scholarly journals Development of a Panel of Genotyping-in-Thousands by Sequencing in Capsicum

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinkwan Jo ◽  
Youngin Kim ◽  
Geon Woo Kim ◽  
Jin-Kyung Kwon ◽  
Byoung-Cheorl Kang
Keyword(s):  
Multiplex Pcr ◽  
Low Cost ◽  
Genotyping By Sequencing ◽  
Illumina Miseq ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Multiple Loci ◽  
Sequencing Method ◽  
Pcr Conditions

Genotyping by sequencing (GBS) enables genotyping of multiple loci at low cost. However, the single nucleotide polymorphisms (SNPs) revealed by GBS tend to be randomly distributed between individuals, limiting their direct comparisons without applying the various filter options to obtain a comparable dataset of SNPs. Here, we developed a panel of a multiplex targeted sequencing method, genotyping-in-thousands by sequencing (GT-seq), to genotype SNPs in Capsicum spp. Previously developed Fluidigm® SNP markers were converted to GT-seq markers and combined with new GT-seq markers developed using SNP information obtained through GBS. We then optimized multiplex PCR conditions: we obtained the highest genotyping rate when the first PCR consisted of 25 cycles. In addition, we determined that 101 primer pairs performed best when amplifying target sequences of 79 bp. We minimized interference of multiplex PCR by primer dimer formation using the PrimerPooler program. Using our GT-seq pipeline on Illumina Miseq and Nextseq platforms, we genotyped up to 1,500 (Miseq) and 1,300 (Nextseq) samples for the optimum panel size of 100 loci. To allow the genotyping of Capsicum species, we designed 332 informative GT-seq markers from Fluidigm SNP markers and GBS-derived SNPs. This study illustrates the first application of GT-seq in crop plants. The GT-seq marker set developed here will be a useful tool for molecular breeding of peppers in the future.

scholarly journals Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

2021 ◽  
Author(s):  
ZHIYONG Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.

scholarly journals Comparative analysis of single nucleotide polymorphisms and microsatellite markers for parentage verification and discovery within the equine Thoroughbred breed

2021 ◽  
Author(s):  
Paul Flynn ◽  
Romy Morrin-O'Donnell ◽  
Rebecca Weld ◽  
Laura M Gargan ◽  
Jens Carlsson ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genotyping By Sequencing ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Thoroughbred Horses ◽  
Snp Panels ◽  
Average Sample ◽  
Short Tandem

Short tandem repeat (STR), also known as microsatellite markers are currently used for genetic parentage verification within equine. Transitioning from STR to single nucleotide polymorphism (SNP) markers to perform equine parentage verification is now a potentially feasible prospect and a key area requiring evaluation is parentage testing accuracies when using SNP based methods, in comparison to STRs. To investigate, we utilised a targeted equine genotyping by sequencing (GBS) panel of 562 SNPs to SNP genotype 309 Thoroughbred horses - inclusive of 55 previously parentage verified offspring. Availability of STR profiles for all 309 horses, enabled comparison of parentage accuracies between SNP and STR panels. An average sample call rate of 97.2% was initially observed, and subsequent removal of underperforming SNPs realised a pruned final panel of 516 SNPs. Simulated trio and partial parentage scenarios were tested across 12-STR, 16-STR, 147-SNP and 516-SNP panels. False-positives (i.e. expected to fail parentage, but pass) ranged from 0% for 147-SNP and 516-SNP panels to 0.003% when using 12-STRs within trio parentage scenarios, and 0% for 516-SNPs to 1.6% for 12-STRs within partial parentage scenarios. Our study leverages targeted GBS methods to generate low-density equine SNP profiles and demonstrates the value of SNP based equine parentage analysis in comparison to STRs - particularly when performing partial parentage discovery.

scholarly journals Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Zhiyong Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms. Results We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264–364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring. Conclusions As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.

scholarly journals Heteroalleles in Common Wheat: Multiple Differences between Allelic Variants of the Gli-B1 Locus

2021 ◽  
Vol 22 (4) ◽  
pp. 1832
Author(s):  
Eugene Metakovsky ◽  
Laura Pascual ◽  
Patrizia Vaccino ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Fragment Length Polymorphism ◽  
Snp Markers ◽  
Group Iv ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Allelic Variants ◽  
B Genome

The Gli-B1-encoded γ-gliadins and non-coding γ-gliadin DNA sequences for 15 different alleles of common wheat have been compared using seven tests: electrophoretic mobility (EM) and molecular weight (MW) of the encoded major γ-gliadin, restriction fragment length polymorphism patterns (RFLPs) (three different markers), Gli-B1-γ-gliadin-pseudogene known SNP markers (Single nucleotide polymorphisms) and sequencing the pseudogene GAG56B. It was discovered that encoded γ-gliadins, with contrasting EM, had similar MWs. However, seven allelic variants (designated from I to VII) differed among them in the other six tests: I (alleles Gli-B1i, k, m, o), II (Gli-B1n, q, s), III (Gli-B1b), IV (Gli-B1e, f, g), V (Gli-B1h), VI (Gli-B1d) and VII (Gli-B1a). Allele Gli-B1c (variant VIII) was identical to the alleles from group IV in four of the tests. Some tests might show a fine difference between alleles belonging to the same variant. Our results attest in favor of the independent origin of at least seven variants at the Gli-B1 locus that might originate from deeply diverged genotypes of the donor(s) of the B genome in hexaploid wheat and therefore might be called “heteroallelic”. The donor’s particularities at the Gli-B1 locus might be conserved since that time and decisively contribute to the current high genetic diversity of common wheat.

scholarly journals Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1042
Author(s):  
Zhuoying Weng ◽  
Yang Yang ◽  
Xi Wang ◽  
Lina Wu ◽  
Sijie Hua ◽  
...  
Keyword(s):  
Fishery Management ◽  
Genotyping By Sequencing ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Individual Identification ◽  
Pedigree Information ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Polymorphic Snps ◽  
Mixed Family

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

scholarly journals Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1074
Author(s):  
Joanna Grzegorczyk ◽  
Artur Gurgul ◽  
Maria Oczkowicz ◽  
Tomasz Szmatoła ◽  
Agnieszka Fornal ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Read Depth ◽  
Model Organisms ◽  
Single Nucleotide Polymorphism Discovery ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Polymorphism Discovery ◽  
Genome Wide ◽  
Plumage Development ◽  
Edar Gene

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

scholarly journals Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

2019 ◽  
Vol 15 ◽  
pp. 117693431988994
Author(s):  
Shulin Zhang ◽  
Yaling Cai ◽  
Jinggong Guo ◽  
Kun Li ◽  
Renhai Peng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Association Analyses ◽  
Genome Wide ◽  
Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

Sign in / Sign up

Export Citation Format

Share Document