High-Density Linkage Map Construction and QTL Identification in a Diploid Blueberry Mapping Population

Genotyping by sequencing approaches have been widely applied in major crops and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of cultivated blueberry, the United States maintains the most diverse blueberry germplasm resources comprised of many species of different ploidy levels. We previously constructed an interspecific mapping population of diploid blueberry by crossing the parent F1#10 (Vaccinium darrowii Fla4B × diploid V. corymbosum W85–20) with the parent W85–23 (diploid V. corymbosum). Employing the Capture-Seq technology developed by RAPiD Genomics, with an emphasis on probes designed in predicted gene regions, 117 F1 progeny, the two parents, and two grandparents of this population were sequenced, yielding 131.7 Gbp clean sequenced reads. A total of 160,535 single nucleotide polymorphisms (SNPs), referenced to 4,522 blueberry genome sequence scaffolds, were identified and subjected to a parent-dependent sliding window approach to further genotype the population. Recombination breakpoints were determined and marker bins were deduced to construct a high density linkage map. Twelve blueberry linkage groups (LGs) consisting of 17,486 SNP markers were obtained, spanning a total genetic distance of 1,539.4 cM. Among 18 horticultural traits phenotyped in this population, quantitative trait loci (QTLs) that were significant over at least 2 years were identified for chilling requirement, cold hardiness, and fruit quality traits of color, scar size, and firmness. Interestingly, in 1 year, a QTL associated with timing of early bloom, full bloom, petal fall, and early green fruit was identified in the same region harboring the major QTL for chilling requirement. In summary, we report here the first high density bin map of a diploid blueberry mapping population and the identification of several horticulturally important QTLs.

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RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG

Plant and Cell Physiology ◽

10.1093/pcp/pcaa056 ◽

2020 ◽

Vol 61 (7) ◽

pp. 1262-1272

Author(s):

Hiromi Kajiya-Kanegae ◽

Hideki Takanashi ◽

Masaru Fujimoto ◽

Motoyuki Ishimori ◽

Norikazu Ohnishi ◽

...

Keyword(s):

Linkage Map ◽

High Density ◽

Genomic Diversity ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genetic Traits ◽

Map Construction ◽

Days To Heading ◽

High Density Linkage Map ◽

Sorghum Bicolor L

Abstract Sorghum [Sorghum bicolor (L.) Moench] grown locally by Japanese farmers is generically termed Takakibi, although its genetic diversity compared with geographically distant varieties or even within Takakibi lines remains unclear. To explore the genomic diversity and genetic traits controlling biomass and other physiological traits in Takakibi, we focused on a landrace, NOG, in this study. Admixture analysis of 460 sorghum accessions revealed that NOG belonged to the subgroup that represented Asian sorghums, and it was only distantly related to American/African accessions including BTx623. In an attempt to dissect major traits related to biomass, we generated a recombinant inbred line (RIL) from a cross between BTx623 and NOG, and we constructed a high-density linkage map based on 3,710 single-nucleotide polymorphisms obtained by restriction-site-associated DNA sequencing of 213 RIL individuals. Consequently, 13 fine quantitative trait loci (QTLs) were detected on chromosomes 2, 3, 6, 7, 8 and 9, which included five QTLs for days to heading, three for plant height (PH) and total shoot fresh weight and two for Brix. Furthermore, we identified two dominant loci for PH as being identical to the previously reported dw1 and dw3. Together, these results corroborate the diversified genome of Japanese Takakibi, while the RIL population and high-density linkage map generated in this study will be useful for dissecting other important traits in sorghum.

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First High-Density Linkage Map and Single Nucleotide Polymorphisms Significantly Associated With Traits of Economic Importance in Yellowtail Kingfish Seriola lalandi

Frontiers in Genetics ◽

10.3389/fgene.2018.00127 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 11

Author(s):

Nguyen H. Nguyen ◽

Pasi M. A. Rastas ◽

H. K. A. Premachandra ◽

Wayne Knibb

Keyword(s):

Single Nucleotide Polymorphisms ◽

Linkage Map ◽

Economic Importance ◽

High Density ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Yellowtail Kingfish ◽

Seriola Lalandi ◽

High Density Linkage Map

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Construction of a high-density linkage map and graphical representation of the arrangement of transcriptome-based unigene markers on the chromosomes of onion, Allium cepa L.

BMC Genomics ◽

10.1186/s12864-021-07803-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Satoshi Fujito ◽

Turgut Yigit Akyol ◽

Takuya Mukae ◽

Tadayuki Wako ◽

Ken-ichiro Yamashita ◽

...

