scholarly journals Genetic Mapping of Prince Rupprecht’s Larch (Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 583
Author(s):  
Dong ◽  
He ◽  
Zhao ◽  
Zhang ◽  
Yuan ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Northern China ◽  
Snp Markers ◽  
Genome Sequence Assembly ◽  
Genome Wide ◽  
Larch Species ◽  
Genomics Research ◽  
Reference Map ◽  
Specific Locus

A high-density genetic linkage map is essential for plant genetics and genomics research. However, due to the deficiency of genomic data and high-quality molecular markers, no genetic map has been published for Prince Rupprecht’s larch (Larix principis-rupprechtii Mayr), a conifer species with high ecological and commercial value in northern China. In this study, 145 F1 progeny individuals from an intraspecific cross between two elite clones of L. principis-rupprechtii and their parents were employed to construct the first genetic map in this important tree species using specific-locus amplified fragment sequencing (SLAF-seq). After preprocessing, the procedure yielded 300.20 Gb of raw data containing 1501.22 M pair-end reads. A total of 324,352 SNP markers were detected and 122,785 of them were polymorphic, with a polymorphism rate of 37.86%. Ultimately, 6099 SNPs were organized into a genetic map containing 12 linkage groups, consistent with the haploid chromosome number of larch and most other species in the Pinaceae family. The linkage map spanned 2415.58 cM and covered 99.6% of the L. principis-rupprechtii genome with an average of 0.4 cM between adjacent markers. To the best of our knowledge, this map is the first reference map for L. principis-rupprechtii, as well as the densest one obtained in larch species thus far. The genome-wide SNPs and the high-resolution genetic map will provide a foundation for future quantitative trait loci mapping, map-based cloning, marker-assisted selection, comparative genomics, and genome sequence assembly for larch trees.

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 Combined QTL and GWAS Analysis to Identify the Growth-Related Gene in Rhopilema Esculentum with the Help of 2b-RAD Sequencing

2021 ◽  
Author(s):  
Bailing Chen ◽  
Yulong Li ◽  
Meilin Tian ◽  
Hao Su ◽  
Wei Sun ◽  
...  
Keyword(s):  
Body Weight ◽  
High Resolution ◽  
Genetic Map ◽  
Calcium Binding ◽  
Genome Wide Association Study ◽  
Snp Markers ◽  
Fishery Resource ◽  
Genetic Breeding ◽  
Marine Fishery ◽  
Genome Wide

Abstract R. esculentum is a popular seafood in Asian countries and an economic marine fishery resource in China. However, the high-resolution genetic map and growth-related molecular markers still lack, hindering the process of the genetic breeding of R. esculentum. Therefore, we firstly used the 2b-RAD method to sequence 152 R. esculentum specimens, identified 9100 single nucleotide polymorphism (SNP) markers and constructed a high-resolution genetic map with a marker interval of 0.58 cM, covering 98.68% of the genome. Then, we separately detected four and three quantitative trait loci (QTLs) associated with umbrella diameter and body weight based on the linkage map, which is located on linkage group (LG) 4, 13, 14 and 15. Finally, 27 genes were found both associated with umbrella diameter and body weight of R. esculentum by genome-wide association study (GWAS), in which one gene named RE13670 containing calcium-binding EGF-like domain may play an important role in controlling the growth. This study will be beneficial for underlying the growth mechanism of R. esculentum and also provide background knowledge for guiding its genetic breeding.

scholarly journals High-density linkage map and QTLs for growth in snapper (Chrysophrys auratus)

2018 ◽  
Author(s):  
David T. Ashton ◽  
Peter A. Ritchie ◽  
Maren Wellenreuther
Keyword(s):  
Linkage Map ◽  
Genome Structure ◽  
Snp Markers ◽  
Biological Research ◽  
Phenotypic Traits ◽  
Strongly Correlated ◽  
Fish Family ◽  
Significant Qtls ◽  
Snp Data ◽  
Genome Wide

