A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.)

Abstract Background Lycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. However, genetic analysis of this plant and molecular breeding for quality improvement are limited by the lack of sufficient molecular markers. Results In this study, two parental strains, ‘Ningqi No. 1’ (Lycium barbarum L.) and ‘Yunnan Gouqi’ (Lycium yunnanense Kuang et A.M. Lu), and 200 F1 hybrid individuals were resequenced for genetic analysis. In total, 8,507 well-selected SNPs were developed, and a high-density genetic map (NY map) was constructed with a total genetic distance of 2,122.24 cM. A consensus genetic map was established by integrating the NY map and a previously published genetic map (NC map) containing 15,240 SNPs, with a total genetic distance of 3,058.19 cM and an average map distance of 0.21 cM. The 12 pseudochromosomes of the Lycium reference genome were anchored using this consensus genetic map, with an anchoring rate of 64.3%. Moreover, weak collinearities between the consensus map and the pepper, potato, and tomato genomes were observed. Twenty-five stable QTLs were identified for leaf- and fruit-related phenotypes, including fruit weight, fruit longitude, leaf length, the fruit index, and the leaf index; these stable QTLs were mapped to four different linkage groups, with LOD scores ranging from 2.51 to 19.37 and amounts of phenotypic variance explained from 6.2% to 51.9%. Finally, 82 out of 188 predicted genes underlying stable QTLs for fruit-related traits were differentially expressed according to RNA-seq analysis. Conclusions A chromosome-level assembly can provide a foundation for further functional genomics research for wolfberry. The genomic regions of these stably expressed QTLs could be used as targets for further fine mapping and development of molecular markers for marker-assisted selection (MAS). The present study provided valuable information on saturated SNP markers and reliable QTLs for map-based cloning of functional genes related to yield and morphological traits in Lycium spp.

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A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.)

10.21203/rs.3.rs-409699/v1 ◽

2021 ◽

Author(s):

Jianhua Zhao ◽

Haoxia Li ◽

Yuhui Xu ◽

Yue Yin ◽

Ting Huang ◽

...

Keyword(s):

Molecular Markers ◽

Genetic Analysis ◽

Genetic Distance ◽

Genetic Map ◽

Fruit Weight ◽

Snp Markers ◽

Leaf Length ◽

Phenotypic Variance ◽

Lycium Barbarum ◽

Stable Qtls

Abstract Background: Lycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. However, genetic analysis of this plant and molecular breeding for quality improvement are limited by the lack of sufficient molecular markers. Results: In this study, two parental strains, ‘Ningqi No. 1’ (Lycium barbarum L.) and ‘Yunnan Gouqi’ (Lycium yunnanense Kuang et A.M. Lu), and 200 F1 hybrid individuals were resequenced for genetic analysis. In total, 8,507 well-selected SNPs were developed, and a high-density genetic map (NY map) was constructed with a total genetic distance of 2,122.24 cM. A consensus genetic map was established by integrating the NY map and a previously published genetic map (NC map) containing 15,240 SNPs, with a total genetic distance of 3,058.19 cM and an average map distance of 0.21 cM. The 12 pseudochromosomes of the Lycium reference genome were anchored using this consensus genetic map, with an anchoring rate of 64.3%. Moreover, weak collinearities between the consensus map and the pepper, potato, and tomato genomes were observed. Twenty-five stable QTLs were identified for leaf- and fruit-related phenotypes, including fruit weight, fruit longitude, leaf length, the fruit index, and the leaf index; these stable QTLs were mapped to four different linkage groups, with LOD scores ranging from 2.51 to 19.37 and amounts of phenotypic variance explained from 6.2% to 51.9%. Finally, 82 out of 188 predicted genes underlying stable QTLs for fruit-related traits were differentially expressed according to RNA-seq analysis. Conclusions: A chromosome-level assembly can provide a foundation for further functional genomics research for wolfberry. The genomic regions of these stably expressed QTLs could be used as targets for further fine mapping and development of molecular markers for marker-assisted selection (MAS). The present study provided valuable information on saturated SNP markers and reliable QTLs for map-based cloning of functional genes related to yield and morphological traits in Lycium spp.

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Construction of a reference linkage map for melon

Genome ◽

10.1139/g01-073 ◽

2001 ◽

Vol 44 (5) ◽

pp. 836-845 ◽

Cited By ~ 45

Author(s):

M Oliver ◽

J Garcia-Mas ◽

M Cardús ◽

N Pueyo ◽

A I López-Sesé ◽

...

