Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping

ABSTRACTThe American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three inter-related cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman Rank Correlations > 0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.

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Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping

BMC Genomics ◽

10.1186/s12864-016-2802-3 ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 24

Author(s):

Giovanny Covarrubias-Pazaran ◽

Luis Diaz-Garcia ◽

Brandon Schlautman ◽

Joseph Deutsch ◽

Walter Salazar ◽

...

Keyword(s):

Linkage Mapping ◽

Genomic Structure ◽

Genotyping By Sequencing ◽

High Density ◽

American Cranberry

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Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping

G3 Genes|Genome|Genetics ◽

10.1534/g3.116.037556 ◽

2017 ◽

Vol 7 (4) ◽

pp. 1177-1189 ◽

Cited By ~ 15

Author(s):

Brandon Schlautman ◽

Giovanny Covarrubias-Pazaran ◽

Luis Diaz-Garcia ◽

Massimo Iorizzo ◽

James Polashock ◽

...

Keyword(s):

Linkage Mapping ◽

Genotyping By Sequencing ◽

High Density ◽

Vaccinium Macrocarpon ◽

American Cranberry

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Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus

PeerJ ◽

10.7717/peerj.12390 ◽

2021 ◽

Vol 9 ◽

pp. e12390

Author(s):

Yaqun Zhang ◽

Chuantao Zhang ◽

Na Yao ◽

Jingxian Huang ◽

Xiangshan Sun ◽

...

Keyword(s):

Sex Determination ◽

Linkage Map ◽

Genetic Linkage ◽

Molecular Mechanisms ◽

Genetic Linkage Map ◽

Genotyping By Sequencing ◽

High Density ◽

Nucleotide Polymorphisms ◽

Penaeus Japonicus ◽

Genetic Mechanisms

Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.

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Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model

International Journal of Molecular Sciences ◽

10.3390/ijms22052679 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2679

Author(s):

Fabio Pértille ◽

Manuel Alvarez-Rodriguez ◽

Arthur Nery da Silva ◽

Isabel Barranco ◽

Jordi Roca ◽

...

Keyword(s):

Animal Model ◽

Semen Quality ◽

Association Studies ◽

Genotyping By Sequencing ◽

Late Summer ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Pig Genome ◽

Selection For ◽

Farrowing Rate

A combined Genotyping By Sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) protocol was used to identify—in parallel—genetic variation (Genomic-Wide Association Studies (GWAS) and epigenetic differences of Differentially Methylated Regions (DMR) in the genome of spermatozoa from the porcine animal model. Breeding boars with good semen quality (n = 11) and specific and well-documented differences in fertility (farrowing rate, FR) and prolificacy (litter size, LS) (n = 7) in artificial insemination programs, using combined FR and LS, were categorized as High Fertile (HF, n = 4) or Low Fertile (LF, n = 3), and boars with Unknown Fertility (UF, n = 4) were tested for eventual epigenetical similarity with those fertility-proven. We identified 165,944 Single Nucleotide Polymorphisms (SNPs) that explained 14–15% of variance among selection lines. Between HF and LF individuals (n = 7, 4 HF and 3 LF), we identified 169 SNPs with p ≤ 0.00015, which explained 58% of the variance. For the epigenetic analyses, we considered fertility and period of ejaculate collection (late-summer and mid-autumn). Approximately three times more DMRs were observed in HF than in LF boars across these periods. Interestingly, UF boars were clearly clustered with one of the other HF or LF groups. The highest differences in DMRs between HF and LF experimental groups across the pig genome were located in the chr 3, 9, 13, and 16, with most DMRs being hypermethylated in LF boars. In both HF and LF boars, DMRs were mostly hypermethylated in late-summer compared to mid-autumn. Three overlaps were detected between SNPs (p ≤ 0.0005, n = 1318) and CpG sites within DMRs. In conclusion, fertility levels in breeding males including FR and LS can be discerned using methylome analyses. The findings in this biomedical animal model ought to be applied besides sire selection for andrological diagnosis of idiopathic sub/infertility.

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Genotyping-by-Sequencing-Based Genome-Wide Association Studies of Fusarium Wilt Resistance in Radishes (Raphanus sativus L.)

