Abstract
Branching angle is a critical factor that determines the morphological establishment and is a typical quantitative trait controlled by multiple genes. In this study, we used SLAF-seq to construct a high-density genetic map, to investigate the genetic architecture of branching angle in poplar (Populus leucopyramidalis). A total of 240,672 SLAF tags were obtained, including 103,691 polymorphic SLAF tags. After filtering, 53,407 polymorphic markers were sorted into eight segregation types, and 11,162 of them were used to construct the genetic map. 8447 were on the female parent map, 8532 were on the male parent map, and 11,162 were on the integrated map. The marker coverage was 4820.84 and 5044.80 cM for the female and male maps, and 3142.61 cM for the integrated map. The average intervals between two adjacent mapped markers were 0.55, 0.59, and 0.28 cM for the three maps, respectively. Two quantitative trait loci (QTLs) were detected. Seven markers that exceeded the threshold in these two regions were considered as being associated with branching angle and the phenotypic variance explained by each of these marker was 10.64–11.66%. After functional annotation, we identified 15 candidate genes and analyzed the expression of candidate genes in narrow and wide crown progenies by qRT-PCR. These results show that the combination of QTL and SLAF-seq will contribute to future breeding plans in poplar breeding, especially in narrow crown poplar breeding.
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Funding
This study was supported by the Major Science and Technology Projects for the Cultivation of New Varieties of Genetically Modified Organisms (2018ZX08020002), the Natural Science Foundation of Shandong Province (ZR2013CM020), and the Agricultural Breeding Program of Shandong Province (201496).
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All authors contributed to the study conception and design. JNW and JHL designed the experiments and wrote the manuscript. RYW, HPG and YTT performed data analysis of SLAF-seq. JNW and LLH participated in RNA isolation and qRT-PCR. DYW and XLW participated in DNA isolation and phenotypic analysis. All authors read and approved of the manuscript.
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Additional File 1
qRT-PCR primers used in the paper.. Supplementary file 1 (XLSX 10 KB)
Additional File 2
Phenotypic traits of 123 Progenies. Phenotypic traits included branch angle, branch number, plant height and ground diameter. Supplementary file 2 (XLSX 14 KB)
Additional File 3
SLAF markers on the 19 linkage groups. The SLAF markers and their locations in each LG on the maps.Supplementary file 3 (XLSX 8113 KB)
Additional File 4
Additional File 3 SNP tag information statistics table. Note: Linkage Group ID: linkage group number; SNP Number: the number of Markers of the SNP type; Trv: SNP transversion; Tri: SNP transitions; Trv/Tri: SNP transversion/SNP transitions; Total: The total number of SNP tags and transversion / transitions of the linkage group. Supplementary file 4 (DOCX 17 KB)
Additional File 5
Haplotype map of the integrated maps. Note: Each row and column is a Marker arranged in the order of the map. Each small square represents the recombination rate between the two Markers. The change of color from yellow to red to purple represents the recombination rate from small to large. The closer the Marker recombination rate is, the closer the color is to yellow. The farther away the Marker recombination rate is, the closer the color to purple. Supplementary file 5 (PDF 322 KB)
Additional File 6
Genetic map and genomic collinearity map. Note:The abscissa indicates the genetic distance of each linkage group, the ordinate indicates the physical length of each linkage group, and the collinearity of Marker in the genome and genetic map is expressed in the form of scatter. Supplementary file 6 (PDF 104 KB)
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Jinnan, W., Ruyue, W., Jihong, L. et al. Construction of a high-density genetic map using specific-length amplified fragment markers and identification of QTLs for branching angle in poplar. Mol Genet Genomics 297, 345–356 (2022). https://doi.org/10.1007/s00438-021-01850-6
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DOI: https://doi.org/10.1007/s00438-021-01850-6