scholarly journals A SNP-Based Genetic Linkage Map of Soybean Using the SoySNP6K Illumina Infinium BeadChip Genotyping Array

2017 ◽  
Vol 1 (3) ◽  
pp. 80-89 ◽  
Author(s):  
Masum Akond ◽  
Shiming Liu ◽  
Lauren Schoener ◽  
James A. Anderson ◽  
Stella K. Kantartzi ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Goodness Of Fit ◽  
Genetic Linkage Map ◽  
Agronomic Traits ◽  
Snp Markers ◽  
High Density ◽  
Genotyping Array ◽  
Glycine Max L ◽  
Average Marker Density

This study reports a high density genetic linkage map based on the ‘Maryland 96-5722’ by ‘Spencer’ recombinant inbred line (RIL) population of soybean [Glycine max (L.) Merr.] and constructed exclusively with single nucleotide polymorphism (SNP) markers. The Illumina Infinium SoySNP6K BeadChip genotyping array produced 5,376 SNPs in the mapping population, with a 96.75% success rate. Significant level of goodness-of-fit for each locus was tested based on the observed vs. expected ratio (1:1). Out of 5,376 markers, 1,465 SNPs fit the 1:1 segregation rate having ≤20% missing data plus heterozygosity among the RILs. Among this 1,456 just 657 were polymorphic between the parents DNAs tested. These 657 SNPs were mapped using the JoinMap 4.0 software and 550 SNPs were distributed on 16 linkage groups (LGs) among the 20 chromosomes of the soybean genome. The total map length was just 201.57 centiMorgans (cM) with an average marker density of 0.37 cM. This is one of the high density SNP-based genetic linkage maps of soybean that will be used by the scientific community to map quantitative trait loci (QTL) and identify candidate genes for important agronomic traits in soybean.

Construction of a high‐density genetic linkage map and identification of QTLs for main agronomic traits of tetraploid hybrid crested wheatgrass

2020 ◽  
Vol 66 (3) ◽  
pp. 161-173 ◽  
Author(s):  
Xiaoxia Yu ◽  
Yanhong Ma ◽  
Zhiyan Jiang ◽  
Yue Shi ◽  
Dongsheng Yang ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Agronomic Traits ◽  
High Density ◽  
Crested Wheatgrass ◽  
Tetraploid Hybrid

scholarly journals An SNP-Based High-Density Genetic Linkage Map for Tetraploid Potato Using Specific Length Amplified Fragment Sequencing (SLAF-Seq) Technology

Agronomy ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 114 ◽  
Author(s):  
Xiaoxia Yu ◽  
Mingfei Zhang ◽  
Zhuo Yu ◽  
Dongsheng Yang ◽  
Jingwei Li ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Genetic Linkage Map ◽  
De Novo ◽  
Snp Markers ◽  
High Density ◽  
Tetraploid Potato ◽  
Specific Length

Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for the discovery of large-scale de novo genotyping of single nucleotide polymorphism (SNP) markers. In the present research, in order to facilitate genome-guided breeding in potato, this strategy was used to develop a large number of SNP markers and construct a high-density genetic linkage map for tetraploid potato. The genomic DNA extracted from 106 F1 individuals derived from a cross between two tetraploid potato varieties YSP-4 × MIN-021 and their parents was used for high-throughput sequencing and SLAF library construction. A total of 556.71 Gb data, which contained 2269.98 million pair-end reads, were obtained after preprocessing. According to bioinformatics analysis, a total of 838,604 SLAF labels were developed, with an average sequencing depth of 26.14-fold for parents and 15.36-fold for offspring of each SLAF, respectively. In total, 113,473 polymorphic SLAFs were obtained, from which 7638 SLAFs were successfully classified into four segregation patterns. After filtering, a total of 7329 SNP markers were detected for genetic map construction. The final integrated linkage map of tetraploid potato included 3001 SNP markers on 12 linkage groups, and covered 1415.88 cM, with an average distance of 0.47 cM between adjacent markers. To our knowledge, the integrated map described herein has the best coverage of the potato genome and the highest marker density for tetraploid potato. This work provides a foundation for further quantitative trait loci (QTL) location, map-based gene cloning of important traits and marker-assisted selection (MAS) of potato.

