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GWAS in tetraploid potato: identification and validation of SNP markers associated with glycoalkaloid content.

التفاصيل البيبلوغرافية
العنوان: GWAS in tetraploid potato: identification and validation of SNP markers associated with glycoalkaloid content.
المؤلفون: Vos PG; Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.; Present Address: Centre for BioSystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands.; Current Address: HZPC, Edisonweg 5, 8501 XG Joure, The Netherlands.; Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, Netherlands., Paulo MJ; Biometris, Wageningen University and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands.; Present Address: Centre for BioSystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands., Bourke PM; Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands., Maliepaard CA; Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands., van Eeuwijk FA; Biometris, Wageningen University and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands., Visser RGF; Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.; Present Address: Centre for BioSystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands., van Eck HJ; Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.; Present Address: Centre for BioSystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands.
المصدر: Molecular breeding : new strategies in plant improvement [Mol Breed] 2022 Dec 13; Vol. 42 (12), pp. 76. Date of Electronic Publication: 2022 Dec 13 (Print Publication: 2022).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Kluwer Academic Publishers Country of Publication: Netherlands NLM ID: 9506703 Publication Model: eCollection Cited Medium: Internet ISSN: 1572-9788 (Electronic) Linking ISSN: 13803743 NLM ISO Abbreviation: Mol Breed Subsets: PubMed not MEDLINE
أسماء مطبوعة: Publication: Dordrecht : Kluwer Academic Publishers
Original Publication: Dordrecht ; Boston : Kluwer Academic Publishers, c1995-
مستخلص: Genome-wide association studies (GWAS) are a useful tool to unravel the genetic architecture of complex traits, but the results can be difficult to interpret. Population structure, genetic heterogeneity, and rare alleles easily result in false positive or false negative associations. This paper describes the analysis of a GWAS panel combined with three bi-parental mapping populations to validate GWAS results, using phenotypic data for steroidal glycoalkaloid (SGA) accumulation and the ratio (SGR) between the two major glycoalkaloids α-solanine and α-chaconine in potato tubers. SGAs are secondary metabolites in the Solanaceae family, functional as a defence against various pests and pathogens and in high quantities toxic for humans. With GWAS, we identified five quantitative trait loci (QTL) of which Sga1.1, Sgr8.1 , and Sga11.1 were validated, but not Sga3.1 and Sgr7.1 . In the bi-parental populations, Sga5.1 and Sga7.1 were mapped, but these were not identified with GWAS. The QTLs Sga1.1 , Sga7.1 , Sgr7.1 , and Sgr8.1 co-localize with genes GAME9, GAME 6/GAME 11 , SGT1 , and SGT2 , respectively. For other genes involved in SGA synthesis, no QTLs were identified. The results of this study illustrate a number of pitfalls in GWAS of which population structure seems the most important. We also show that introgression breeding for disease resistance has introduced new haplotypes to the gene pool involved in higher SGA levels in certain pedigrees. Finally, we show that high SGA levels remain unpredictable in potato but that α-solanine/α-chaconine ratio has a predictable outcome with specific SGT1 and SGT2 haplotypes.
Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01344-2.
Competing Interests: Conflict of interestThe authors declare no competing interests.
(© The Author(s), under exclusive licence to Springer Nature B.V. 2022. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)
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فهرسة مساهمة: Keywords: Haplotypes; Marker-assisted selection; QTL-mapping; Solanum tuberosum; Steroidal glycoalkaloids
تواريخ الأحداث: Date Created: 20230614 Latest Revision: 20231214
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC10248624
DOI: 10.1007/s11032-022-01344-2
PMID: 37313326
قاعدة البيانات: MEDLINE
الوصف
تدمد:1572-9788
DOI:10.1007/s11032-022-01344-2