Genetic polymorphism of Malus sieversii populations in Xinjiang, China

Yan, Guorong; Hong, Liu; Song, Wenqin; Chen, Ruiyang

doi:10.1007/s10722-007-9226-5

Cited by 42 publications

(33 citation statements)

References 12 publications

(10 reference statements)

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“…Moreover, the estimated F st value at two of the most significant SNPs (ss475879551 on LG9 and ss475881697 on LG16) was 0.12 and 0.09, respectively, so these SNPs were not outliers as per the observed F st distribution (Fig. The M. sieversii gene pool has shown significant resistance to apple scab and fire blight (Luby et al, 2002;Forsline and Aldwinckle, 2004) and may well hold genes that allow M. sieversii to adapt to cold and dry regions (Yan et al, 2008). A lack of strong marker-trait associations for most of the studied traits indicated that the SNP array used in this study comprised mainly neutral markers, so our inferences on admixture and population structure of Malus accessions would not be biased.…”

Section: Ld and Marker-trait Associationmentioning

confidence: 83%

Molecular-level and trait-level differentiation between the cultivated apple (Malus× domesticaBorkh.) and its main progenitorMalussieversii

et al. 2014

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The present study is the first to compare the trait-level differentiation (Q st ) and the molecular-level differentiation (F st ) between Malus £ domestica and Malus sieversii. A set of 115 accessions representing M. £ domestica (99) and M. sieversii (16) were genotyped using the International RosBREED SNP Consortium apple 8K SNP array and phenotyped for eight fruit quality traits in a clonally replicated experiment. A set of 3521 single nucleotide polymorphisms (SNPs) with an average call rate of 98% was retained following SNP data quality filters. About 86% of the total SNPs were polymorphic in M. sieversii, while all but three SNPs were polymorphic in M. £ domestica. The patterns of linkage disequilibrium were different, especially at the longer distances, between the two species. No differentiation (F st ¼ 0) was observed for nearly 23% of the SNPs, but about 20% of the SNPs exhibited a high genetic differentiation (F st $ 0.15). A highly significant (P , 0.001) genome-level F st ¼ 0.12 was observed between M. £ domestica and M. sieversii. The average estimated Q st value was 0.20 (range 0.08-0.40), and for three of the eight studied traits (crispness, flavour intensity and fruit weight), Q st value was more than twice the estimated genome-level F st value. A higher Q st value than F st value for four of the eight fruit quality traits indicated differential (or directional) selection for these traits in M. £ domestica. The average posterior probability of assignment of M. £ domestica accessions to the M. sieversii gene pool was 11%, supporting the hypothesis of M. sieversii being one of the progenitors of the domesticated apple.

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Section: Ld and Marker-trait Associationmentioning

confidence: 83%

Molecular-level and trait-level differentiation between the cultivated apple (Malus× domesticaBorkh.) and its main progenitorMalussieversii

et al. 2014

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“…Malus sieversii has been considered an important germplasm resource for potential cultivar breeding of cultivated apples, making effective preservation of M. sieversii's genetic resources a major conservation target. Previous studies have identified priority conservation areas as areas displaying high levels of genetic diversity (Zhang et al 2007, Li et al 2008, Yan et al 2008, Zhang 2008. This approach has also been used to propose priority areas for conservation action on other endangered plants in the same region (Su et al 2, SRAP in Zhang 2008;3, SSR in Li et al 2008;4, SSR in Qin et al 2012;5, SSR in Dong et al 2013;6, LEAFY gene in Zhang et al 2015;7, SSR in the current study; 8, genome-wide SNPs in the current study.…”

Section: Discussionmentioning

confidence: 99%

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

Zhang

2018

Nordic Journal of Botany

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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.

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“…The use of molecular marker data has been extremely useful for organizing and managing collections of genetic resources (Bretting and Widrlechner 1995;Van Treuren et al 2001). In particular, genetic analyses have been performed with microsatellite markers in cultivated and wild Malus collections for fingerprinting (Galli et al 2005;Guilford et al 1997;Hokanson et al 1998;Oraguzie et al 2005), genomic mapping (Hemmat et al 2003;Liebhard et al 2002;Liebhard et al 2003), marker-assisted breeding (Gianfranceschi et al 1999;Gygax et al 2004), and assessments of diversity within domesticated and wild collections (Coart et al 2003;Gaurino et al 2006;Hokanson et al 2001;Kitahara et al 2005;Lamboy et al 1996;Pereira-Lorenzo et al 2003;Ramos-Cabrer et al 2007;Volk et al 2005;Volk et al 2008;Yan et al 2008;Zhang et al 2007).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple

Richards

Volk

Reilley

et al. 2008

Tree Genetics & Genomes

125

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Malus sieversii (Lebed.) M. Roem. is a wild progenitor species of the domesticated apple. It is found across a mountainous region of central Asia and has been the focus of several collection expeditions by the USDA-ARS-National Plant Germplasm System. This study used microsatellite variation at seven loci to estimate diversity and differentiation within M. sieversii using several complimentary approaches. Multilocus genotypes were amplified from 949 individuals representing seedling trees from 88 half-sib families from eight M. sieversii populations collected in Kazakhstan. Apportioning of genetic variation was estimated at both the family and site level. Analyses using a hierarchical model to estimate F st showed that differentiation among individual families is more than three times greater than differentiation among sites. In addition, average gene diversity and allelic richness varied significantly among sites. A rendering of a genetic network among all sites showed that differentiation is largely congruent with geographical location. In addition, nonhierarchical Bayesian assignment methods were used to infer genetic clusters across the collection area. We detected four genetic clusters in the data set. The quality of these assignments was evaluated over multiple Markov Chain Monte Carlo runs using both posterior likelihood and stability of the assignments. The spatial pattern of genetic assignments among the eight collection sites shows two broadly distributed and two narrowly distributed clusters. These data indicate that the southwestern collection sites are more admixed and more diverse than the northern sites.

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Genetic polymorphism of Malus sieversii populations in Xinjiang, China

Cited by 42 publications

References 12 publications

Molecular-level and trait-level differentiation between the cultivated apple (Malus× domesticaBorkh.) and its main progenitorMalussieversii

Molecular-level and trait-level differentiation between the cultivated apple (Malus× domesticaBorkh.) and its main progenitorMalussieversii

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

Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple

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