Dataset Information

Development of a MAGIC population and high-resolution quantitative trait mapping for nicotine content in tobacco.

ABSTRACT: Multiparent Advanced Generation Inter-Cross (MAGIC) population is an ideal genetic and breeding material for quantitative trait locus (QTL) mapping and molecular breeding. In this study, a MAGIC population derived from eight tobacco parents was developed. Eight parents and 560 homozygous lines were genotyped by a 430K single-nucleotide polymorphism (SNP) chip assay and phenotyped for nicotine content under different conditions. Four QTLs associated with nicotine content were detected by genome-wide association mapping (GWAS), and one major QTL, named qNIC7-1, was mapped repeatedly under different conditions. Furthermore, by combining forward mapping, bioinformatics analysis and gene editing, we identified an ethylene response factor (ERF) transcription factor as a candidate gene underlying the major QTL qNIC7-1 for nicotine content in tobacco. A presence/absence variation (PAV) at qNIC7-1 confers changes in nicotine content. Overall, the large size of this MAGIC population, diverse genetic composition, balanced parental contributions and high levels of recombination all contribute to its value as a genetic and breeding resource. The application of the tobacco MAGIC population for QTL mapping and detecting rare allelic variation was demonstrated using nicotine content as a proof of principle.

SUBMITTER: Yuan G

PROVIDER: S-EPMC9871594 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Development of a MAGIC population and high-resolution quantitative trait mapping for nicotine content in tobacco.

Yuan Guangdi G Sun Kefan K Yu Wenlong W Jiang Zipeng Z Jiang Caihong C Liu Dan D Wen Liuying L Si Huan H Wu Fengyan F Meng He H Cheng Lirui L Yang Aiguo A Wang Yuanying Y

Frontiers in plant science 20230110

Multiparent Advanced Generation Inter-Cross (MAGIC) population is an ideal genetic and breeding material for quantitative trait locus (QTL) mapping and molecular breeding. In this study, a MAGIC population derived from eight tobacco parents was developed. Eight parents and 560 homozygous lines were genotyped by a 430K single-nucleotide polymorphism (SNP) chip assay and phenotyped for nicotine content under different conditions. Four QTLs associated with nicotine content were detected by genome-w ...[more]

PMID: 36704165

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Project description:Manganese (Mn), iron (Fe), copper (Cu), zinc (Zn), and selenium (Se) are essential micronutrients for human health. However, the genetic basis for the content of Mn, Fe, Cu, Zn, and Se in wheat grains remains unclear. A recombinant inbred lines (RIL) population derived from Yangmai 4/Yanzhan 1 (YM4/YZ1) with wheat 55K single nucleotide polymorphism (SNP) arrays and micronutrient content of two environments was used to construct a genetic linkage map and dissect the quantitative trait loci (QTL) for the content of Mn, Fe, Cu, Zn, and Se in wheat. A total of 8 QTL were detected and located on chromosomes 1A, 1B, 2D, 4D, 7A, and 7D, respectively. Among them, QFe.yaas-2D and QSe.yaas-2D were co-located on chromosome 2D, while QMn.yaas-4D and QZn.yaas-4D were co-located on chromosome 4D, which were in the dwarfing locus of Rht-D1 region. The positive alleles of QCu.yaas-1A, QMn.yaas-1B, and QZn.yaas-7D were contributed by YZ1 and explained 7.66-19.92% of the phenotypic variances, while the positive alleles of QFe.yaas-2D, QSe.yaas-2D, QMn.yaas-4D, QZn.yaas-4D, and QCu.yaas-7A were contributed by YM4 and explained 5.77-20.11% of the phenotypic variances. The positive alleles of QCu.yaas-1A, QMn.yaas-1B, and QMn/Zn.yaas-4D increased TGW by 3.52%, 3.45%, and 7.51% respectively, while the positive alleles of QFe/Se.yaas-2D decreased TGW by 6.45%. Six SNP markers flanked the target QTL were converted into Kompetitive allele specific PCR (KASP) markers, and their effects were validated in a panel of one hundred and forty-nine wheat advanced lines. Twenty-five advanced lines harboring at least five positive alleles were identified in the validation populations. A total of 60 and 51 high-confidence annotated genes for QFe/Se.yaas-2D and QMn/Zn.yaas-4D were identified using the International Wheat Genome Sequencing Consortium Reference Sequence v2.1 (IWGSC RefSeq v2.1), respectively. Some genes in these two regions were involved in stress tolerance, growth development, Zn synthesis in plants. These results provide the basis for fine-mapping the target QTL of micronutrient content and marker-assisted selection in grain quality breeding programs.

Dataset Information

Development of a MAGIC population and high-resolution quantitative trait mapping for nicotine content in tobacco.

Publications

Development of a MAGIC population and high-resolution quantitative trait mapping for nicotine content in tobacco.

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