Strawberry (Fragaria spp.) Structural Genomics

Davis, Thomas M.; Simpson, D. W.

doi:10.1007/978-0-387-77491-6_21

Cited by 9 publications

(11 citation statements)

References 91 publications

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“…This result is in line with that of previous studies [6,15-17,22]. However, we did find some discrepancies, which in most cases showed that the octoploid genetic map had better collinearity with the diploid Fv × Fb genetic map [51] than with the diploid Fragaria vesca pseudo chromosomes (v1.1). This result indicates that most of the divergence between our genetic maps and the physical map are due to limitations of the physical map.…”

Section: Discussionsupporting

confidence: 92%

“…The octoploid genetic map was represented by the homoeologue that had a good density of segregating markers and showed few inconsistencies in marker order with the other homoeologues. The diploid genetic map of Sargent et al [ 51 ] was chosen as it had most primer pairs in common with our map. The genetic positions of the CO–and CX-series of markers [ 18 ], were imputed using data from a recent diploid genetic map [ 50 ].…”

Section: Methodsmentioning

confidence: 99%

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Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

et al. 2014

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BackgroundBreeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic organisation.ResultsThe linkage map incorporates 508 segregating loci and represents each of the 28 chromosome pairs of octoploid strawberry, spanning an estimated length of 2050 cM. The sub-genomes are denoted according to their sequence divergence from F. vesca as revealed by marker performance. The map revealed high overall synteny between the sub-genomes, but also revealed two large inversions on LG2C and LG2D, of which the latter was confirmed using a separate mapping population. We discovered interesting breeding features within the parental cultivars by in-depth analysis of our haplotype data. The linkage map-derived homozygosity level of Holiday was similar to the pedigree-derived inbreeding level (33% and 29%, respectively). For Korona we found that the observed homozygosity level was over three times higher than expected from the pedigree (13% versus 3.6%). This could indicate selection pressure on genes that have favourable effects in homozygous states. The level of kinship between Holiday and Korona derived from our linkage map was 2.5 times higher than the pedigree-derived value. This large difference could be evidence of selection pressure enacted by strawberry breeders towards specific haplotypes.ConclusionThe obtained SSR linkage map provides a good base for QTL discovery. It also provides the first biologically relevant basis for the discernment and notation of sub-genomes. For the first time, we revealed genomic rearrangements that were verified in a separate mapping population. We believe that haplotype information will become increasingly important in identifying marker-trait relationships and regions that are under selection pressure within breeding material. Our attempt at providing a biological basis for the discernment of sub-genomes warrants follow-up studies to streamline the naming of the sub-genomes among different octoploid strawberry maps.

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Section: Discussionsupporting

confidence: 92%

Section: Methodsmentioning

confidence: 99%

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

et al. 2014

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“…The 269 primer pairs were comprised of 194 published Rubus primer pairs (Amsellem et al 2001;Castillo et al 2010;Graham et al 2004Graham et al , 2006Lewers et al 2008;Lopes et al 2006;Sargent et al 2009;Woodhead et al 2008Woodhead et al , 2010Zorrilla-Fontanesi et al 2011 …”

Section: Genetic Markersmentioning

confidence: 99%

Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach

Bushakra

Stephens²,

Atmadjaja

et al. 2012

Theor Appl Genet

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The genus Rubus belongs to the Rosaceae and is comprised of 600-800 species distributed world-wide. To date, genetic maps of the genus consist largely of non-transferable markers such as amplified fragment length polymorphisms. An F(1) population developed from a cross between an advanced breeding selection of Rubus occidentalis (96395S1) and R. idaeus 'Latham' was used to construct a new genetic map consisting of DNA sequence-based markers. The genetic linkage maps presented here are constructed of 131 markers on at least one of the two parental maps. The majority of the markers are orthologous, including 14 Rosaceae conserved orthologous set markers, and 60 new gene-based markers developed for raspberry. Thirty-four published raspberry simple sequence repeat markers were used to align the new maps to published raspberry maps. The 96395S1 genetic map consists of six linkage groups (LG) and covers 309 cM with an average of 10 cM between markers; the 'Latham' genetic map consists of seven LG and covers 561 cM with an average of 5 cM between markers. We used BLAST analysis to align the orthologous sequences used to design primer pairs for Rubus genetic mapping with the genome sequences of Fragaria vesca 'Hawaii 4', Malus × domestica 'Golden Delicious', and Prunus 'Lovell'. The alignment of the orthologous markers designed here suggests that the genomes of Rubus and Fragaria have a high degree of synteny and that synteny decreases with phylogenetic distance. Our results give unprecedented insights into the genome evolution of raspberry from the putative ancestral genome of the single ancestor common to Rosaceae.

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“…Aroma of strawberry is due to esters, alcohols, aldehydes, and sulfur compounds. Hundreds of volatile esters have been correlated with strawberry ripening and aroma [57]. Volatile esters are the major constituents of floral scent.…”

Section: Functional Genomicsmentioning

confidence: 99%

Insight on Rosaceae Family with Genome Sequencing and Functional Genomics Perspective

Soundararajan

Won

Kim

2019

BioMed Research International

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Rosaceae is one of the important families possessing a variety of diversified plant species. It includes many economically valuable crops that provide nutritional and health benefits for the human. Whole genome sequences of valuable crop plants were released in recent years. Understanding of genomics helps to decipher the plant physiology and developmental process. With the information of cultivating species and its wild relative genomes, genome sequence-based molecular markers and mapping loci for economically important traits can be used to accelerate the genome assisted breeding. Identification and characterization of disease resistant capacities and abiotic stress tolerance related genes are feasible to study across species with genome information. Further breeding studies based on the identification of gene loci for aesthetic values, flowering molecular circuit controls, fruit firmness, nonacid fruits, etc. is required for producing new cultivars with valuable traits. This review discusses the whole genome sequencing reports of Malus, Pyrus, Fragaria, Prunus, and Rosa and status of functional genomics of representative traits in individual crops.

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Strawberry (Fragaria spp.) Structural Genomics

Cited by 9 publications

References 91 publications

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach

Insight on Rosaceae Family with Genome Sequencing and Functional Genomics Perspective

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