Keyword(s):

Molecular Markers ◽

Genetic Distance ◽

Linkage Map ◽

Genetic Map ◽

Cucumis Melo ◽

Morphological Trait ◽

Linkage Groups ◽

Resistant Gene ◽

Anchor Points ◽

Cucumis Melo L

A map of melon (Cucumis melo L.) with 411 markers (234 RFLPs, 94 AFLPs, 47 RAPDs, 29 SSRs, five inter-SSRs, and two isozymes) and one morphological trait (carpel number) was constructed using the F2 progeny of a cross between the Korean accession PI161375 and the Spanish melon type 'Pinyonet Piel de Sapo'. RFLPs were obtained using 212 probes from different genomic and cDNA melon libraries, including 16 Arabidopsis ESTs, 13 Cucumis known genes, and three resistant gene homologues. Most loci (391) mapped to 12 major linkage groups, spanning a total genetic distance of 1197 cM, with an average map interval of 3 cM/marker. The remaining 21 loci (six RAPDs and 15 AFLPs) were not linked. A majority (66%) of the markers were codominant (RFLPs, SSRs, and isozymes), making them easily transferable to other melon crosses. Such markers can be used as a reference, to merge other melon and cucumber maps already constructed. Indeed, some of them (23 SSRs, 14 RFLPs, one isozyme, and one morphological trait) could act as anchor points with other published cucurbit maps.Key words: Cucumis melo, genetic map, molecular markers, RFLPs, SSRs.

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The Liability Threshold Model for Predicting the Risk of Cardiovascular Disease in Patients with Type 2 Diabetes: A Multi-Cohort Study of Korean Adults

Metabolites ◽

10.3390/metabo11010006 ◽

2020 ◽

Vol 11 (1) ◽

pp. 6

Author(s):

Eun Pyo Hong ◽

Seong Gu Heo ◽

Ji Wan Park

Keyword(s):

Type 2 Diabetes ◽

Cardiovascular Disease ◽

Risk Prediction ◽

Linear Mixed Model ◽

Threshold Model ◽

Snp Markers ◽

Polygenic Risk Score ◽

Phenotypic Variance ◽

Prediction Approach

Personalized risk prediction for diabetic cardiovascular disease (DCVD) is at the core of precision medicine in type 2 diabetes (T2D). We first identified three marker sets consisting of 15, 47, and 231 tagging single nucleotide polymorphisms (tSNPs) associated with DCVD using a linear mixed model in 2378 T2D patients obtained from four population-based Korean cohorts. Using the genetic variants with even modest effects on phenotypic variance, we observed improved risk stratification accuracy beyond traditional risk factors (AUC, 0.63 to 0.97). With a cutoff point of 0.21, the discrete genetic liability threshold model consisting of 231 SNPs (GLT231) correctly classified 87.7% of 2378 T2D patients as high or low risk of DCVD. For the same set of SNP markers, the GLT and polygenic risk score (PRS) models showed similar predictive performance, and we observed consistency between the GLT and PRS models in that the model based on a larger number of SNP markers showed much-improved predictability. In silico gene expression analysis, additional information was provided on the functional role of the genes identified in this study. In particular, HDAC4, CDKN2B, CELSR2, and MRAS appear to be major hubs in the functional gene network for DCVD. The proposed risk prediction approach based on the liability threshold model may help identify T2D patients at high CVD risk in East Asian populations with further external validations.

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Multi-year analyses on three populations reveal the first stable QTLs for tolerance to rain-induced fruit cracking in sweet cherry (Prunus avium L.)

Horticulture Research ◽

10.1038/s41438-021-00571-6 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

José Quero-García ◽

Philippe Letourmy ◽

José Antonio Campoy ◽

Camille Branchereau ◽

Svetoslav Malchev ◽

...

Keyword(s):

Confidence Intervals ◽

Sweet Cherry ◽

Prunus Avium ◽

Linear Models ◽

Basic Research ◽

Fruit Weight ◽

Phenotypic Variance ◽

Fruit Cracking ◽

The Stability ◽

Sweet Cherry Cultivars

AbstractRain-induced fruit cracking is a major problem in sweet cherry cultivation. Basic research has been conducted to disentangle the physiological and mechanistic bases of this complex phenomenon, whereas genetic studies have lagged behind. The objective of this work was to disentangle the genetic determinism of rain-induced fruit cracking. We hypothesized that a large genetic variation would be revealed, by visual field observations conducted on mapping populations derived from well-contrasted cultivars for cracking tolerance. Three populations were evaluated over 7–8 years by estimating the proportion of cracked fruits for each genotype at maturity, at three different areas of the sweet cherry fruit: pistillar end, stem end, and fruit side. An original approach was adopted to integrate, within simple linear models, covariates potentially related to cracking, such as rainfall accumulation before harvest, fruit weight, and firmness. We found the first stable quantitative trait loci (QTLs) for cherry fruit cracking, explaining percentages of phenotypic variance above 20%, for each of these three types of cracking tolerance, in different linkage groups, confirming the high complexity of this trait. For these and other QTLs, further analyses suggested the existence of at least two-linked QTLs in each linkage group, some of which showed confidence intervals close to 5 cM. These promising results open the possibility of developing marker-assisted selection strategies to select cracking-tolerant sweet cherry cultivars. Further studies are needed to confirm the stability of the reported QTLs over different genetic backgrounds and environments and to narrow down the QTL confidence intervals, allowing the exploration of underlying candidate genes.

