single QTL in different environments explaining 3.495–30.130% of the phenotypic variation. There were four loci for KLW, five for KA, five for KL, three for KP, two for KW, and two for TKW among the detected QTLs. We used BSA + 660 K gene chip technology to reveal the positions of major novel QTLs for KLW. A total of 670 out of 5285 polymorphic SNPs were detected on chromosome 2A. The SNPs in 2A are most likely related to the major QTL, and there may be minor QTLs on 5B, 7A, 3A and 4B. SSR markers were developed to verify the chromosome region associated with KLW. A linkage map was constructed with 7 SSR markers, and a major effect QTL was identified within a 21.55 cM interval, corresponding to a physical interval of 10.8 Mb in the Chinese Spring RefSeq v1.0 sequence. This study can provide useful information for subsequent construction of fine mapping and marker-assisted selection breeding.

scholarly journals Evidence for hexasomic inheritance in Chrysanthemum morifolium Ramat. based on analysis of EST-SSR markers

Genome ◽  
2021 ◽  
pp. 1-7
Author(s):  
Min Fan ◽  
Yike Gao ◽  
Zhiping Wu ◽  
Saba Haider ◽  
Qixiang Zhang
Keyword(s):  
Genetic Analysis ◽  
Ssr Markers ◽  
Segregation Analysis ◽  
Expressed Sequence Tag ◽  
Chrysanthemum Morifolium ◽  
Random Pairing ◽  
Disomic Inheritance ◽  
Inheritance Mode ◽  
Marker Alleles ◽  
Chrysanthemum Morifolium Ramat

Chrysanthemums (Chrysanthemum morifolium Ramat.) are ornamental flowers, which are famous worldwide. The mode of inheritance has great implications for the genetic analysis of polyploid species. However, genetic analysis of chrysanthemum has been hampered because of its controversial inheritance mode (disomic or hexasomic). To classify the inheritance mode of chrysanthemums, an analysis of three approaches was carried out in an F1 progeny of 192 offspring using 223 expressed sequence tag-simple sequence repeat (EST-SSR) markers. The analysis included segregation analysis, the ratio of simplex marker alleles linked in coupling to repulsion, as well as the transmission and segregation patterns of EST-SSR marker alleles. After segregation analysis, 204 marker alleles fit hexasomic inheritance and 150 marker alleles fit disomic inheritance, showing that marker alleles were inherited predominantly in a hexasomic manner. Furthermore, the results of the analysis of allele configuration and segregation behavior of five EST-SSR markers also suggested random pairing of chromosomes. Additionally, the ratio of simplex marker alleles linked in coupling to repulsion was 1:0, further supporting hexasomic inheritance. Therefore, it could be inferred that chrysanthemum is a complete or near-complete hexasome.

scholarly journals Characterization and Development of EST-SSR Markers from Transcriptome Sequences of Chrysanthemum (Chrysanthemum ×morifolium Ramat.)

HortScience ◽  
2019 ◽  
Vol 54 (5) ◽  
pp. 772-778 ◽  
Author(s):  
Min Fan ◽  
Yike Gao ◽  
Yaohui Gao ◽  
Zhiping Wu ◽  
Hua Liu ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Principal Component ◽  
Chrysanthemum Morifolium ◽  
Dinucleotide Repeats ◽  
Population Structure Analysis ◽  
Ssr Loci ◽  
Chrysanthemum Morifolium Ramat ◽  
Diversity Studies ◽  
Expressed Sequence

Simple sequence repeat (SSR) markers are valuable for genetic and breeding applications, but SSR resources for the ornamental genus chrysanthemum (Chrysanthemum ×morifolium Ramat.) are still limited. Expressed sequence tags (ESTs) are sources of SSRs that represent an opportunity to develop SSRs to accelerate molecular breeding in chrysanthemum. In total, 4661 SSR loci were identified from 3823 SSR-containing unigenes in the chrysanthemum transcriptome with an average of one SSR per 6.98 kb. Of these SSR sequences, trinucleotide repeats (30.0%) predominated, followed by dinucleotide repeats (17.9%). In total, 1584 primer pairs were subsequently synthesized. By screening the parents and six individuals of the F1 progeny, 831 (52.5%) valid EST-SSR markers were identified, of which 361 (43.4%) were polymorphic. The annotation of unigenes containing polymorphic SSRs indicated that 330 (93.5%) demonstrated significant homology to other plant protein sequences. Twenty-five polymorphic EST-SSR markers were further selected for transferability analysis and exhibited 93% amplification in six Ajania species and six other Chrysanthemum species. Based on genotyping of the 59 samples, neighbor-joining analysis revealed six phylogenetic groupings, which was confirmed by population structure analysis and principal component analysis (PCA). Phylogenetic relationships among the 59 samples revealed by SSRs were highly consistent with the traditional taxonomic classification of Chrysanthemum and Ajania. The polymorphism information content (PIC) values ranged from 0.29 to 0.86, with a mean of 0.67, indicating high levels of informativeness. This research reveals the SSR distribution characteristics of chrysanthemum and provides a large number of new EST-SSR markers for further genetic diversity studies, genetic mapping, and molecular marker-assisted selection breeding for chrysanthemum.

