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SNP detection and population structure evaluation of Salix gordejevii Y. L. Chang et Skv. in Hunshandake Sandland, Inner Mongolia, China

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Abstract

Single nucleotide polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism and, hence, are highly favorable markers for genetic map construction and genome-wide association studies. Based on the DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection, the genetic diversity and population structure of Salix gordejevii Y. L. Chang et Skv., a valuable sand-fixing shrub, was assessed in 199 accessions from 20 populations in Hunshandake Sandland of northern China. A total of 623.15 M reads resulted in 30.49 × sequencing depth on average and a mean Q30 of 95.70%, and 2,287,715 SNPs in 178,509 polymorphic SLAF tags were obtained. By discarding minor allele frequency > 0.05 and integrity > 0.8, a total of 93,600 SNPs were retained for population genetic analyses, which revealed that 199 individuals could be divided into six groups based on cross-validation errors. However, this grouping pattern did not match the geographical distribution, indicating that there is no apparent geographic barrier in the blank areas where S. gordejevii was not distributed in Hunshandake Sandland. In addition, the physical distance of linkage disequilibrium decay in the analyzed S. gordejevii individuals was 18.5 kb when r2 = 0.1. The linkage disequilibrium decay distances for different chromosomes varied from 4.6 kb (chromosome 16) to 37.8 kb (chromosome 3). The obtained SNPs offer suitable marker resources for further genetic and genomic studies and will benefit S. gordejevii breeding programs.

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Funding

This research was financially supported by the program of Research Program of Science and Technology at Universities of Inner Mongolia Autonomous Region (NJZZ19185) and “The biogeographical feature and competitive hybridization of Maple (Acer L.) in East Asia” of National Natural Science Foundation of China (41901063) to J.G., the Program of Science and Technology of Inner Mongolia Autonomous Region (201605052) to X.-L.N.

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  1. Faculty of Resources and Environment, Baotou Teachers’ College, Inner Mongolia University of Science and Technology, Baotou, 014030, China

    Jian Gao & Xiao-Li Ning

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  1. Jian Gao
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  2. Xiao-Li Ning
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Contributions

J.G. and X.-L.N. conceived and designed the work; J.G. collected samples; J.G. performed the experiments and analysed the data; J.G. wrote the manuscript; X.-L.N. critically reviewed the manuscript. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Xiao-Li Ning.

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The authors declare that all experiments described herein comply with the law of government in which they were carried out. All plant materials used in this study are legally obtained and/or collected.

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Gao, J., Ning, XL. SNP detection and population structure evaluation of Salix gordejevii Y. L. Chang et Skv. in Hunshandake Sandland, Inner Mongolia, China. Physiol Mol Biol Plants 27, 997–1005 (2021). https://doi.org/10.1007/s12298-021-00994-4

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