Identifying genetic diversity and a preliminary core collection of Pyrus pyrifolia cultivars by a genome-wide set of SSR markers

2014 ◽  
Vol 167 ◽  
pp. 5-16 ◽  
Author(s):  
Yue Song ◽  
Lian Fan ◽  
Hui Chen ◽  
Mingyue Zhang ◽  
Qianqian Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Core Collection ◽  
Pyrus Pyrifolia ◽  
Genome Wide ◽  
A Genome

Genome-wide identification of SSR markers in the Brassica A genome and their utility in breeding

2016 ◽  
Vol 96 (5) ◽  
pp. 808-818 ◽  
Author(s):  
Neil Hobson ◽  
Habibur Rahman
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Low Cost ◽  
Pak Choi ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Genetic Pools ◽  
High Level ◽  
Simple Sequence

Simple sequence repeat (SSR) markers can be applied to genotyping projects at low cost with inexpensive equipment. The objective of this study was to develop SSR markers from the publically-available genome sequence of Brassica rapa and provide the physical position of these markers on the chromosomes for use in breeding and research. To assess the utility of these new markers, a subset of 60 markers were used to genotype 43 accessions of B. rapa. Fifty-five markers from the 10 chromosome scaffolds produced a total of 730 amplicons, which were then used to perform a phylogenetic analysis of the accessions, illustrating their utility in distinguishing between a wide range of germplasm. In agreement with similar studies of genetic diversity, our markers separated accessions into distinct genetic pools including Chinese cabbage, Chinese winter oilseed, European winter oilseed, Canadian spring oilseed, pak-choi, turnip, and yellow sarson. The results further illustrate the presence of a high level of genetic diversity in B. rapa, and demonstrate the potential of these SSR markers for use in breeding and research.

scholarly journals 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

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.

scholarly journals Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1479
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Dhiman Biswas ◽  
Jennifer Ann Harikrishna ◽  
Yuxuan Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Comparative Mapping ◽  
In Silico ◽  
Large Scale ◽  
Crop Improvement ◽  
Musa Spp ◽  
Population Structure Analysis ◽  
A Genome ◽  
Development And Validation

Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.

Genetic Diversity of Angelica gigas Nakai Collected in Korea using Genome-Wide SSR Markers

2019 ◽  
Vol 27 (6) ◽  
pp. 376-382
Author(s):  
Dae Hui Jeong ◽  
Yun Mi Park ◽  
Ki Yoon Kim ◽  
Hong Woo Park ◽  
Kwon Seok Jeon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Angelica Gigas ◽  
Angelica Gigas Nakai ◽  
Genome Wide

scholarly journals Genome-wide development of lncRNA-derived-SSR markers for Dongxiang wild rice (Oryza rufipogon Griff.)

2021 ◽  
Author(s):  
Wanling Yang ◽  
Yuanwei Fan ◽  
Yong Chen ◽  
Gumu Ding ◽  
Hu Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Stress Responses ◽  
Wild Rice ◽  
Diversity Index ◽  
Oryza Rufipogon ◽  
Coding Sequences ◽  
Genome Wide ◽  
Ssr Loci ◽  
Dongxiang Wild Rice

AbstractDongxiang wild rice (Oryza rufipogon Griff., DXWR) is the northernmost distributed common wild rice found in the world. It contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in crop breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice materials. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content (PIC) values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research, including genetic diversity analysis, QTL mapping, and molecular breeding programs, to make good use of the elite lncRNA genes from DXWR.

scholarly journals Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica with their transferability analysis to gramineae and non- gramineae species

2019 ◽  
Author(s):  
Gisele Kanzana ◽  
Yufei Zhang ◽  
Tiantian Ma ◽  
Wenxian Liu ◽  
Fan Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Target Genes ◽  
Stress Conditions ◽  
Biotic And Abiotic Stress ◽  
Marker Assisted Breeding ◽  
Map Construction ◽  
Expected Heterozygosity ◽  
Genome Wide ◽  
Precursor Mirnas

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.

scholarly journals Genome-Wide Association Study Reveals Genetic Architecture of Septoria Tritici Blotch Resistance in a Historic Landrace Collection

2021 ◽  
Author(s):  
Anik Dutta ◽  
Daniel Croll ◽  
Bruce A. McDonald ◽  
Simon G. Krattinger
Keyword(s):  
Genetic Diversity ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Phenotypic Variability ◽  
Genome Wide Association ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Genome Wide ◽  
A Genome ◽  
Wheat Landraces

Abstract Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is a major constraint in global wheat production. The lack of genetic diversity in modern elite wheat cultivars largely hinders the improvement of STB resistance. Wheat landraces are reservoirs of untapped genetic diversity, which can be exploited to find novel STB resistance genes or alleles. Here, we characterized 188 Swiss wheat landraces for resistance to STB using four Swiss Z. tritici isolates. We used a genome-wide association study (GWAS) to identify genetic variants associated with the amount of lesion and pycnidia production by the fungus. The majority of the landraces were highly resistant for both traits to the isolate 1E4, indicating a gene-for-gene relationship, while higher phenotypic variability was observed against other isolates. GWAS detected a significant SNP on chromosome 3A that was associated with both traits in the isolate 1E4. The resistance response against 1E4 was likely controlled by the Stb6 gene. Sanger sequencing revealed that the majority of these ~100-year-old landraces carry the Stb6 resistance allele. This indicates the importance of this gene in Switzerland during the early 1900s for disease control in the field. Our study demonstrates the importance of characterizing historic landrace collections for STB resistance to provide valuable information on resistance variability and contributing alleles. This will help breeders in the future to make decisions on integrating such germplasms in STB resistance breeding.

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