Construction of an Integrated High Density Simple Sequence Repeat Linkage Map in Cultivated Strawberry (Fragaria x ananassa) and its Applicability

Abstract

The cultivated strawberry (Fragaria× ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA′A′BBB′B′ model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. × ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. × ananassa EST-derived SSR markers) from F. × ananassa ESTs, and 125 markers (F. × ananassa transcriptome-derived SSR markers) from F. × ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. × ananassa and the genome of F. vesca. Variety distinction on 129 F. × ananassa lines was demonstrated using 45 selected SSR markers.

The History Of Genome Mapping In Fragaria Spp.

“…Therefore, all F. × ananassa maps were built on F1 progeny obtained from inter/intraspecific cross pollination (CP) of highly heterozygous cultivars (Haymes et al 1997;Lerceteau-Köhler et al 2003, 2012Rousseau-Gueutin et al 2008;Sargent et al 2009Sargent et al , 2012Goldberg et al 2010;Isobe et al 2012;Gaston et al 2013;van Dijk et al 2014;Mohamed 2014).…”

“…Since more abundant progeny carries a greater number of meiotic recombination events, thus, it determines the resolution and accuracy of the linkage map more precisely (Paterson 1996), larger segregating populations of over 100 individuals were introduced in the study on F. vesca (Koskela et al 2012), F. virginiana and F. chiloensis (Spigler et al 2008Goldberg et al 2010) as well as F. × ananassa (Lerceteau-Köhler et al 2003, 2012Rousseau-Gueutin et al 2008Weebadde et al 2008;Sargent et al 2009Isobe et al 2012;Gaston et al 2013;van Dijk et al 2014). Nevertheless, as some economic factors may limit the progeny number, the bin (selective) mapping appears to be a strategy of choice (Vision et al 2000).…”

The Development of a Primed <i>In Situ</i> Hybridization Technique for Chromosome Labeling in Cultivated Strawberry (<i>Fragaria</i>×<i>ananassa</i>)

“…In addition, it has been proposed that this species is an allopolyploid, having three kinds of complex genome compositions: AABBBBCC (Fedorova 1946), AAA′A′BBBB (Senanayake and Bringhurst 1967), or AAA′A′BBB′B′ (Bringhurst 1990). Of these three models, AAA′A′BBB′B′ is considered the most likely candidate based on DNA analysis (Kunihisa 2011, Sargent et al 2012, Isobe et al 2013. The allooctoploidy of cultivated strawberry is a serious obstacle for conducting genetic analyses due to the existence of similar sub-genomes, which lead to multiple alleles and complex segregation ratios (van Dijk et al 2012), making it difficult to conduct theoretical genetic analyses based on Mendel s laws of inheritance.…”

“…For the purposes of conducting theoretical genetic analyses and efficient breeding in cultivated and wild octoploid strawberries, several linkage maps have recently been constructed using various types of DNA markers (Yamamoto et al 2003, Rousseau-Gueutin et al 2008, Spigler et al 2008, Weebadde et al 2008, Sargent et al 2009, Isobe et al 2013. However, mis-integration appeared to occur during the calculation process because many of the markers were mapped on multiple homologous regions across linkage groups.…”

Modification of the filter-inserted tip method for simple and rapid DNA extraction from strawberry

“…Condition of PCR was same as described above. Two primer pairs for strawberry simple sequence repeat (SSR) marker FVES1038 and FVES2619 (Isobe et al 2013) were tested along with the two primer pairs described above. The Reaction mixture (reaction volume: 15 µl) contained 3 µl DNA solution, 0.11 µl Paq5000 DNA polymerase (Agilent Technologies, Tokyo, Japan), 1.5 µl 10X PCR buffer, 1.2 µl 2.5 mM dNTPs, and 0.6 µl each of primers (10 µM).…”