Development of Genome-wide SSR Markers for Physical Map Construction with PCR-based Polymorphic SSRs in Jute (Corchorus Spp.)

AbstractSSR markers are commonly used for many genetic applications, such as map construction, fingerprinting and genetic diversity analysis due to their high reproducibility, levels of polymorphism and abundance. As endogenous, small RNAs, miRNAs have essential roles in plant development and gene expression under diverse stress conditions, including various biotic and abiotic stress conditions. In the present study, we predicted 110 pre-miRNAs sequences from 287 precursor miRNAs and used them as queries for SSR marker development. Among 110 primer pairs, 85 were successfully amplified and examined for transferability to other gramineae and non-gramineae species. The results showed that all 82 primer pairs yielded unambiguous and strong amplification, and across the 23 studied Cleistogenes accessions, a total of 385 alleles were polymorphic. The number of alleles produced per primer varied from 3 to 11, with an average of 4.69 per locus. The expected heterozygosity (He) ranged from 0.44 to 0.88, with an average of 0.74 per locus, and the PIC (Polymorphism Information Content) values ranged from 0.34 to 0.87, with an average of 0.69 per locus. In this study, 1422 miRNA target genes were predicted and analyzed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. The results showed that this miRNA-based microsatellite marker system can be very useful for genetic diversity and marker-assisted breeding studies.

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Genome-wide SSR Markers in Bottle Gourd: Development, Characterization, Utilization in Assessment of Genetic Diversity of National Genebank of India and Synteny With Other Related Cucurbits

10.21203/rs.3.rs-990222/v1 ◽

2021 ◽

Author(s):

Bhawna Bonthala ◽

Manjusha Verma ◽

M Z Abdin ◽

Lalit Arya ◽

Chithra D Pandey ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Bottle Gourd ◽

Map Construction ◽

Phylogenetic Studies ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome ◽

Tetranucleotide Repeats ◽

Nucleotide Repeats

Abstract Lagenaria siceraria (Molina) Standley is an important cultivated crop with its immense importance in pharmaceutical industry and as vegetable. Its seed, root, stem, leaves, flower and fruit are used as an ointment for ailment of various diseases throughout Asia. Despite its worldwide importance,informative co-dominant microsatellite markers in the bottle gourd crop are very restricted, impeding geneticimprovement, cultivar identification and phylogenetic studies. Next generation sequencing has revolutionizedthe approaches for discovery, assessment and validation of molecular markers. We conducted a genome wideanalysis, for developing SSR markers by utilizing restriction site-associated DNA sequencing (RAD-Seq) data.By performing in silico mining of microsatellite repeat-motifs, we developed 45,066 perfect SSR markers. Ofwhich 203 markers were successfully validated and 101 (49.75%) polymorphic primer pairs were utilized for anin depth genetic diversity and population structure analysis of 96 accessions from the National Genebank ofIndia. Tetranucleotide repeats (∼34.3%) were the most prevalent followed by trinucleotide repeats (∼30.73%),further 21.03%, 9.6% and 4.3% of di-, penta- and hexa- nucleotide repeats in the bottle gourd genome. Syntenyof SSR markers on 11 bottle gourd linkage groups was correlated with the 7 chromosomes of cucumber(93.2%), 12 chromosomes of melon (87.4%) and 11 watermelon (90.8%). The generated SSR markers providea valuable tool for germplasm characterization, genetic linkage map construction, studying synteny, genediscovery and for breeding in bottle gourd and other cucurbits species.

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Barley Genomics: An Overview

International Journal of Plant Genomics ◽

10.1155/2008/486258 ◽

2008 ◽

Vol 2008 ◽

pp. 1-13 ◽

Cited By ~ 43

Author(s):

Nese Sreenivasulu ◽

Andreas Graner ◽

Ulrich Wobus

Keyword(s):

Sequence Data ◽

Physical Map ◽

Association Studies ◽

Genetic Maps ◽

Map Construction ◽

Genome Wide ◽

Technological Developments ◽

Genome Sequencing Effort ◽

Agronomically Important Traits ◽

Made In

Barley (Hordeum vulgare), first domesticated in the Near East, is a well-studied crop in terms of genetics, genomics, and breeding and qualifies as a model plant for Triticeae research. Recent advances made in barley genomics mainly include the following: (i) rapid accumulation of EST sequence data, (ii) growing number of studies on transcriptome, proteome, and metabolome, (iii) new modeling techniques, (iv) availability of genome-wide knockout collections as well as efficient transformation techniques, and (v) the recently started genome sequencing effort. These developments pave the way for a comprehensive functional analysis and understanding of gene expression networks linked to agronomically important traits. Here, we selectively review important technological developments in barley genomics and related fields and discuss the relevance for understanding genotype-phenotype relationships by using approaches such as genetical genomics and association studies. High-throughput genotyping platforms that have recently become available will allow the construction of high-density genetic maps that will further promote marker-assisted selection as well as physical map construction. Systems biology approaches will further enhance our knowledge and largely increase our abilities to design refined breeding strategies on the basis of detailed molecular physiological knowledge.

