Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping

ABSTRACTThe American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three inter-related cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman Rank Correlations > 0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.

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QTL Mapping of Fruit and Seed-related Traits in Watermelon Using Genotyping-by-Sequencing-based High-density Linkage Mapping

10.21203/rs.3.rs-107825/v1 ◽

2020 ◽

Author(s):

Meiling Gao ◽

Xiaoxue Liang ◽

Xiujie Liu ◽

Yu Guo ◽

Hongguo Xu ◽

...

Keyword(s):

Qtl Mapping ◽

Seed Size ◽

Fruit Quality ◽

Linkage Mapping ◽

Genotyping By Sequencing ◽

Fruit Shape ◽

High Density ◽

Chromosome 2 ◽

Phenotypic Data ◽

Stripe Pattern

Abstract BackgroundWatermelon is an important vegetable crop with dual use of both fruit and seeds. Understanding the genetic basis of fruit quality and seed size-related traits is important for efficient marker-assisted breeding in watermelon. Linkage mapping in watermelon segregating populations using genotyping-by-sequencing (GBS) provides insights into genetic control of fruit- and seed-related traits and genome collinearity in commercial watermelon cultivars. ResultsIn the present study, we conducted QTL mapping of 12 horticulturally important traits on external and internal fruit quality and seed size/weight using segregating populations derived a cross between two commercial varieties. A high-density genetic map was developed with GBS which contained more than 6,000 SNP loci in 1,004 bins with a total map length of 1261.1 cM and average marker interval of 1.26 cM or 329 kb. Phenotypic data of fruit rind color (RC), rind stripe pattern (RSP), flesh color (FFC), fruit diameter (FD), fruit length (FL), fruit shape index (FSI), fruit weight (FW), Brix content central (BCC), Brix content edge (BCE), seed length (SL), width (SW), and weight (20SWT) were collected from two locations in two years. QTL analysis identified 47 QTL for the 12 traits, of which 24 had moderate- or major-effects, and 34 were novel QTL not identified in previous studies. The QTL for RSP were identified overlapped with previous reports, and mapped the QTL to a small interval on chromosome 6. From the detected novel QTL, we identify FD (qfd2.1), FL (qfl2.1) co-located with FSI (qfsi2.1) QTL on chromosome 2, and the minor QTL qfw3.2 co-located with previously reported fruit shape QTL (qfd3.1, qfl3.1, qfsi3.1), and SW (qsw10.1) co-located with 20SWT QTL (q20swt10.1) on chromosome 10, and 5 minor QTL (qbcc2.1, qbcc5.1, qbce2.1, qbce2.2, qbce5.1) were found to be likely new locus for Brix content.ConclusionWe conducted GBS consisting of 120 F2 individuals and developed a high-density linkage map with more than 6,000 SNP loci in 1004 bins in watermelon. We identified 47 QTL for 12 fruit and seed related traits including 34 novel QTL. Our work expands the molecular breeding toolbox for watermelon to improve the yield and fruit quality.

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High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes

Frontiers in Plant Science ◽

10.3389/fpls.2020.00448 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 2

Author(s):

Mulatu Geleta ◽

Cecilia Gustafsson ◽

Jeffrey C. Glaubitz ◽

Rodomiro Ortiz

Keyword(s):

Linkage Mapping ◽

Genetic Linkage ◽

Genotyping By Sequencing ◽

High Density ◽

Genetic Linkage Mapping

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High-density linkage mapping for agronomic and physiological traits of rice (Oryza sativa L.) under reproductive-stage salt stress

Journal of Genetics ◽

10.1007/s12041-021-01301-6 ◽

2021 ◽

Vol 100 (2) ◽

Author(s):

Mostafa Ahmadizadeh ◽

Nadali Babaeian-Jelodar ◽

Ghasem Mohammadi-Nejad ◽

Nadali Bagheri ◽

Rakesh Kumar Singh

Keyword(s):

Oryza Sativa ◽

Salt Stress ◽

Linkage Mapping ◽

Oryza Sativa L ◽

High Density ◽

Reproductive Stage ◽

Physiological Traits

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Drought response QTLs in a Super Basmati × Azucena population by high‐density GBS‐based SNP linkage mapping

Plant Breeding ◽

10.1111/pbr.12961 ◽

2021 ◽

Author(s):

Raheela Waheed ◽

John Carlos Ignacio ◽

Juan David Arbelaez ◽

Venice Margarette Juanillas ◽

Muhammad Asif ◽

...

Keyword(s):

Linkage Mapping ◽

High Density ◽

Drought Response

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Alteration of Anthocyanin Glycosylation in Cranberry Through Interspecific Hybridization

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.130.5.711 ◽

2005 ◽

Vol 130 (5) ◽

pp. 711-715 ◽

Cited By ~ 21

Author(s):

Nicholi Vorsa ◽

James J. Polashock

Keyword(s):

Human Health ◽

Interspecific Hybridization ◽

Interspecific Hybrids ◽

Parental Species ◽

Genetic Manipulation ◽

Vaccinium Macrocarpon ◽

Antioxidant Potential ◽

Backcross Population ◽

American Cranberry

The flavonoids of american cranberry (Vaccinium macrocarpon Ait.) are documented to be beneficial for human health. Among their benefits is a high antioxidant potential, with anthocyanin glycosides being the main contributors. Flavonoid glucose conjugates are reported to be more bioavailable than those with other sugar conjugates. The anthocyanin glycosides of V. macrocarpon fruit are mainly galactosides and arabinosides of the aglycones, cyanidin and peonidin, with less than 8% glucosides. In contrast, the fruit anthocyanins of another cranberry species, V. oxycoccus L. were found to be largely glucosides of cyanidin and peonidin. Interspecific hybrids between these two species were intermediate to the parental species in the proportion of fruit anthocyanin glucosides. About half the progeny (1:1 segregation) in a backcross population (to V. macrocarpon) maintained the relatively high anthocyanin glucoside ratio. In this study, we demonstrate the genetic manipulation of anthocyanin glycosylation in cranberry using interspecific hybridization, resulting in dramatically increased glucose-conjugated anthocyanins.

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