Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology

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Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology. / Zhigunov, Anatoly V.; Ulianich, Pavel S.; Lebedeva, Marina V.; Chang, Peter L.; Nuzhdin, Sergey V.; Potokina, Elena K.

In: BMC Plant Biology, Vol. 17, 180, 14.11.2017, p. 87-98.

Research output: Contribution to journal › Article › peer-review

Author

Zhigunov, Anatoly V. ; Ulianich, Pavel S. ; Lebedeva, Marina V. ; Chang, Peter L. ; Nuzhdin, Sergey V. ; Potokina, Elena K. / Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology. In: BMC Plant Biology. 2017 ; Vol. 17. pp. 87-98.

BibTeX

@article{c645373d76cd4b3e9b19ee9ac5472940,

title = "Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology",

abstract = "Background: Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe. Results: We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation. Conclusions: The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen.",

keywords = "European aspen, Full-sibling population, Growth-related traits, High resolution linkage map, Intra-specific cross, QTL mapping, RADseq, SNP",

author = "Zhigunov, {Anatoly V.} and Ulianich, {Pavel S.} and Lebedeva, {Marina V.} and Chang, {Peter L.} and Nuzhdin, {Sergey V.} and Potokina, {Elena K.}",

year = "2017",

month = nov,

day = "14",

doi = "10.1186/s12870-017-1127-y",

language = "English",

volume = "17",

pages = "87--98",

journal = "BMC Plant Biology",

issn = "1471-2229",

publisher = "BioMed Central Ltd.",

}

RIS

TY - JOUR

T1 - Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology

AU - Zhigunov, Anatoly V.

AU - Ulianich, Pavel S.

AU - Lebedeva, Marina V.

AU - Chang, Peter L.

AU - Nuzhdin, Sergey V.

AU - Potokina, Elena K.

PY - 2017/11/14

Y1 - 2017/11/14

N2 - Background: Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe. Results: We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation. Conclusions: The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen.

AB - Background: Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe. Results: We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation. Conclusions: The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen.

KW - European aspen

KW - Full-sibling population

KW - Growth-related traits

KW - High resolution linkage map

KW - Intra-specific cross

KW - QTL mapping

KW - RADseq

KW - SNP

UR - http://www.scopus.com/inward/record.url?scp=85033771625&partnerID=8YFLogxK

U2 - 10.1186/s12870-017-1127-y

DO - 10.1186/s12870-017-1127-y

M3 - Article

C2 - 29143610

AN - SCOPUS:85033771625

VL - 17

SP - 87

EP - 98

JO - BMC Plant Biology

JF - BMC Plant Biology

SN - 1471-2229

M1 - 180

ER -

ID: 9326781