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.
Highlights
Prince Rupprecht’s larch (Larix principis-rupprechtii Mayr, 2n = 24), as a member of the genusLarix, plays a crucial role in reforestation programs and commercial activities in North China due to its superior biological characteristics, including rapid growth at early ages, wide ecological adaptability, and desirable wood properties [1,2]
A high-density genetic map was constructed based on an F1 mapping population derived from an intraspecific cross of two elite clones deployed in a clonal seed orchard of L. principis-rupprechtii
single nucleotide polymorphism (SNP) markers detected by SLAF-seq, which enables identification and genotyping of SNPs in species with or without reference genomes [25]
Summary
The economic importance and ecological benefits of this species have prompted breeders to carry out genetic improvement measures based on recurrent selection schemes, with the ultimate goal of developing new varieties characterized by fast growth, high timber quality, and strong disease resistance [3]. This is a complicated process and difficult to achieve in a short time using traditional breeding methods (e.g., cross breeding, recurrent selection), mainly because of the long lifecycle and highly heterozygous nature of L. principis-rupprechtii, like other conifers [4]. A prerequisite for successfully implementing MAS is the use of genomic tools, genetic linkage maps with high quality
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