Construction of a genetic linkage map based on RAPD, AFLP, and SSR markers for tea plant (Camellia sinensis)

Chang, Yali; Oh, Eun Ui; Lee, Min Seuk; Kim, Ho Bang; Moon, Doo-Gyung; Song, Kwan Jeong

doi:10.1007/s10681-017-1979-0

Cited by 20 publications

(11 citation statements)

References 25 publications

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“…Then, markers were selected according to the lowest missing rate from each bin. By using JoinMap 4.0, the markers were ordered into corresponding groups with LOD scores ranging from 2 to 10, and each group was then used to construct a linkage map by using the Kosambi mapping function with an LOD ≥ 5 [20,41]. To obtain the physical locations of the SNPs and divide the long and short chromosome arms of the genetic map, the flanking sequences were subjected to BLAST searches with the IWGSC wheat contig sequences (http://www.wheatgenome.org/).…”

Section: Molecular Genotyping and Genetic Linkage Map Constructionmentioning

confidence: 99%

Mapping Quantitative Trait Loci for 1000-Grain Weight in a Double Haploid Population of Common Wheat

Liu

Gan

et al. 2020

IJMS

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Thousand-grain weight (TGW) is a very important yield trait of crops. In the present study, we performed quantitative trait locus (QTL) analysis of TGW in a doubled haploid population obtained from a cross between the bread wheat cultivar “Superb” and the breeding line “M321” using the wheat 55-k single-nucleotide polymorphism (SNP) genotyping assay. A genetic map containing 15,001 SNP markers spanning 2209.64 cM was constructed, and 9 QTLs were mapped to chromosomes 1A, 2D, 4B, 4D, 5A, 5D, 6A, and 6D based on analyses conducted in six experimental environments during 2015–2017. The effects of the QTLs qTgw.nwipb-4DS and qTgw.nwipb-6AL were shown to be strong and stable in different environments, explaining 15.31–32.43% and 21.34–29.46% of the observed phenotypic variance, and they were mapped within genetic distances of 2.609 cM and 5.256 cM, respectively. These novel QTLs may be used in marker-assisted selection in wheat high-yield breeding.

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Section: Molecular Genotyping and Genetic Linkage Map Constructionmentioning

confidence: 99%

Mapping Quantitative Trait Loci for 1000-Grain Weight in a Double Haploid Population of Common Wheat

Liu

Gan

et al. 2020

IJMS

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“…Genetic maps are constructed according to the linkage relationships between molecular markers in the genome, including random amplified polymorphic DNA (RAPD) [25, 26], amplified fragment length polymorphisms (AFLPs) [26–28], simple sequence repeats (SSRs) [26, 28–30], sequence-related amplified polymorphisms (SRAPs) [31], single nucleotide polymorphisms (SNPs) [32], and insertions-deletions (InDels) [33]. Among these types of markers, SNPs and InDels are considered potential applied molecular markers [34].…”

Section: Introductionmentioning

confidence: 99%

Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode

Zhang

Xiao

et al. 2019

BMC Plant Biol

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BackgroundCatalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies.ResultsRestriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F1 population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16–60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9–1, Q18–66 and Q18–73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis.ConclusionsThis is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.

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“…Based on genotyping for molecular markers, some genetic maps have recently been constructed by using various types of markers in tea plants. For example, Chang et al [17] constructed a genetic map using 678 markers including 143 RAPDs, 11 public SSRs, 495 AFLPs, and 29 newly mined SSRs, and the map covered 1441.6 cM with an average distance of 4.7 cM between adjacent markers. Ma et al [18] developed an SSR genetic map containing 406 SSRs spanning 1143.5 cM with an average distance of 2.9 cM between markers.…”

Section: Introductionmentioning

confidence: 99%

High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

Wang

Wei

et al. 2018

BMC Genomics

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BackgroundFlavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content is time consuming and labour intensive. High-density genetic map construction associated with quantitative trait locus (QTL) mapping provides an effective way to facilitate trait improvement in plant breeding. In this study, an F1 population (LJ43×BHZ) was genotyped using 2b-restriction site-associated DNA (2b-RAD) sequencing to obtain massive single nucleotide polymorphism (SNP) markers to construct a high-density genetic map for a tea plant. Furthermore, QTLs related to flavonoids were identified using our new genetic map.ResultsA total of 13,446 polymorphic SNP markers were developed using 2b-RAD sequencing, and 4,463 of these markers were available for constructing the genetic linkage map. A 1,678.52-cM high-density map at an average interval of 0.40 cM with 4,217 markers, including 427 frameset simple sequence repeats (SSRs) and 3,800 novel SNPs, mapped into 15 linkage groups was successfully constructed. After QTL analysis, a total of 27 QTLs related to flavonoids or caffeine content (CAF) were mapped to 8 different linkage groups, LG01, LG03, LG06, LG08, LG10, LG11, LG12, and LG13, with an LOD from 3.14 to 39.54, constituting 7.5% to 42.8% of the phenotypic variation.ConclusionsTo our knowledge, the highest density genetic map ever reported was constructed since the largest mapping population of tea plants was adopted in present study. Moreover, novel QTLs related to flavonoids and CAF were identified based on the new high-density genetic map. In addition, two markers were located in candidate genes that may be involved in flavonoid metabolism. The present study provides valuable information for gene discovery, marker-assisted selection breeding and map-based cloning for functional genes that are related to flavonoid content in tea plants.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5291-8) contains supplementary material, which is available to authorized users.

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Construction of a genetic linkage map based on RAPD, AFLP, and SSR markers for tea plant (Camellia sinensis)

Cited by 20 publications

References 25 publications

Mapping Quantitative Trait Loci for 1000-Grain Weight in a Double Haploid Population of Common Wheat

Mapping Quantitative Trait Loci for 1000-Grain Weight in a Double Haploid Population of Common Wheat

Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode

High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

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