Keyword(s):

Linkage Map ◽

Allium Cepa ◽

Doubled Haploid ◽

Graphical Representation ◽

Mapping Population ◽

Sequence Data ◽

Doubled Haploids ◽

Snp Markers ◽

High Density ◽

Genotype Information

Abstract Background Genomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosomic addition lines (MALs) and doubled haploids (DHs). These were the parental lines of an A. cepa mapping population for transcriptome-based SNP genotyping. Results We mapped the transcriptome sequence reads from a series of A. fistulosum-A. cepa MALs onto the unigene sequence of the doubled haploid shallot A. cepa Aggregatum group (DHA) and compared the MAL genotype call for parental bunching onion and shallot transcriptome mapping data. We identified SNP sites with at least four reads on 25,462 unigenes. They were anchored on eight A. cepa chromosomes. A single SNP site was identified on 3,278 unigenes and multiple SNPs were identified on 22,184 unigenes. The chromosome marker information was made public via the web database Allium TDB (http://alliumtdb.kazusa.or.jp/). To apply transcriptome based genotyping approach for genetic mapping, we gathered RNA sequence data from 96 lines of a DHA × doubled haploid bulb onion A. cepa common onion group (DHC) mapping population. After selecting co-dominant SNP sites, 16,872 SNPs were identified in 5,339 unigenes. Of these, at least two SNPs with identical genotypes were found in 1,435 unigenes. We developed a linkage map using genotype information from these unigenes. All unigene markers mapped onto the eight chromosomes and graphical genotyping was conducted based on the unigene order information. Another 2,963 unigenes were allocated onto the eight chromosomes. To confirm the accuracy of this transcriptome-based genetic linkage map, conventional PCR-based markers were used for linkage analysis. All SNP - and PCR-based markers were mapped onto the expected linkage groups and no inconsistency was found among these chromosomal locations. Conclusions Effective transcriptome analysis with unique Allium resources successfully associated numerous chromosome markers with unigene information and a high-density A. cepa linkage map. The information on these unigene markers is valuable in genome sequencing and useful trait detection in Allium.

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The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don

BMC Genomics ◽

10.1186/1471-2164-13-95 ◽

2012 ◽

Vol 13 (1) ◽

pp. 95 ◽

Cited By ~ 36

Author(s):

Yoshinari Moriguchi ◽

Tokuko Ujino-Ihara ◽

Kentaro Uchiyama ◽

Norihiro Futamura ◽

Maki Saito ◽

...

Keyword(s):

Male Sterility ◽

Linkage Map ◽

Cryptomeria Japonica ◽

Major Gene ◽

Snp Markers ◽

High Density ◽

High Density Linkage Map

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High-density linkage map around the root aerenchyma locus Qaer1.06 in the backcross populations of maize Mi29 × teosinte “Zea nicaraguensis”

Breeding Science ◽

10.1270/jsbbs.59.427 ◽

2009 ◽

Vol 59 (4) ◽

pp. 427-433 ◽

Cited By ~ 27

Author(s):

Yoshiro Mano ◽

Fumie Omori

Keyword(s):

Linkage Map ◽

High Density ◽

Root Aerenchyma ◽

Backcross Populations ◽

High Density Linkage Map

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High-density linkage map construction and identification of loci regulating fruit quality traits in blueberry

Horticulture Research ◽

10.1038/s41438-021-00605-z ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Molla F. Mengist ◽

Hamed Bostan ◽

Elisheba Young ◽

Kristine L. Kay ◽

Nicholas Gillitt ◽

...

Keyword(s):

Linkage Map ◽

Fruit Quality ◽

Titratable Acidity ◽

Fruit Weight ◽

High Density ◽

Soluble Solids ◽

Quality Traits ◽

Total Soluble Solids ◽

Fruit Quality Traits ◽

High Density Linkage Map

AbstractFruit quality traits play a significant role in consumer preferences and consumption in blueberry (Vaccinium corymbosum L). The objectives of this study were to construct a high-density linkage map and to identify the underlying genetic basis of fruit quality traits in blueberry. A total of 287 F1 individuals derived from a cross between two southern highbush blueberry cultivars, ‘Reveille’ and ‘Arlen’, were phenotyped over three years (2016–2018) for fruit quality-related traits, including titratable acidity, pH, total soluble solids, and fruit weight. A high-density linkage map was constructed using 17k single nucleotide polymorphisms markers. The linkage map spanned a total of 1397 cM with an average inter-loci distance of 0.08 cM. The quantitative trait loci interval mapping based on the hidden Markov model identified 18 loci for fruit quality traits, including seven loci for fruit weight, three loci for titratable acidity, five loci for pH, and three loci for total soluble solids. Ten of these loci were detected in more than one year. These loci explained phenotypic variance ranging from 7 to 28% for titratable acidity and total soluble solid, and 8–13% for pH. However, the loci identified for fruit weight did not explain more than 10% of the phenotypic variance. We also reported the association between fruit quality traits and metabolites detected by Proton nuclear magnetic resonance analysis directly responsible for these fruit quality traits. Organic acids, citric acid, and quinic acid were significantly (P < 0.05) and positively correlated with titratable acidity. Sugar molecules showed a strong and positive correlation with total soluble solids. Overall, the study dissected the genetic basis of fruit quality traits and established an association between these fruit quality traits and metabolites.

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