Genes ◽

10.3390/genes12060858 ◽

2021 ◽

Vol 12 (6) ◽

pp. 858

Author(s):

O New Lee ◽

Hyunjin Koo ◽

Jae Woong Yu ◽

Han Yong Park

Keyword(s):

Fusarium Wilt ◽

Association Studies ◽

Genotyping By Sequencing ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Gwas Study ◽

F2 Population ◽

Genome Wide ◽

Resistant Varieties

Fusarium wilt (FW) is a fungal disease that causes severe yield losses in radish production. The most effective method to control the FW is the development and use of resistant varieties in cultivation. The identification of marker loci linked to FW resistance are expected to facilitate the breeding of disease-resistant radishes. In the present study, we applied an integrated framework of genome-wide association studies (GWAS) using genotyping-by-sequencing (GBS) to identify FW resistance loci among a panel of 225 radish accessions, including 58 elite breeding lines. Phenotyping was conducted by manual inoculation of seedlings with the FW pathogen, and scoring for the disease index was conducted three weeks after inoculation during two constitutive years. The GWAS analysis identified 44 single nucleotide polymorphisms (SNPs) and twenty putative candidate genes that were significantly associated with FW resistance. In addition, a total of four QTLs were identified from F2 population derived from a FW resistant line and a susceptible line, one of which was co-located with the SNPs on chromosome 7, detected in GWAS study. These markers will be valuable for molecular breeding programs and marker-assisted selection to develop FW resistant varieties of R. sativus.

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Adapting genotyping-by-sequencing and variant calling for heterogeneous stock rats

10.1101/523043 ◽

2019 ◽

Cited By ~ 2

Author(s):

Alexander F. Gileta ◽

Jianjun Gao ◽

Apurva S. Chitre ◽

Hannah V. Bimschleger ◽

Celine L. St. Pierre ◽

...

Keyword(s):

Association Studies ◽

Variant Calling ◽

Genotyping By Sequencing ◽

Genetic Maps ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Heterogeneous Stock ◽

Genotype Information ◽

Genotype By Sequencing ◽

Inbred Rat

ABSTRACTThe heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We also evaluate multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We also compared various rat genetic maps, which are necessary for imputation, including a recently developed map specific to the HS. Using our approach, we obtained concordance rates of 99% with data obtained using data from a genotyping array. The principles and computational pipeline that we describe could easily be adapted for use in other species for which reliable reference genome sets are available.

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Genomic regions associated with herbicide tolerance in a worldwide faba bean (Vicia faba L.) collection

Scientific Reports ◽

10.1038/s41598-021-03861-0 ◽

2022 ◽

Vol 12 (1) ◽

Author(s):

Lynn Abou-Khater ◽

Fouad Maalouf ◽

Abdulqader Jighly ◽

Alsamman M. Alsamman ◽

Diego Rubiales ◽

...

Keyword(s):

Protein Kinase ◽

Faba Bean ◽

Field Experiments ◽

Core Protein ◽

Association Studies ◽

Herbicide Tolerance ◽

Genotyping By Sequencing ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Herbicide Treatments

AbstractWeeds represent one of the major constraints for faba bean crop. The identification of molecular markers associated with key genes imparting tolerance to herbicides can facilitate and fasten the efficient and effective development of herbicide tolerant cultivars. We phenotyped 140 faba bean genotypes in three open field experiments at two locations in Lebanon and Morocco against three herbicide treatments (T1 metribuzin 250 g ai/ha; T2 imazethapyr 75 g ai/ha; T3 untreated) and one in greenhouse where T1 and T3 were applied. The same set was genotyped using genotyping by sequencing (GBS) which yield 10,794 high quality single nucleotide polymorphisms (SNPs). ADMIXTURE software was used to infer the population structure which revealed two ancestral subpopulations. To identify SNPs associated with phenological and yield related traits under herbicide treatments, Single-trait (ST) and Multi-trait (MT) Genome Wide Association Studies (GWAS) were fitted using GEMMA software, showing 10 and 14 highly significant associations, respectively. Genomic sequences containing herbicide tolerance associated SNPs were aligned against the NCBI database using BLASTX tool using default parameters to annotate candidate genes underlying the causal variants. SNPs from acidic endochitinase, LRR receptor-like serine/threonine-protein kinase RCH1, probable serine/threonine-protein kinase NAK, malate dehydrogenase, photosystem I core protein PsaA and MYB-related protein P-like were significantly associated with herbicide tolerance traits.

