Abstract
The Chinese elm is an important tree ecologically; however, little is known about its genetic diversity and adaptation mechanisms. In this study, a total of 107 individuals collected from seven natural populations in eastern China were investigated by specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) detected by SLAF-seq, genetic diversity and markers associated with climate variables were identified. All seven populations showed medium genetic diversity, with PIC values ranging from 0.2632 to 0.2761. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Environmental association analyses with three climate variables (annual rainfall, annual average temperature, and altitude) resulted in, altogether, 43 and 30 putative adaptive loci by Bayenv2 and LFMM, respectively. Five adaptive genes were annotated, which were related to the functions of glycosylation, peroxisome synthesis, nucleic acid metabolism, energy metabolism, and signaling. This study was the first on the genetic diversity and local adaptation in Chinese elms, and the results will be helpful in future work on molecular breeding.
Highlights
Chinese elm (Ulmus parvifolia), which is native to China, Japan and Korea, has become a widely distributed ornamental tree that is frequently planted on lawns, along streets and in parks [1]
Our study identified a total of 4,138,972 single nucleotide polymorphisms (SNPs) and selected 457,888 SNPs with minor allele frequency (MAF) > 5% and a missing rate < 0.2 for further analysis
The trees were genotyped by SLAF-seq technology, and identification of SNPs was carried out
Summary
Chinese elm (Ulmus parvifolia), which is native to China, Japan and Korea, has become a widely distributed ornamental tree that is frequently planted on lawns, along streets and in parks [1]. In China, the wild resources of U. parvifolia are mainly located in the northern and eastern areas, exhibiting a wide range of adaptation. Within this area, Chinese elm is recognized as a drought, heat, and cold tolerant tree [2,3,4]. As global climate alteration will happen in the near future, it remains questionable to what degree the speed of future adaptation can keep up with the pace of climate change [5]. Revealing polymorphisms and genes that determine adaptation would provide the basis for breeding genetically improved germplasms that could be used in changing environments
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