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The distribution of SNP marker effects for faecal worm egg count in sheep, and the feasibility of using these markers to predict genetic merit for resistance to worm infections

Genetics Research ◽

10.1017/s0016672311000097 ◽

2011 ◽

Vol 93 (3) ◽

pp. 203-219 ◽

Cited By ~ 51

Author(s):

KATHRYN E. KEMPER ◽

DAVID L. EMERY ◽

STEPHEN C. BISHOP ◽

HUTTON ODDY ◽

BENJAMIN J. HAYES ◽

...

Keyword(s):

Complex Traits ◽

Sampling Error ◽

Snp Markers ◽

Snp Marker ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

Phenotypic Variance ◽

Breeding Values ◽

Genetic Merit ◽

Independent Population

SummaryGenetic resistance to gastrointestinal worms is a complex trait of great importance in both livestock and humans. In order to gain insights into the genetic architecture of this trait, a mixed breed population of sheep was artificially infected with Trichostrongylus colubriformis (n=3326) and then Haemonchus contortus (n=2669) to measure faecal worm egg count (WEC). The population was genotyped with the Illumina OvineSNP50 BeadChip and 48 640 single nucleotide polymorphism (SNP) markers passed the quality controls. An independent population of 316 sires of mixed breeds with accurate estimated breeding values for WEC were genotyped for the same SNP to assess the results obtained from the first population. We used principal components from the genomic relationship matrix among genotyped individuals to account for population stratification, and a novel approach to directly account for the sampling error associated with each SNP marker regression. The largest marker effects were estimated to explain an average of 0·48% (T. colubriformis) or 0·08% (H. contortus) of the phenotypic variance in WEC. These effects are small but consistent with results from other complex traits. We also demonstrated that methods which use all markers simultaneously can successfully predict genetic merit for resistance to worms, despite the small effects of individual markers. Correlations of genomic predictions with breeding values of the industry sires reached a maximum of 0·32. We estimate that effective across-breed predictions of genetic merit with multi-breed populations will require an average marker spacing of approximately 10 kbp.

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SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽

10.1139/g10-079 ◽

2010 ◽

Vol 53 (11) ◽

pp. 948-956 ◽

Cited By ~ 35

Author(s):

G. Durstewitz ◽

A. Polley ◽

J. Plieske ◽

H. Luerssen ◽

E. M. Graner ◽

...

Keyword(s):

Genetic Analysis ◽

Oilseed Rape ◽

Expressed Sequence Tag ◽

Diploid Species ◽

Amplicon Sequencing ◽

Snp Markers ◽

Snp Analysis ◽

Genome Wide ◽

A Genome ◽

Illumina Goldengate

Oilseed rape ( Brassica napus ) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

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Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

Biology ◽

10.3390/biology10010036 ◽

2021 ◽

Vol 10 (1) ◽

pp. 36

Author(s):

Te-Hua Hsu ◽

Yu-Ting Chiu ◽

Hung-Tai Lee ◽

Hong-Yi Gong ◽

Chang-Wen Huang

Keyword(s):

Molecular Markers ◽

Expressed Sequence Tag ◽

De Novo ◽

Growth Traits ◽

Gene Diversity ◽

Snp Markers ◽

Cdna Libraries ◽

Functional Markers ◽

Genetic Management ◽

Ssr And Snp Markers

The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.

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On Genetic Map Functions

Genetics ◽

10.1093/genetics/142.4.1369 ◽

1996 ◽

Vol 142 (4) ◽

pp. 1369-1377

Author(s):

Hongyu Zhao ◽

Terence P Speed

Keyword(s):

Genetic Distance ◽

Genetic Map ◽

Probability Model ◽

Recombination Fraction ◽

Renewal Processes ◽

Gamma Distributions ◽

Multilocus Analysis ◽

Map Function ◽

Better Than

Abstract Various genetic map functions have been proposed to infer the unobservable genetic distance between two loci from the observable recombination fraction between them. Some map functions were found to fit data better than others. When there are more than three markers, multilocus recombination probabilities cannot be uniquely determined by the defining property of map functions, and different methods have been proposed to permit the use of map functions to analyze multilocus data. If for a given map function, there is a probability model for recombination that can give rise to it, then joint recombination probabilities can be deduced from this model. This provides another way to use map functions in multilocus analysis. In this paper we show that stationary renewal processes give rise to most of the map functions in the literature. Furthermore, we show that the interevent distributions of these renewal processes can all be approximated quite well by gamma distributions.