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Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus)

Science Progress ◽

10.1177/00368504211035597 ◽

2021 ◽

Vol 104 (3) ◽

pp. 003685042110355

Author(s):

Hai-feng Tian ◽

Qiao-mu Hu ◽

Zhong Li

Keyword(s):

Genetic Diversity ◽

Capillary Electrophoresis ◽

Ssr Markers ◽

Simple Sequence Repeats ◽

Breeding Population ◽

Monopterus Albus ◽

Polymorphic Ssrs ◽

Genome Wide ◽

Swamp Eel ◽

Simple Sequence

Objectives: Swamp eel is one model species for sexual reversion and an aquaculture fish in China. One local strain with deep yellow and big spots of Monopterus albus has been selected for consecutive selective breeding. The objectives of this study were characterizing the Simple Sequence Repeats (SSRs) of M. albus in the assembled genome obtained recently, and developing polymorphic SSRs for future breeding programs. Methods: The genome wide SSRs were mined by using MISA software, and their types and genomic distribution patterns were investigated. Based on the available flanking sequences, primer pairs were batched developed, and Polymorphic SSRs were identified by using Polymorphic SSR Retrieval tool. The obtained polymorphic SSRs were validated by using e-PCR and capillary electrophoresis, then they were used to investigate genetic diversity of one breeding population. Results: A total of 364,802 SSRs were identified in assembled M. albus genome. The total length, density and frequency of SSRs were 8,204,641 bp, 10,259 bp/Mb, and 456.16 loci/Mb, respectively. Mononucleotide repeats were predominant among SSRs (33.33%), and AC and AAT repeats were the most abundant di- and tri-nucleotide repeats motifs. A total of 287,189 primer pairs were designed, and a high-density physical map was constructed (359.11 markers per Mb). A total of 871 polymorphic SSRs were identified, and 38 SSRs of 101 randomly selected ones were validated by using e-PCR and capillary electrophoresis. Using these 38 polymorphic SSRs, 201 alleles were detected and genetic diversity level (Na, PIC, HO, and He) was evaluated. Conclusions: The genome-wide SSRs and newly developed SSR markers will provide a useful tool for genetic mapping, diversity analysis studies in swamp eel in the future. The high level of genetic diversity (Na = 5.29, PIC = 0.5068, HO = 0.4665, He = 0.5525) but excess of homozygotes ( FIS = 0.155) in one breeding population provide baseline information for future breeding program.

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Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia)

BMC Genomics ◽

10.1186/s12864-021-07499-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Junjie Cui ◽

Jiazhu Peng ◽

Jiaowen Cheng ◽

Kailin Hu

Keyword(s):

Genetic Map ◽

Average Density ◽

Momordica Charantia ◽

Bitter Gourd ◽

Map Construction ◽

Indel Markers ◽

Genome Wide ◽

Indel Polymorphisms ◽

Molecular Marker Development ◽

Development And Validation

Abstract Background The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers. Results Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Then we developed a total of 2502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines ‘47–2–1-1-3’ and ‘04–17,’ indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 ‘47–2–1-1-3’ × ‘04–17’ F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome. Conclusions This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.

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QTL mapping of fruit nutritional and flavor components in tomato (Solanum lycopersicum) using genome-wide SSR markers and recombinant inbred lines (RILs) from an intra-specific cross

Euphytica ◽

10.1007/s10681-018-2295-z ◽

2018 ◽

Vol 214 (11) ◽

Cited By ~ 5

Author(s):

Junji Kimbara ◽

Akio Ohyama ◽

Hiroshi Chikano ◽

Hirotaka Ito ◽

Katsutoshi Hosoi ◽

...