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.

Genetic linkage and physical mapping for an oyster mushroom Pleurotus cornucopiae and QTL analysis for the trait cap color

2021 ◽  
Author(s):  
Yan Zhang ◽  
Wei Gao ◽  
Anton Sonnenberg ◽  
Qiang Chen ◽  
Jinxia Zhang ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
De Novo ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Biological Efficiency ◽  
Solid Base ◽  
Marker Assisted Breeding ◽  
Oyster Mushrooms

Oyster mushrooms are grown commercially worldwide especially in many developing countries for their easy cultivation and high biological efficiency. Pleurotus cornucopiae is one of the main oyster mushrooms species for its gastronomic value and nutraceutical properties. Cap color is an important trait since consumers prefer dark colored mushrooms, which are now only represented by a small portion of the commercial varieties. Breeding efforts are greatly required to improve quality-related traits to satisfy various demands of consumers. Here we present a saturated genetic linkage map of P. cornucopiae constructed by using a segregating population of 122 monokaryons and 3449 SNP markers generated by 2b-RAD approach. The map contains 11 linkage groups covering 961.6 cM (centimorgan) with an average marker spacing of 0.27 cM. The genome of P. cornucopiae was de novo sequenced resulting in 425 scaffolds (>1000 bp) with a total genome size of 35.1 Mb. The scaffolds were assembled to pseudo-chromosome level with the assistance of the genetic linkage map. A total of 97% SNP markers (3357) were physically localized on 140 scaffolds that were assigned to 11 pseudo-chromosomes with a total of 32.5 Mb representing 92.5% of the whole genome. Six QTL controlling cap color of P. cornucopiae were detected explaining a total phenotypic variation of 65.6% with the highest value for the QTL on pseudo-chromosome 5 (18%). The results of our study provide a solid base for marker-assisted breeding for agronomic traits and especially for studies on biological mechanisms controlling cap color in oyster mushrooms. Importance Oyster mushrooms are produced and consumed over the world. Pleurotus cornucopiae is one of the main oyster mushrooms species. Dark cap oyster mushrooms are more and more popular to a consumer’s preferences, but dark varieties are rare to see on the market. Prerequisites for efficient breeding programs are the availability of high-quality whole genomes and genetic linkage maps. Genetic studies to fulfill some of these prerequisites have hardly been done for P. cornucopiae . In this study, we de novo sequenced the genome and constructed a saturated genetic linkage map for P. cornucopiae . The genetic linkage map was effectively used to assist the genome assembly and identify QTL that genetically control the trait cap color. Besides, the genome characteristics of P. cornucopiae was compared to its closely related species P . ostreatus . The results provided a basis for understanding the genetic background and marker-assisted breeding of this economic important mushroom species.

Construction of genetic linkage map and identification of QTLs related to agronomic traits in DH population of maize (Zea mays L.) using SSR markers

2019 ◽  
Vol 41 (6) ◽  
pp. 667-678 ◽  
Author(s):  
Jae-Keun Choi ◽  
Kyu Jin Sa ◽  
Dae Hyun Park ◽  
Su Eun Lim ◽  
Si-Hwan Ryu ◽  
...  
Keyword(s):  
Zea Mays ◽  
Linkage Map ◽  
Ssr Markers ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Zea Mays L ◽  
Agronomic Traits ◽  
Dh Population

scholarly journals A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guosong Zhang ◽  
Jie Li ◽  
Jiajia Zhang ◽  
Xia Liang ◽  
Tao Wang ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Candidate Genes ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Hypoxia Tolerance ◽  
Genome Wide ◽  
Pelteobagrus Vachelli

Abstract Background A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits. Results By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. Conclusions We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

scholarly journals Construction of genetic linkage map and identification of QTLs related to agronomic traits in maize using DNA transposon-based markers

2018 ◽  
Vol 68 (4) ◽  
pp. 465-473 ◽  
Author(s):  
Rahul Vasudeo Ramekar ◽  
Kyu Jin Sa ◽  
Kyong-Cheul Park ◽  
Neha Roy ◽  
Nam-Soo Kim ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Agronomic Traits ◽  
Dna Transposon
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