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Genetic Mapping of Prince Rupprecht’s Larch (Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing

1
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
2
National Key Seed Base of Larch, Weichang, Chengde 068450, China
*
Author to whom correspondence should be addressed.
Genes 2019, 10(8), 583; https://doi.org/10.3390/genes10080583
Received: 9 June 2019 / Revised: 12 July 2019 / Accepted: 29 July 2019 / Published: 31 July 2019
(This article belongs to the Section Plant Genetics and Genomics)
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Abstract

A high-density genetic linkage map is essential for plant genetics and genomics research. However, due to the deficiency of genomic data and high-quality molecular markers, no genetic map has been published for Prince Rupprecht’s larch (Larix principis-rupprechtii Mayr), a conifer species with high ecological and commercial value in northern China. In this study, 145 F1 progeny individuals from an intraspecific cross between two elite clones of L. principis-rupprechtii and their parents were employed to construct the first genetic map in this important tree species using specific-locus amplified fragment sequencing (SLAF-seq). After preprocessing, the procedure yielded 300.20 Gb of raw data containing 1501.22 M pair-end reads. A total of 324,352 SNP markers were detected and 122,785 of them were polymorphic, with a polymorphism rate of 37.86%. Ultimately, 6099 SNPs were organized into a genetic map containing 12 linkage groups, consistent with the haploid chromosome number of larch and most other species in the Pinaceae family. The linkage map spanned 2415.58 cM and covered 99.6% of the L. principis-rupprechtii genome with an average of 0.4 cM between adjacent markers. To the best of our knowledge, this map is the first reference map for L. principis-rupprechtii, as well as the densest one obtained in larch species thus far. The genome-wide SNPs and the high-resolution genetic map will provide a foundation for future quantitative trait loci mapping, map-based cloning, marker-assisted selection, comparative genomics, and genome sequence assembly for larch trees. View Full-Text
Keywords: genetic map; SLAF-seq; SNP; larch; Larix principis-rupprechtii genetic map; SLAF-seq; SNP; larch; Larix principis-rupprechtii
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Dong, M.; He, Q.; Zhao, J.; Zhang, Y.; Yuan, D.; Zhang, J. Genetic Mapping of Prince Rupprecht’s Larch (Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing. Genes 2019, 10, 583.

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