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ANÁLISE BIOMÉTRICA DE FRUTOS E SEMENTES DE Passiflora cristalina Vanderplank & Zappi

Nativa ◽

10.31413/nativa.v7i2.6554 ◽

2019 ◽

Vol 7 (2) ◽

pp. 138

Author(s):

Greiciele Farias da Silveira ◽

Ana Aparecida Bandini Rossi ◽

Uéliton Alves de Oliveira ◽

Tatiane Lemos Varella ◽

Fernanda Saragosa Rossi ◽

...

Keyword(s):

Fruit Weight ◽

Food Distribution ◽

Soluble Solids ◽

Volume Index ◽

Phenotypic Variance ◽

Bark Thickness ◽

Mato Grosso ◽

Biometric Analysis ◽

Solids Content ◽

Number Of Seeds

O objetivo do presente trabalho é caracterizar biometricamente os frutos e sementes de Passiflora cristalina Vanderplank & Zappi ocorrentes na região de Alta Floresta, Mato Grosso. Foram coletados em 2013 um total de 100 frutos maduros de 15 genótipos e destes foram selecionadas 300 sementes aleatoriamente. Os frutos foram analisados quanto ao comprimento, largura, espessura, peso, espessura da casca, o peso da polpa, o peso das sementes/fruto, número de sementes/fruto e teor de sólidos solúveis. As sementes foram avaliadas em relação ao comprimento, largura, espessura e índice de volume. As características biométricas foram analisadas mediante distribuição de frequência calculando-se o coeficiente de correlação de Spearman e o nível de significância através do teste T. O comprimento do fruto correlacionou-se positivamente com a largura e peso do fruto, espessura da casca e com peso das sementes, não havendo uma correlação com o número de sementes por fruto. Houve uma ampla distribuição de frequência das características avaliadas nos frutos, com exceção do peso das sementes. A alta variação fenotípica encontrada para a maioria das características avaliadas nos frutos e sementes de P. cristalina revela que a espécie tem divergência genética a ser utilizado em programas de seleção e conservação de recursos genéticos.Palavras-chave: divergência genética, maracujá, recursos genéticos. BIOMETRIC ANALYSIS OF FRUITS AND SEEDS OF Passiflora cristalina Vanderplank & Zappi ABSTRACT: The present work has presented the fruits and seeds of Passiflora cristalina Vanderplank & Zappi occurring in the region of Alta Floresta, Mato Grosso. A total of 100 mature fruits of 15 genotypes were collected in 2013 and 300 seeds were randomly selected. The fruits were inert to the length, thickness, thickness, weight, bark thickness, pulp weight, seed/fruit weight, number of seeds / fruit and soluble solids content. The seeds were evaluated for length, width, thickness and volume index. The biometric characteristics were analyzed with the calculation frequency calculated with the Spearman correlation coefficient and the level of significance throughout the T test. Fruit weight was correlated with fruit width and weight, bark thickness and weight of the fruits. Seeds without a key with the number of seeds per fruit. There is an offer of food distribution in the fruits, with the exception of the weight of the seeds. The high phenotypic variance found for a greater number of species evaluated in fruits and seeds of P.cristalina reveals that a type of genetics has been characterized in programs of selection and conservation of genetic resources.Keywords: genetic divergence, passion fruit, genetic resources.

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Centromere-Linkage Analysis and Consolidation of the Zebrafish Genetic Map

Genetics ◽

10.1093/genetics/142.4.1277 ◽

1996 ◽

Vol 142 (4) ◽

pp. 1277-1288

Author(s):

Stephen L Johnson ◽

Michael A Gates ◽

Michele Johnson ◽

William S Talbot ◽

Sally Horne ◽

...

Keyword(s):

Linkage Group ◽

Linkage Analysis ◽

Genetic Analysis ◽

Linkage Map ◽

Rapid Method ◽

Genetic Map ◽

Dna Polymorphisms ◽

Linkage Groups

Abstract The ease of isolating mutations in zebrafish will contribute to an understanding of a variety of processes common to all vertebrates. To facilitate genetic analysis of such mutations, we have identified DNA polymorphisms closely linked to each of the 25 centromeres of zebrafish, placed centromeres on the linkage map, increased the number of mapped PCR-based markers to 652, and consolidated the number of linkage groups to the number of chromosomes. This work makes possible centromere-linkage analysis, a novel, rapid method to assign mutations to a specific linkage group using half-tetrads.

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