1. A genetic linkage map of Pinus massoniana based on SRAP, SSR and ESTP markers

Abstract Pinus massoniana (masson pine) is the most important native pine in southern China. High-density genetic maps have not been constructed for the species. In this study, a genetic linkage map with 251 markers (47 SSRs, 23 ESTPs and 181 SRAPs) was constructed using a F1 progeny mapping population derived from controlled pollination of two parents of different provenances. At LOD 7.0, a total of 17 linkage groups were constructed with twelve groups having nine or more markers and five other groups of two to four markers each. The total map length was 1,956 cM with an average of 8.4 cM among individual loci. The current linkage map represented 93% of the estimated genome length of 2,114 cM for masson pine. Such linkage map are useful for future genomic studies of masson pine including comparative mapping in Pinaceae and quantitative trait loci (QTL) mapping for economically important traits.

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Construction of a genetic linkage map for Saccharum officinarum incorporating both simplex and duplex markers to increase genome coverage

Genome ◽

10.1139/g07-056 ◽

2007 ◽

Vol 50 (8) ◽

pp. 742-756 ◽

Cited By ~ 40

Author(s):

K.S. Aitken ◽

P.A. Jackson ◽

C.L. McIntyre

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Saccharum Officinarum ◽

Basic Chromosome Number ◽

Genetic Maps ◽

Sugarcane Cultivar ◽

Repulsion Phase ◽

Preferential Chromosome Pairing ◽

Segregating Population

Saccharum officinarum L. is an octoploid with 80 chromosomes and a basic chromosome number of x = 10. It has high stem sucrose and contributes 80% of the chromosomes to the interspecific sugarcane cultivars that are grown commercially for sucrose. A genetic linkage map was developed for S. officinarum (clone IJ76-514) using a segregating population generated from a cross between Q165 (a commercial sugarcane cultivar) and IJ76-514. In total, 40 AFLP and 72 SSR primer pairs were screened across the population, revealing 595 polymorphic bands inherited from IJ76-514. These 595 markers displayed a frequency distribution different from all other sugarcane genetic maps produced, with only 40% being simplex markers (segregated 1:1). Of these 240 simplex markers, 178 were distributed on 47 linkage groups (LGs) and 62 remained unlinked. With the addition of 234 duplex markers and 80 biparental simplex markers (segregating 3:1), 534 markers formed 123 LGs. Using the multi-allelic SSR markers, repulsion phase linkage, and alignment with the Q165 linkage map, 105 of the 123 LGs could be grouped into 10 homology groups (HGs). These 10 HGs were further assigned to the 8 HGs observed in cultivated sugarcane and S. spontaneum . Analysis of repulsion phase linkage indicated that IJ76-514 is neither a complete autopolyploid nor an allopolyploid. Detection of 28 repulsion linkages that occurred between 6 pairs of LGs located in 4 HGs suggested the occurrence of limited preferential chromosome pairing in this species.

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A genetic linkage map of crested wheatgrass based on AFLP and RAPD markers

Genome ◽

10.1139/g2012-014 ◽

2012 ◽

Vol 55 (4) ◽

pp. 327-335 ◽

Cited By ~ 10

Author(s):

Xiaoxia Yu ◽

Xiaolei Li ◽

Yanhong Ma ◽

Zhuo Yu ◽

Zaozhe Li

Keyword(s):

Molecular Markers ◽

Linkage Map ◽

Genetic Linkage ◽

Rapd Markers ◽

Genetic Linkage Map ◽

Mapping Population ◽

Gene Localization ◽

Linkage Groups ◽

Crested Wheatgrass ◽

Map Distance

Using a population of 105 interspecific F2 hybrids derived from a cross between Agropyron mongolicum Keng and Agropyron cristatum (L.) Gaertn. ‘Fairway’ as a mapping population, a genetic linkage map of crested wheatgrass was constructed based on AFLP and RAPD molecular markers. A total of 175 markers, including 152 AFLP and 23 RAPD markers, were ordered in seven linkage groups. The map distance was 416 cM, with a mean distance of 2.47 cM between markers. The number of markers ranged from 13 to 46 in each linkage group and the length of groups ranged from 18 to 104 cM. The research found that 30 out of 175 molecular markers showed segregation distortion, accounting for 17% of all markers. This is the first genetic linkage map of crested wheatgrass. This map will facilitate gene localization, cloning, and molecular marker-assisted selection in the future.

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QTL mapping for growth-related traits by constructing the first genetic linkage map in Simao pine

10.21203/rs.3.rs-49639/v2 ◽

2020 ◽

Author(s):

dawei Wang ◽

chen Shi ◽

Siguang Li ◽

Hongyan Tang ◽

Chenzhong He ◽

...

