Simple sequence repeat (SSR) markers linked to E1, E3, E4, and E7 maturity genes in soybean

Genome ◽  
2003 ◽  
Vol 46 (6) ◽  
pp. 1024-1036 ◽  
Author(s):  
Stephen J Molnar ◽  
Satish Rai ◽  
Martin Charette ◽  
Elroy R Cober
Keyword(s):  
Molecular Markers ◽  
Reproductive Period ◽  
Soybean Genome ◽  
Isogenic Line ◽  
Near Isogenic Lines ◽  
Marker Assisted Breeding ◽  
Trait Locus ◽  
First Time ◽  
Map Location ◽  
Simple Sequence

Soybean near isogenic lines (NILs), contrasting for maturity and photoperiod sensitivity loci, were genotyped with approximately 430 mapped simple sequence repeats (SSRs), also known as microsatellite markers. By analysis of allele distributions across the NILs, it was possible to confirm the map location of the Dt1 indeterminate growth locus, to refine the SSR mapping of the T tawny pubescence locus, to map E1 and E3 maturity loci with molecular markers, and to map the E4 and E7 maturity loci for the first time. Molecular markers flanking these loci are now available for marker-assisted breeding for these traits. Analysis of map locations identified a putative homologous relationship among four chromosomal regions; one in the middle of linkage group (LG) C2 carrying E1 and E7, one on LG I carrying E4, one at the top of LG C2, at which there is a reproductive period quantitative trait locus (QTL), and the fourth on LG B1. Other evidence suggests that homology also exists between the E1 + E7 region on LG C2 and a region on LG L linked to a pod maturity QTL. Homology relationships predict possible locations in the soybean genome of additional maturity loci, as well as which maturity loci may share a common evolutionary origin and similar mechanism(s) of action.Key words: soybean, maturity, photoperiod, microsatellite marker, near isogenic line.

scholarly journals Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Fritillaria hupehensis

Life ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 287
Author(s):  
Kunyuan Guo ◽  
Jie Chen ◽  
Yan Niu ◽  
Xianming Lin
Keyword(s):  
Average Length ◽  
Flavonoid Biosynthesis ◽  
Full Length ◽  
Marker Assisted Breeding ◽  
Pacbio Rs Ii ◽  
Secondary Metabolite Biosynthesis ◽  
Non Coding Rnas ◽  
First Time ◽  
Flavonoid Biosynthesis Pathway ◽  
Simple Sequence

One of the most commonly utilized medicinal plants in China is Fritillaria hupehensis (Hsiao et K.C. Hsia). However, due to a lack of genomic resources, little is known about the biosynthesis of relevant compounds, particularly the flavonoid biosynthesis pathway. A PacBio RS II sequencing generated a total of 342,044 reads from the bulb, leaf, root, and stem, of which 316,438 were full-length (FL) non-redundant reads with an average length of 1365 bp and a N50 of 1888 bp. There were also 38,607 long non-coding RNAs and 7914 simple sequence repeats detected. To improve our understanding of processes implicated in regulating secondary metabolite biosynthesis in F. hupehensis tissues, we evaluated potential metabolic pathways. Overall, this study provides a repertoire of FL transcripts in F. hupehensis for the first time, and it will be a valuable resource for marker-assisted breeding and research into bioactive compounds for medicinal and pharmacological applications.

Implementing molecular marker technology in forage improvement

2003 ◽  
pp. 229-238
Author(s):  
M. Faville ◽  
B. Barrett ◽  
A. Griffiths ◽  
M. Schreiber ◽  
C. Mercer ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Genetic Variation ◽  
White Clover ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Seedling Vigour ◽  
Genome Map ◽  
Trait Locus ◽  
Simple Sequence

