Abstract
Kiwifruit breeding still largely relies on phenotypic observation of cross progeny grown in the field to fruiting maturity, without any selection prior to the juvenility being overcome. Developing markers for the selection of traits of interest would greatly help breeders to rapidly screen breeding populations. With the aim of mapping several traits of interest in kiwifruit, a F1 population of diploid (2n = 58) Actinidia chinensis was produced by combining parents with contrasting phenotypic traits. Ninety-four individuals were preliminarily analyzed to obtain a saturated genetic map based on 167 SSRs from the literature and 12,586 segregating restriction-site-associated DNA (RAD) loci obtained through an approach known as genotyping-by-sequencing (GBS) based on haplotype calling of SNP markers identified by a modified double digest restriction-associated DNA sequencing (ddRADseq) protocol as proposed by Peterson et al. (2012). To improve the accuracy of genotype calling, restriction-site-associated reads were aligned to the scaffolds of the recently published kiwifruit genome (Huang et al. 2013). This strategy provided genetic anchoring to 557 Mbp (90 %) of the assembly, helping also to anchor some 120 unmapped Mbp and to identify some mis-joined scaffolds. The analysis of the region controlling the dioecy in kiwifruit, spanning 16 scaffolds in the pseudomolecule 25 of the genome assembly (approximately 4.9 Mbp), with RAD markers that co-segregated with the gender determinant, allowed to sort out markers suitable for marker-assisted selection for the gender in the mapping population with successful extension to further controlled crosses having parents at different ploidy level and belonging to the A. chinensis/Actinidia deliciosa complex.
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References
Catchen J, Amores A, Hohenlohe P, Cresko W, Postlethwait J (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics 1:171–182
Chakravarti A, Lasher LK, Reefer JE (1991) A maximum likelihood method for estimating genome length using genetic linkage data. Genetics 128:175–182
Cipriani G, Morgante M (1993) Evidence of chloroplast variation DNA variation in the genus Actinidia revealed by restriction analysis of PCR - amplified fragments. J Genet Breeding 47:319–326
Crowhurst RN, Gleave AP, MacRae EA et al (2008) Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics 9:351
Fraser LG, Tsang GK, Datson PM, De Silva HN, Harvey CF, Gill GP, Crowhurst RN, McNeilage MA (2009) A gene-rich linkage map in the dioecious species Actinidia chinensis (kiwifruit) reveals putative X/Y sex-determining chromosomes. BMC Genomics 10:102. doi:10.1186/1471-2164-10-102
Hackett CA, Broadfoot LB (2003) Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity 90:33–38. doi:10.1038/sj.hdy.6800173
Huang WG, Cipriani G, Morgante M, Testolin R (1998) Microsatellite DNA in Actinidia chinensis: isolation, characterisation, and homology in related species. Theor Appl Genet 97:1269–1278
Huang S-X, Ding J, Deng D et al (2013) Draft genome of the kiwifruit Actinidia chinensis. Nat Communications 4:2640. doi:10.1038/ncomms3640
Kumar S, Chagné D, Bink MCAM, Volz RK, Whitworth C, Carlisle C (2012) Genomic selection for fruit quality traits in apple (Malus x domestica Borkh.). PLoS ONE 7(5):e36674. doi:10.1371/ journal.pone.0036674
Langmead B, Salzberg S (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359
McNeilage MA, Fraser LG, Tsang GK, Datson PM, De Silva HN, Crowhurst RN, Ferguson AR (2012) Molecular genetics and genomics and kiwifruit breeding. Acta Horticulturae 913:63–70
Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829
Morgante M, Hanafey M, Powell W (2001) Microsatellites are preferentially associated with non repetitive DNA in plant genomes. Nat Genet 30:194–200
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7(5), e37135. doi:10.1371/journal.pone.003
Ronin Y, Mester D, Minkov D, Belotserkovski R, Jackson BN, Schnable PS, Aluru S, Korol A (2012) Two-phase analysis in consensus genetic mapping. G3 Genes Genomes Genetics 2(5):537–549. doi:10.1534/g3.112.002428
Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Methods Mol Biol, vol 132. Humana Press, Totowa, pp 365–386
Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744
Testolin R (2012) Breeding the future: what fruit breeders can learn from breeders of cows and chickens. Chronica Horticulturae 52(2):6–8
Testolin R (2013) Kiwifruit breeding: from the phenotypic analysis of parents to the genomic estimation of their breeding value (GEBV). Acta Horticulturae 913:123–130
Testolin R, Cipriani G, Costa G (1995) Sex segregation ratio and gender expression in the genus Actinidia. Sexual Plant Reprod 8:129–132
Van Ooijen JW (2006) JoinMap® 4, Software for the mapping of quantitative trait loci in experimental populations. Kyazma B.V, Wageningen
Van Os H, Stam P, Visser RGF, Eck HJ (2005) SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data. Theor Appl Genet 112:187–194
Wu Y, Bhat PR, Close TJ, Lonardi S (2008) Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. Plos ONE. doi:10.1371/ journal.pgen.1000212
Acknowledgments
This research was developed within the program Chile-Italia D09I1136 “Mejoramiento Genético del Kiwi apoyado en la Selección Asistida por Marcadores” supported by the Chilean Government- FONDEF. Authors are grateful to Dr. Ross Ferguson for the manuscript revision.
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Communicated by M. Wirthensohn
Data Archiving Statement
Raw Illumina reads used for this study are publicly available at NCBI SRA under the accession SRA293705 (project PRJNA294589, “Actinidia chinensis Map”) as run SRR2229880, SRR2239887, SRR2239888, and SRR2239889.
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ESM 1
Adapter sequences used for the generation of the ddRAD library. (XLSX 9 kb)
ESM 2
Linkage maps with all markers information and scoring matrices. (XLSX 5176 kb)
ESM 3
Figures of parental maps alignment for each linkage group. (PPTX 455 kb)
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Scaglione, D., Fornasiero, A., Pinto, C. et al. A RAD-based linkage map of kiwifruit (Actinidia chinensis Pl.) as a tool to improve the genome assembly and to scan the genomic region of the gender determinant for the marker-assisted breeding. Tree Genetics & Genomes 11, 115 (2015). https://doi.org/10.1007/s11295-015-0941-3
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DOI: https://doi.org/10.1007/s11295-015-0941-3