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Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401325 ◽

2020 ◽

Vol 10 (7) ◽

pp. 2195-2205 ◽

Cited By ~ 1

Author(s):

Alexander F. Gileta ◽

Jianjun Gao ◽

Apurva S. Chitre ◽

Hannah V. Bimschleger ◽

Celine L. St. Pierre ◽

...

Keyword(s):

Association Studies ◽

Variant Calling ◽

Genotyping By Sequencing ◽

Genetic Maps ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Heterogeneous Stock ◽

Genotype Information ◽

Genotype By Sequencing ◽

Inbred Rat

The heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We evaluated multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We have also compared various rat genetic maps, which are necessary for imputation, including a recently developed map specific to the HS. Using our approach, we obtained concordance rates of 99% with data obtained using data from a genotyping array. The principles and computational pipeline that we describe could easily be adapted for use in other species for which reliable reference genome sets are available.

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Molecular Characterization of Global Finger Millet (Eleusine coracana, L. Gaertn) germplasm Reaction to Striga in Kenya

Asian Journal of Biochemistry, Genetics and Molecular Biology ◽

10.9734/ajbgmb/2018/v1i2493 ◽

2018 ◽

pp. 1-14

Author(s):

Sirengo Peter Nyongesa ◽

Wamalwa Dennis Simiyu ◽

Oduor Chrispus ◽

Odeny Damaris Achieng ◽

Dangasuk Otto George

Keyword(s):

Finger Millet ◽

Association Studies ◽

Block Design ◽

Principal Component ◽

Genotyping By Sequencing ◽

Eleusine Coracana ◽

Striga Hermonthica ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Striga Resistance

Finger millet (Eleusine coracana, L. Gaertn) is an important food crop in Africa and Asia. The parasitic weed Striga hermonthica (Del.) Benth limits finger millet production through reduced yield in agro-ecologies where they exist. The damage of Striga to cereal crops is more severe under drought and low soil fertility. This study aims to determine genetic basis for reaction to Striga hermonthica among the selected germplasm of finger millets through genotyping by sequencing (GBS). One hundred finger millet genotypes were evaluated for reaction to Striga hermonthica infestation under field conditions at Alupe and Kibos in Western Kenya. The experiment was laid out in a randomized complete block design (RCBD) consisting of 10 x 10 square (triple lattice) under Striga (inoculated) and no Striga conditions and plant growth monitored to maturity after 110 days. All genotypes were genotyped by genotyping by sequencing (GBS) and data analyzed using the non-reference based Universal Network Enabled Analysis Kit (UNEAK) pipeline. Genome wide association studies (GWAS) were done to establish the association of detected Single Nucleotide Polymorphisms (SNPs) with Striga reaction based on field results. In molecular analysis 117,542 SNPs from raw GBS data used in GWAS revealed that markers TP 85424 and TP 88244 were associated with Striga resistance in the 95 genotypes. Principal Component Analysis revealed that the first and third component axes accounted for 2.5 and 8% of total variance respectively and the genotypes were distributed according to their reaction to Striga weed. Genetic diversity analysis grouped the 95 accessions into three major clusters containing; 32 (A), 56 (B), and 7 (C) genotypes. All finger millet genotypes that showed high resistance to Striga in the field were from cluster B while the most susceptible genotypes were from clusters A and C. Results revealed genetic variation for Striga resistance in cultivated finger millet genotypes and hence the possibility of marker –assisted breeding for resistance to Striga.

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A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia

Frontiers in Genetics ◽

10.3389/fgene.2021.802738 ◽

2022 ◽

Vol 12 ◽

Author(s):

Yang Cui ◽

Baolian Fan ◽

Xu Xu ◽

Shasha Sheng ◽

Yuhui Xu ◽

...

Keyword(s):

Genetic Map ◽

Molecular Genetic ◽

Genetic Research ◽

Genotyping By Sequencing ◽

Leaf Traits ◽

Coffea Canephora ◽

High Density ◽

Specific Pcr ◽

True Hybrid ◽

Allele Specific

The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F1 population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F1 individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.

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