Accelerated improvement of two cornerstones of New Zealand's pastoral industries, per ennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.), may be realised through the application of markerassisted selection (MAS) strategies to enhance traditional plant breeding programmes. Genome maps constructed using molecular markers represent the enabling technology for such strategies and we have assembled maps for each species using EST-SSR markers - simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) representing genes. A comprehensive map of the white clover genome has been completed, with 464 EST-SSR and genomic SSR marker loci spanning 1125 cM in total, distributed across 16 linkage groups. These have been further classified into eight pairs of linkage groups, representing contributions from the diploid progenitors of this tetraploid species. In perennial ryegrass a genome map based exclusively on EST-SSR loci was constructed, with 130 loci currently mapped to seven linkage groups and covering a distance of 391 cM. This map continues to be expanded with the addition of ESTSSR loci, and markers are being concurrently transferred to other populations segregating for economically significant traits. We have initiated gene discovery through quantitative trait locus (QTL) analysis in both species, and the efficacy of the white clover map for this purpose was demonstrated with the initial identification of multiple QTL controlling seed yield and seedling vigour. One QTL on linkage group D2 accounts for 25.9% of the genetic variation for seed yield, and a putative QTL accounting for 12.7% of the genetic variation for seedling vigour was detected on linkage group E1. The application of MAS to forage breeding based on recurrent selection is discussed. Keywords: genome map, marker-assisted selection, perennial ryegrass, QTL, quantitative trait locus, SSR, simple sequence repeat, white clover

Genetic Diversity of Basil (Ocimum spp. - Lamiaceae) Based on RAPD Markers and Volatile Oil Constituents

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 492f-493
Author(s):  
Roberto F. Vieira ◽  
James E. Simon ◽  
Peter Goldsbrough ◽  
Antonio Figueira
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Volatile Oil ◽  
Essential Oil Composition ◽  
Oil Composition ◽  
Traditional Medicines ◽  
The Tropics ◽  
High Degree ◽  
First Time

Essential oils extracted from basil (Ocimum spp.) by steam distillation are used to flavor foods, oral products, in fragrances, and in traditional medicines. The genus Ocimum contains around 30 species native to the tropics and subtropics, with some species naturalized and/or cultivated in temperate areas. Interand intraspecific hybridization have created significant confusion in the botanical systematics of this genus. Taxonomy of basil (O. basilicum) is also complicated by the existence of numerous varieties, cultivars, and chemotypes within the species that do not differ significantly in morphology. In this study we are using RAPD markers and volatile oil composition to characterize the genetic diversity among the most economically important Ocimum species. We hypothesize that the genetic similarity revealed by molecular markers will more accurately reflect the morphological and chemical differences in Ocimum than essential oil composition per se. Preliminary research using five Ocimum species, four undetermined species, and eight varieties of O. basilicum (a total of 19 accessions) generated 107 polymorphic fragments amplified with 19 primers. RAPDs are able to discriminate between Ocimum species, but show a high degree of similarity between O. basilicum varieties. The genetic distance between nine species and among 55 accessions within the species O. americanum, O. basilicum, O. campechianum, O. × citriodorum, O. gratissimum, O. kilimandscharium, O. minimum, O. selloi, and O. tenuiflorum will be analyzed by matrix of similarity and compared to the volatile oil profile. This research will for the first time apply molecular markers to characterize the genetic diversity of Ocimum associate with volatile oil constituent.

scholarly journals Development of Molecular Markers for Predicting Radish (Raphanus sativus) Flesh Color Based on Polymorphisms in the RsTT8 Gene

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1386
Author(s):  
Soyun Kim ◽  
Keunho Yun ◽  
Han Yong Park ◽  
Ju Young Ahn ◽  
Ju Yeon Yang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Raphanus Sativus ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cosmetic Industry ◽  
Natural Colorants ◽  
Health Promoting ◽  
Primer Sets ◽  
Red Radish ◽  
Simple Sequence