Keyword(s):

Qtl Mapping ◽

Solanum Lycopersicum ◽

Ssr Markers ◽

Recombinant Inbred ◽

Recombinant Inbred Lines ◽

Inbred Lines ◽

Flavor Components ◽

Genome Wide

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Application of Microsatellite and Inter Simple Sequence Markers for Certifying Trueness to Type of Grafted Ramets and Clustering of Persian Walnut Varieties

10.21203/rs.3.rs-542091/v1 ◽

2021 ◽

Author(s):

Masoomeh Hosseini Nickravesh ◽

Kourosh Vahdati ◽

fatemeh amini ◽

Reza Amiri ◽

Keith Woeste

Keyword(s):

Ssr Markers ◽

Issr Markers ◽

Principal Coordinate Analysis ◽

Dna Fingerprint ◽

Polymorphic Ssrs ◽

Persian Walnut ◽

Inter Simple Sequence Repeats ◽

Ssr Loci ◽

Ssrs Markers ◽

Simple Sequence

Abstract The utility of seventeen Microsatellite (SSR) markers and fifteen inter simple sequence repeats (ISSR) markers for the identification of twenty eight ramets of 11 varieties of walnut (Juglans regia) was explored. Thirty nine individual genomes were screened using 61 and 38 scorable fragments from SSR and ISSR markers, respectively. The least polymorphic SSR locus was WGA004 (two alleles) and the most polymorphic (5 alleles) was WGA276. Polymorphism information content values ranged from 0.08 (WGA004) to 0.43 (WGA032) in SSR markers and from 0.11 (AGA (AC)7) to 0.49 (CAC(TGT)5) in ISSR markers, with an average of 0.29 and 0.19, respectively. In most cases, grafted varieties with identical names also had the same microsatellites profile. The principal coordinate analysis and clustering (UPGMA) based on the combined marker set emphasized two failures in grafting or off-types, ramets identified as Serr 4 (S4) and Vina 1 (V1). The presence of two off-type ramets in the walnut research orchard emphasizes the importance of using molecular certification for proving true-to-type of walnut orchards. Using 13 polymorphic SSRs, we tabulated a DNA fingerprint chart of 11 walnut varieties. Except for ‘Chandler’, each cultivar could be distinguished using a combination of only two SSR loci. The 13 SSRs markers evaluated in this study could be used in future to identify clones produced from the varieties.

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Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing

Genes ◽

10.3390/genes8100238 ◽

2017 ◽

Vol 8 (10) ◽

pp. 238 ◽

Cited By ~ 5

Author(s):

Jinsu Gil ◽

Yurry Um ◽

Serim Kim ◽

Ok Kim ◽

Sung Koo ◽

...

Keyword(s):

Next Generation Sequencing ◽

Ssr Markers ◽

Next Generation ◽

Angelica Gigas ◽

Angelica Gigas Nakai ◽

Genome Wide ◽

Generation Sequencing

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Genetic Basis of Maize Resistance to Multiple Insect Pests: Integrated Genome-Wide Comparative Mapping and Candidate Gene Prioritization

Genes ◽

10.3390/genes11060689 ◽

2020 ◽

Vol 11 (6) ◽

pp. 689

Author(s):

A. Badji ◽

D. B. Kwemoi ◽

L. Machida ◽

D. Okii ◽

N. Mwila ◽

...

Keyword(s):

Insect Resistance ◽

Defense Mechanisms ◽

Genome Wide Association Study ◽

Insect Pests ◽

Physical Map ◽

Fall Armyworm ◽

Nucleotide Polymorphisms ◽

Multiple Traits ◽

Maize Weevil ◽

Genome Wide

Several species of herbivores feed on maize in field and storage setups, making the development of multiple insect resistance a critical breeding target. In this study, an association mapping panel of 341 tropical maize lines was evaluated in three field environments for resistance to fall armyworm (FAW), whilst bulked grains were subjected to a maize weevil (MW) bioassay and genotyped with Diversity Array Technology’s single nucleotide polymorphisms (SNPs) markers. A multi-locus genome-wide association study (GWAS) revealed 62 quantitative trait nucleotides (QTNs) associated with FAW and MW resistance traits on all 10 maize chromosomes, of which, 47 and 31 were discovered at stringent Bonferroni genome-wide significance levels of 0.05 and 0.01, respectively, and located within or close to multiple insect resistance genomic regions (MIRGRs) concerning FAW, SB, and MW. Sixteen QTNs influenced multiple traits, of which, six were associated with resistance to both FAW and MW, suggesting a pleiotropic genetic control. Functional prioritization of candidate genes (CGs) located within 10–30 kb of the QTNs revealed 64 putative GWAS-based CGs (GbCGs) showing evidence of involvement in plant defense mechanisms. Only one GbCG was associated with each of the five of the six combined resistance QTNs, thus reinforcing the pleiotropy hypothesis. In addition, through in silico co-functional network inferences, an additional 107 network-based CGs (NbCGs), biologically connected to the 64 GbCGs, and differentially expressed under biotic or abiotic stress, were revealed within MIRGRs. The provided multiple insect resistance physical map should contribute to the development of combined insect resistance in maize.

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