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Phenotypic Variance ◽

Basal Diameter ◽

Exploitation And Utilization ◽

Information Construction ◽

Genomic Studies ◽

Needle Diameter

Abstract Background: Simao pine is one of the primary economic tree species for resin and timber production in southwest China. The exploitation and utilization of Simao pine are constrained by the relatively lacking of genetic information. Construction a fine genetic linkage map and detecting quantitative trait locis (QTLs) for growth-related traits is a prerequisite section of Simao Pine's molecular breeding program. Results: In our study, a high-resolution Simao pine genetic map employed specific locus amplified fragment sequencing (SLAF-seq) technology and based on an F1 pseudo-testcross population has been constructed. There were 11,544 SNPs assigned to 12 linkage groups (LGs), and the total length of the map was 2,062.85 cM with a mean distance of 0.37 cM between markers. According to the phenotypic variation analysis for three consecutive years, a total of seventeen QTLs for four traits were detected. Among 17 QTLs, there were six for plant height (Dh.16.1, Dh16.2, Dh17.1, Dh18.1-3), five for basal diameter (Dbd.17.1-5), four for needle length (Dnl17.1-3, Dnl18.1) and two for needle diameter (Dnd17.1 and Dnd18.1) respectively. These QTLs individually explained phenotypic variance from 11.0-16.3 %, and the logarithm of odds (LOD) value ranged from 2.52 to 3.87. Conclusions: In our study, a fine genetic map of Simao pine applied the technology of SLAF-seq has been constructed for the first time. Based on the map, a total of 17 QTLs for four growth-related traits were identified. It provides helpful information for genomic studies and marker-assisted selection (MAS) in Simao pine.

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Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map

Horticulturae ◽

10.3390/horticulturae7020025 ◽

2021 ◽

Vol 7 (2) ◽

pp. 25

Author(s):

Xingbo Wu ◽

Amanda M. Hulse-Kemp ◽

Phillip A. Wadl ◽

Zach Smith ◽

Keithanne Mockaitis ◽

...

Keyword(s):

Genetic Resources ◽

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Mapping Population ◽

High Density ◽

Linkage Maps ◽

Map Construction ◽

Hydrangea Macrophylla ◽

Genetic Linkage Maps

Hydrangea (Hydrangea macrophylla) is an important ornamental crop that has been cultivated for more than 300 years. Despite the economic importance, genetic studies for hydrangea have been limited by the lack of genetic resources. Genetic linkage maps and subsequent trait mapping are essential tools to identify and make markers available for marker-assisted breeding. A transcriptomic study was performed on two important cultivars, Veitchii and Endless Summer, to discover simple sequence repeat (SSR) markers and an F1 population based on the cross ‘Veitchii’ × ‘Endless Summer’ was established for genetic linkage map construction. Genotyping by sequencing (GBS) was performed on the mapping population along with SSR genotyping. From an analysis of 42,682 putative transcripts, 8780 SSRs were identified and 1535 were validated in the mapping parents. A total of 267 polymorphic SSRs were selected for linkage map construction. The GBS yielded 3923 high quality single nucleotide polymorphisms (SNPs) in the mapping population, resulting in a total of 4190 markers that were used to generate maps for each parent and a consensus map. The consensus linkage map contained 1767 positioned markers (146 SSRs and 1621 SNPs), spanned 1383.4 centiMorgans (cM), and was comprised of 18 linkage groups, with an average mapping interval of 0.8 cM. The transcriptome information and large-scale marker development in this study greatly expanded the genetic resources that are available for hydrangea. The high-density genetic linkage maps presented here will serve as an important foundation for quantitative trait loci mapping, map-based gene cloning, and marker-assisted selection of H. macrophylla.

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A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander

BMC Genomics ◽

10.1186/s12864-021-07550-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Qiaomu Hu ◽

Yang Liu ◽

Xiaolin Liao ◽

Haifeng Tian ◽

Xiangshan Ji ◽

...

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Economic Value ◽

Genetic Research ◽

High Density ◽

Amphibian Species ◽

Genomic Studies ◽

Chinese Giant Salamander

Abstract Background The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Its large genome presents challenges to genetic research. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci. Results In this study, we constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data of members from an full-sib family which sex had been determined. A total of 10,896 markers were grouped and oriented into 30 linkage groups, representing 30 chromosomes of A. davidianus. The genetic length of LGs ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26). The total genetic map length was 2643.10 cM with an average inter-locus distance of 0.24 cM. Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively. Conclusion We constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. Current results are expected to be a useful tool for future genomic studies aiming at the marker-assisted breeding of the species.