High-density Genetic Linkage Map Construction in Sunflower (Helianthus annuus L.) Using SNP and SSR Markers

2021 ◽  
Vol 15 (8) ◽  
pp. 889-897
Author(s):  
Pin Lyu ◽  
Jianhua Hou ◽  
Haifeng Yu ◽  
Huimin Shi
Keyword(s):  
Linkage Map ◽  
Helianthus Annuus ◽  
Ssr Markers ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Snp Markers ◽  
High Density ◽  
Helianthus Annuus L ◽  
Density Maps

Background: Sunflower (Helianthus annuus L.) is an important oil crop only after soybean, canola and peanuts. A high-quality genetic map is the foundation of marker-assisted selection (MAS). However, for this species, the high-density maps have been reported limitedly. Objective: In this study, we proposed the construction of a high-density genetic linkage map by the F7 population of sunflowers using SNP and SSR Markers. Methods: The SLAF-seq strategy was employed to further develop SNP markers with SSR markers to construct the high-density genetic map by the HighMap software. Results: A total of 1,138 million paired-end reads (226Gb) were obtained and 518,900 SLAFs were detected. Of the polymorphic SLAFs, 2,472,245 SNPs were developed and finally, 5,700 SNPs were found to be ideal to construct a genetic map after filtering. The final high-density genetic map included 4,912 SNP and 93 SSR markers distributed in 17 linkage groups (LGs) and covered 2,425.05 cM with an average marker interval of 0.49 cM. Conclusion: The final result demonstrated that the SLAF-seq strategy is suitable for SNP markers detection. The genetic map reported in this study can be considered as one of the most highdensity genetic linkage maps of sunflower and could lay a foundation for quantitative trait loci (QTLs) fine mapping or map-based gene cloning.

Daminozide Alters Anthocyanin Metabolism in Ray Florets of Bronze Chrysanthemum (Chrysanthemum morifolium Ramat.)

2013 ◽  
Vol 32 (3) ◽  
pp. 453-460 ◽  
Author(s):  
Jonathon Roepke ◽  
Tyler Jean ◽  
Kayla J. Perkel ◽  
Theo Blom ◽  
Gale G. Bozzo
Keyword(s):  
Chrysanthemum Morifolium ◽  
Ray Florets ◽  
Chrysanthemum Morifolium Ramat

scholarly journals An Extended Intervarietal Microsatellite Linkage Map of Cucumber, Cucumis sativus L.

HortScience ◽  
2010 ◽  
Vol 45 (6) ◽  
pp. 882-886 ◽  
Author(s):  
Yiqun Weng ◽  
Shanna Johnson ◽  
Jack E. Staub ◽  
Sanwen Huang
Keyword(s):  
Linkage Map ◽  
Cucumis Sativus ◽  
Ssr Markers ◽  
Genetic Map ◽  
Chromosomal Rearrangements ◽  
Recombination Suppression ◽  
Cucumis Sativus L ◽  
Sequence Characterized Amplified Region ◽  
Ril Population ◽  
Marker Loci

A recombinant inbred line (RIL) population derived from two cultivated cucumber (Cucumis sativus var. sativus L., 2n = 2x = 14) lines, Gy7 (synonym G421) and H-19, was previously used to map yield and fruit quality components. However, the map consisted mainly of dominant markers (i.e., random amplified polymorphic DNAs or amplified fragment length polymorphisms) limiting its use in plant improvement and map-based gene cloning. We report here a moderately saturated genetic map derived from this RIL population that incorporates codominant microsatellite [simple sequence repeat (SSR)] markers and two architectural traits, little leaf (ll) and determinate (de), growth habit. Of 821 cucumber genomic SSR primer pairs evaluated for map construction, 140 (17.0%) were polymorphic between the mapping parents. In combination with 42 previously mapped sequence characterized amplified region (SCAR) and SSR makers, these polymorphic markers were used to construct a linkage map with 46 RILs and 176 mapped loci spanning ≈400 cM across seven linkage groups (LG). The numbers of loci mapped on LG 1 through 7 were 11, 6, 35, 18, 46, 45, and 15, respectively. The ll locus was flanked by SSR02355 and SSR03940 (4.2 and 3.6 cM from ll, respectively), and de was flanked by CSWCTT14b and SSR13251 (1.4 and 4.2 cM from the de, respectively). The SSR markers linked with the de and ll genes were mapped to Chromosome 6. No recombination suppression was detected among the mapped loci examined. This Gy7 × H-19 RIL-based genetic map shared 94 marker loci with a previously reported RIL-based linkage map derived from a wide cross between C. sativus var. sativus line Gy14 and C. sativus var. hardwickii Alef. R. PI 183967. Comparative mapping supported previous findings that genomic differences (likely chromosomal rearrangements) exist between Gy14 and PI 183967.

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