Red radish (Raphanus sativus L.) cultivars are a rich source of health-promoting anthocyanins and are considered a potential source of natural colorants used in the cosmetic industry. However, the development of red radish cultivars via conventional breeding is very difficult, given the unusual inheritance of the anthocyanin accumulation trait in radishes. Therefore, molecular markers linked with radish color are needed to facilitate radish breeding. Here, we characterized the RsTT8 gene isolated from four radish genotypes with different skin and flesh colors. Sequence analysis of RsTT8 revealed a large number of polymorphisms, including insertion/deletions (InDels), single nucleotide polymorphisms (SNPs), and simple sequence repeats (SSRs), between the red-fleshed and white-fleshed radish cultivars. To develop molecular markers on the basis of these polymorphisms for discriminating between radish genotypes with different colored flesh tissues, we designed four primer sets specific to the RsTT8 promoter, InDel, SSR, and WD40/acidic domain (WD/AD), and tested these primers on a diverse collection of radish lines. Except for the SSR-specific primer set, all primer sets successfully discriminated between red-fleshed and white-fleshed radish lines. Thus, we developed three molecular markers that can be efficiently used for breeding red-fleshed radish cultivars.

scholarly journals Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xingyi Wang ◽  
Hui Liu ◽  
Kadambot H. M. Siddique ◽  
Guijun Yan
Keyword(s):  
Candidate Genes ◽  
Quantitative Trait ◽  
Genomic Region ◽  
Nucleotide Polymorphisms ◽  
Near Isogenic Lines ◽  
Gene Effects ◽  
Isogenic Lines ◽  
Trait Locus ◽  
Grain Yield And Quality ◽  
Sprouting Resistance

Abstract Background Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated. Results Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines. Conclusions The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.

scholarly journals Genotyping of Peach and Nectarine Cultivars with SSR and SRAP Molecular Markers

2004 ◽  
Vol 129 (2) ◽  
pp. 204-210 ◽  
Author(s):  
Riaz Ahmad ◽  
Dan Potter ◽  
Stephen M. Southwick
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sweet Cherry ◽  
Prunus Persica ◽  
Sequence Repeat ◽  
Srap Markers ◽  
Upgma Cluster Analysis ◽  
Commercially Important ◽  
Simple Sequence

Simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) molecular markers were evaluated for detecting intraspecific variation in 38 commercially important peach and nectarine (Prunus persica) cultivars. Out of the 20 SSR primer pairs 17 were previously developed in sweet cherry and three in peach. The number of putative alleles revealed by SSR primer pairs ranged from one to five showing a low level of genetic variability among these cultivars. The average number of alleles per locus was 2.2. About 76% of cherry primers produced amplification products in peach and nectarine, showing a congeneric relationship within Prunus species. Only nine cultivars out of the 38 cultivars could be uniquely identified by the SSR markers. For SRAP, the number of fragments produced was highly variable, ranging from 10 to 33 with an average of 21.8 per primer combination. Ten primer combinations resulted in 49 polymorphic fragments in this closely related set of peaches and nectarines. Thirty out of the 38 peach and nectarine cultivars were identified by unique SRAP fingerprints. UPGMA Cluster analysis based on the SSR and SRAP polymorphic fragments was performed; the relationships inferred are discussed with reference to the pomological characteristics and pedigree of these cultivars. The results indicated that SSR and SRAP markers can be used to distinguish the genetically very close peach and nectarine cultivars as a complement to traditional pomological studies. However, for fingerprinting, SRAP markers appear to be much more effective, quicker and less expensive to develop than are SSR markers.

scholarly journals Lipoxygenase activities during development of root and nodule of soybean

2004 ◽  
Vol 39 (7) ◽  
pp. 625-630 ◽  
Author(s):  
Tatiana Góes Junghans ◽  
Maria Goreti de Almeida Oliveira ◽  
Maurilio Alves Moreira
Keyword(s):  
Growth And Development ◽  
Root Formation ◽  
Lipoxygenase Activity ◽  
Post Inoculation ◽  
Isogenic Line ◽  
Near Isogenic Line ◽  
Near Isogenic Lines ◽  
Isogenic Lines ◽  
Bradyrhizobium Elkanii ◽  
Over Time