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Construction of a genetic linkage map in Lilium using a RIL mapping population based on SRAP marker

Genetika ◽

10.2298/gensr1502425c ◽

2015 ◽

Vol 47 (2) ◽

pp. 425-438 ◽

Cited By ~ 2

Author(s):

Li-Jing Chen ◽

Hong-Mei Li ◽

Shao-Kun Sun ◽

Muhammad Irfan ◽

Jing-Wei Lin ◽

...

Keyword(s):

Linkage Map ◽

Recombinant Inbred ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Mapping Population ◽

Recombinant Inbred Lines ◽

Inbred Lines ◽

Linkage Groups ◽

Marker Interval ◽

Interval Distance

A genetic linkage map of lily was constructed using RILs (recombinant inbred lines) population of 180 individuals. This mapping population was developed by crossing Raizan No.1 (Formolongo) and Gelria (Longiflomm) cultivars through single-seed descent (SSD). SRAPs were generated by using restriction enzymes EcoRI in combination with either MseI. The resulting products were separated by electrophoresis on 6% denaturing polyacrylamide gel and visualized by silver staining. The segregation of each marker and linkage analysis was done using the program Mapmaker3.0. With 50 primer pairs, a total of 189 parental polymorphic bands were detected and 78 were used for mapping. The total map length was 2,135.5 cM consisted of 16 linkage groups. The number of markers in the linkage groups varied from 1 to 12. The length of linkage groups was range from 11.2 cM to 425.9 cM and mean marker interval distance range from 9.4 cM to 345.4 cM individually. The mean marker interval distance between markers was 27.4 cM. The map developed in the present study was the first sequence-related amplified polymorphism markers map of lily constructed with recombinant inbred lines, it could be used for genetic mapping and molecular marker assisted breeding and quantitative trait locus mapping of Lilium.

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QTL Mapping for Growth-Related Traits by Constructing the First Genetic Linkage Map in Simao pine

10.21203/rs.3.rs-49639/v1 ◽

2020 ◽

Author(s):

dawei Wang ◽

chen Shi ◽

Siguang Li ◽

Hongyan Tang ◽

Chenzhong He ◽

...

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Phenotypic Variance ◽

Basal Diameter ◽

Exploitation And Utilization ◽

Information Construction ◽

Genomic Studies ◽

Specific Locus ◽

Needle Diameter

Abstract Simao pine is one of primary economic tree species for resin and timber production in southwest China, the exploitation and utilization are constrained by relatively lacking the genetic information. Construction a fine genetic linkage map and detecting QTLs for growth-related traits is an important section in molecular breeding program for Simao Pine. In our study, a high-resolution Simao pine genetic map employing specific locus amplified fragment sequencing (SLAF-seq) with an F1 population has been constructed. There were 11,544 SNPs assigned to 12 linkage groups in the map, and the total length of the map was 2,062.85 cM with a mean distance of 0.37 cM between markers. According to the phenotypic variation analysis during three consecutive years, seventeen QTLs for four traits which including six for plant height (Dh.16.1, Dh16.2, Dh17.1, Dh18.1-3), five for basal diameter (Dbd.17.1-5), four for needle length (Dnl17.1-3, Dnl18.1) and two for needle diameter (Dnd17.1 and Dnd18.1) were identified. These QTLs individually explained phenotypic variance from 11.0-16.3 %, and the LOD value ranged from 2.52 to 3.87. The result in this study provide helpful information for genomic studies and marker-assisted selection (MAS) in Simao pine.

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A genetic linkage map of Silene vulgaris based on AFLP markers

Genome ◽

10.1139/g05-114 ◽

2006 ◽

Vol 49 (4) ◽

pp. 320-327 ◽

Cited By ~ 21

Author(s):

Martin Bratteler ◽

Christian Lexer ◽

Alex Widmer

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Genome Mapping ◽

Mapping Population ◽

Segregation Ratio ◽

Aflp Markers ◽

Transmission Ratio Distortion ◽

Silene Vulgaris ◽

Ratio Distortion

A genetic linkage map of an intraspecific cross between 2 Silene vulgaris s.l. ecotypes is presented. Three-hundred AFLP markers from 2 different restriction enzyme combinations were used to genotype an F2 mapping population. Maternal and paternal pure-coupling phase maps with 114 and 186 markers on 12 and 13 linkage groups, respectively, were constructed. Total map length of the paternal and maternal maps are 547 and 446 Kosambi cM, respectively. Nearly half of the markers (49%) exhibited significant transmission ratio distortion. Genome coverage and potential causes of the observed segregation ratio distortions are discussed. The maps represent a first step towards the identification of quantitative trait loci associated with habitat adaptation in the non-model species Silene vulgaris.Key words: AFLP, genome mapping, segregation distortion, Silene vulgaris.

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