ABSTRACTCharacterizing the genetic variation underlying phenotypic traits is a central objective in biological research. This research has been hampered in the past by the limited genomic resources available for most non-model species. However, recent advances in sequencing technology and related genotyping methods are rapidly changing this. Here we report the use of genome-wide SNP data from the ecologically and commercially important marine fish species Chrysophrys auratus (snapper) to 1) construct the first linkage map for this species, 2) scan for growth QTLs, and 3) search for candidate genes in the surrounding QTL regions. The newly constructed linkage map contained ~11K SNP markers and is the densest map to date in the fish family Sparidae. Comparisons with available genome scaffolds indicated that overall marker placement was strongly correlated between the scaffolds and linkage map (R = 0.7), but at fine scales (< 5 cM) there were some precision limitations. Of the 24 linkage groups, which reflect the 24 chromosomes of this species, three were found to contain QTLs with genome-wide significance for growth-related traits. A scan for 13 known candidate growth genes located the genes for growth hormone, parvalbumin, and myogenin within 13.2, 2.6, and 5.0 cM of these genome-wide significant QTLs, respectively. The linkage map and QTLs found in this study will advance the investigation of genome structure and selective breeding in snapper.

scholarly journals Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0125583 ◽  
Author(s):  
Yash Paul Khajuria ◽  
Maneesha S. Saxena ◽  
Rashmi Gaur ◽  
Debasis Chattopadhyay ◽  
Mukesh Jain ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Linkage Map ◽  
Genetic Map ◽  
High Density ◽  
Genome Wide ◽  
Polymorphic Microsatellite

scholarly journals Construction of a High-Density Genetic Map for Pitaya Using the Whole Genome Resequencing Approach

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 534
Author(s):  
Zhijiang Wu ◽  
Haiyan Deng ◽  
Guidong Liang ◽  
Xiaoying Ye ◽  
Yonghua Qin ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Snp Markers ◽  
High Density ◽  
Genetic Maps ◽  
Fleshy Fruit ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Hylocereus Undatus ◽  
Whole Genome Resequencing

Pitaya (Hylocereus undatus) is one of the most economic fleshy fruit tree crops. This study aimed at producing a high-density linkage genetic map of pitaya based on the whole genome resequencing (WGrS) approach. For this purpose, a bi-parental F1 population of 198 individuals was generated and genotyped by WGrS. High-quality polymorphic 6434 single polymorphism nucleotide (SNP) markers were extracted and used to construct a high-density linkage map. A total of 11 linkage groups were resolved as expected in accordance with the chromosome number. The map length was 14,128.7 cM with an average SNP interval of 2.2 cM. Homology with the sequenced reference genome was described, and the physical and genetic maps were compared with collinearity analysis. This linkage map in addition to the available genomic resources will help for quantitative trait mapping, evolutionary studies and marker-assisted selection in the important Hylocereus species.

scholarly journals A high-density SNP-based genetic map in Pelteobagrus vachelli and mapping of growth, sex determination and hypoxia tolerance related loci

2019 ◽  
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: As is known to all, when we are doing QTL fine mapping, analyzing comparative genome, identifying candidate genes, making marker-assisted selection in aquaculture species, the high-density genetic linkage map is of great significance. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters made it difficult to do traditional selective breeding based on phenotypes. For instance, potential problems include lacking in genomic resource which is in large scale and short of markers that is related tightly to 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. It is reflected that bu using comparative genome mapping, a large majority (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 gene 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.

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.

scholarly journals High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata

2021 ◽  
Vol 22 (11) ◽  
pp. 5723
Author(s):  
Yuan-Yuan Xu ◽  
Sheng-Rui Liu ◽  
Zhi-Meng Gan ◽  
Ren-Fang Zeng ◽  
Jin-Zhi Zhang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Map ◽  
Expression Patterns ◽  
High Density ◽  
Poncirus Trifoliata ◽  
Leaf Abscission ◽  
Comparative Genomic ◽  
Map Comparison ◽  
Genomic Studies

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.

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