The objective of this work was to evaluate root and nodule soybean lipoxygenases in Doko cultivar and in a near isogenic line lacking seed lipoxygenases, inoculated and uninoculated with Bradyrhizobium elkanii. The lipoxygenase activities from roots collected at 3, 5, 9, 13, 18 and 28 days post-inoculation and from nodules collected at 13, 18 and 28 days post-inoculation were measured. The pH-activity profiles from root and nodules suggested that the lipoxygenases pool expressed in these organs from Doko cultivar and triple-null near isogenic lines are similar. The root lipoxygenase activity of Doko and triple-null lines, inoculated and uninoculated, reduced over time. The highest lipoxygenase activity observed at the beginning of root formation suggests the involvement of this enzyme in growth and development of this organ. However, for nodules an expressive increase of lipoxygenase activity was noticed 28 days post-inoculation. Root and nodule showed, at least, two mobility groups for lipoxygenases in immunoblottings, with approximately 94 and 97 kDa.

scholarly journals Study of Plant Genetic Variation through Molecular Markers: An Overview

2021 ◽  
pp. 464-473
Author(s):  
Zeina S. M. Al-Hadeithi ◽  
Saade Abdalkareem Jasim
Keyword(s):  
Molecular Markers ◽  
Simple Sequence Repeat Marker ◽  
Fragment Length ◽  
Simple Sequence Repeat ◽  
Plant Biotechnology ◽  
Molecular Techniques ◽  
Basic Material ◽  
Sequence Repeat ◽  
Simple Sequence

This article refers to viewing the role of molecular markers during analyzing the genome of plants and their importance in plant biotechnology. In recent years, we observed the role of molecular techniques in programs for improving plant breeding and preserving genetic resources has been observed, and molecular and biochemical indicators which represent basic material through determining the diversity between genotypes for indicators it is never affected by external surrounding conditions as always in the phenotype features. Molecular markers of DNA have been widely applied to answer a range of questions related to taxonomy, molecular evolution, population genetics, and genetic diversity, as well as monitoring trade in plants and food products , in addition to its having a role in studying gene expression , genetic mapping, and studies of species evolution providing fast and accurate results. In this work, the advantages and limitations of the molecular techniques applied in plant sciences such as: RAPD (Random Amplification Polymorphic DNA Marker); ISSR (Inter Simple Sequence Repeat Marker); SSR (Simple Sequence Repeat Marker); AFLP (Amplified Fragment Length Polymorphic Marker); RFLP (Restriction Fragment Length Polymorphism Marker); SNP (Single Nucleotide Polymorphism) and Real Time PCR.

Assessment of Genetic Diversity of Rheum species (Endangered Medicinal Herb of Indian Himalayan Region) using Molecular Markers

2021 ◽  
Vol 16 (11) ◽  
pp. 147-154
Author(s):  
Anjali Uniyal ◽  
Akhilesh Kumar ◽  
Sweta Upadhyay ◽  
Vijay Kumar ◽  
Sanjay Gupta
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Fragment Length Polymorphism ◽  
Dna Polymorphisms ◽  
Inter Simple Sequence Repeats ◽  
Pharmaceutical Industries ◽  
Endangered Medicinal Herb ◽  
Identification And Characterization ◽  
Simple Sequence

The Rheum species are important medicinal plants that are facing extinction due to their unplanned development and overexploitation by pharmaceutical industries. DNA polymorphisms are not prone to environmental modifications, thus they are widely used for the identification and characterization of plants. The use of different molecular markers has enabled the researchers for the valuation of genetic variability and diversity in its natural zone of distribution. The conventional approach may take several years to yield this information. For the estimation of molecular and genetic variations in geographical zone of distribution, various molecular markers technique are available like RAPD (Randomly Amplified Polymorphic DNA), RFLP (Restriction fragment length polymorphism), ISSR (Inter-Simple Sequence Repeats), SSR and AFLP. The uses of different molecular markers for the study of genetic diversity have been discussed in the review.

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