Identifying evolutionarily significant units for conservation of the endangered Malus sieversii using genome‐wide RADseq data

Abstract

Malus sieversii, a wild progenitor of the domesticated apple, is an endangered species and is assigned second conservation priority by the China Plant Red Data Book. It is urgent to carry out in situ conservation of this species, but previous studies have not identified evolutionarily significant units (ESUs) for conservation management. In this study, we investigated the genetic diversity and relationships of six M. sieversii populations from China using integrated analysis of microsatellite (nSSR) data, genome‐wide SNPs and previous results in order to propose a reasonable conservation management. The results showed that levels of genetic diversity were inconsistently reflected by our nSSR and previous studies, suggesting that indices of genetic diversity are not effective to identify priority conservation areas for M. sieversii. Based on the selection criteria of ESUs for endangered species conservation, ESUs should reflect lineage divergence, geographical separation and different adaptive variation. Our phylogenetic tree based on genome‐wide SNPs yielded a clear relationship of divergent lineages among M. sieversii populations, leading to new different from those of previous studies. Three independent lineages, including the pairs of populations Huocheng‐Yining, Gongliu‐Xinyuan and Tuoli‐Emin, were identified. The geographic distances between populations among the different phylogenetic lineages were much greater than those within the same phylogenetic lineage. A cluster analysis on environmental variables showed that the three independent lineages inhabit different environmental conditions, suggesting that they may have adapted to different environments. Based on the results, we propose that three independent ESUs should be recognized as conservation units for M. sieversii in China.

Genetic diversity, population structure, and relationships of apricot (Prunus) based on restriction site-associated DNA sequencing

“…To clarify the genetic relationships among the five ecological groups, phylogenetic trees were constructed. We used the published RAD-seq data of M. sieversii 46 (NCBI accession number SRX2934932) as an outgroup. TreeBeST (version 1.9.2) 47 was used to calculate the distance matrix, RAxML (version 8.2.12) 48 was used to construct the ML phylogenetic tree, and 1000 bootstrap replicates were used.…”

Insights into the aridification history of Central Asian Mountains and international conservation strategy from the endangered wild apple tree

“…This study is the first to report on M. sieversii genetic diversity and structure across the species' entire range. We used genome‐wide SNPs that allowed us to reveal a clear phylogenetic relationship among M. sieversii populations, an improvement over previous research that used traditional molecular markers, such as SSR makers (Omasheva et al., 2017; Richards et al., 2009; Zhang et al., 2018) and DNA fragment sequences (Zhang et al., 2015, 2018). The 15 fragmented populations were divided into three different groups, characterized by geographical separation and lineage divergence (Figure 1).…”

“…Its distribution covers several countries, including China, Kazakhstan, Kyrgyzstan and Tajikistan (Figure 1a). Due to recent habitat loss and population decline, M. sieversii is an endangered species in the ‘China Plant Red Data Book’ (Zhang et al., 2018) and in the ‘Red Book of Kazakh SSR’ (Omasheva et al., 2017). A typical conservation strategy is to identify priority protected areas and conservation units.…”

“…In addition to benefiting conservation efforts, clarifying overall genetic structure would also provide basic data on apple germplasm for breeding. To date, M. sieversii genetic structure has only been obtained from the Chinese (Zhang et al., 2018) and Kazakhstan populations (Omasheva et al., 2017; Richards et al., 2009).…”

“…Genome‐wide single nucleotide polymorphisms (SNP) are more effective than traditional molecular markers at distinguishing genetic relationships (Lu et al., 2020; Zhang et al., 2018). Next‐generation sequencing (NGS) has helped clarify M. sieversii genetic structure and evolutionary history; thousands of SNPs throughout the genome have been identified for phylogenetic analyses (McCormack et al., 2013) and for deep examination of population structures (Binks et al., 2019; Emerson et al., 2010; Mason et al., 2019).…”