title: De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila.
abstract: Salix psammophila, a sandy shrub known as desert willow, is regarded as a potential biomass feedstock and plays an important role in maintaining local ecosystems. However, a lack of genomic data and efficient molecular markers limit the study of its population evolution and genetic breeding. In this study, chromosome counts, flow cytometry and SSR analyses indicated that S. psammophila is tetraploid. A total of 6,346 EST-SSRs were detected based on 71,458 de novo assembled unigenes from transcriptome data. Twenty-seven EST-SSR markers were developed to evaluate the genetic diversity and population structure of S. psammophila from eight natural populations in Northern China. High levels of genetic diversity (mean 10.63 alleles per locus; mean HE0.689) were dectected in S. psammophila. The weak population structure and little genetic differentiation (pairwise FST= 0.006-0.016) were found among Population 1-Population 7 (Pop1-Pop7; Inner Mongolia and Shaanxi), but Pop8 (Ningxia) was clearly separated from Pop1-Pop7 and moderate differentiation (pairwise FST= 0.045-0.055) was detected between them, which may be influenced by local habitat conditions. Molecular variance analyses indicated that most of the genetic variation (94.27%) existed within populations. These results provide valuable genetic informations for natural resource conservation and breeding programme optimisation of S. psammophila.
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.|Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
authors.forename: Huixia
authors.initials: H
authors.lastname: Jia
authors.affiliation: College of Forestry, Inner Mongolia Agricultural University, Hohhot, 010019, China.
authors.forename: Haifeng
authors.initials: H
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
authors.forename: Pei
authors.initials: P
authors.lastname: Sun
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
authors.forename: Jianbo
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
authors.forename: Yinghua
authors.initials: Y
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
authors.forename: Xiaojiao
authors.initials: X
authors.lastname: Han
authors.affiliation: College of Forestry, Inner Mongolia Agricultural University, Hohhot, 010019, China.
authors.forename: Guosheng
authors.initials: G
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.|Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
authors.forename: Mengzhu
authors.initials: M
authors.lastname: Lu
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.|Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
authors.forename: Jianjun
authors.initials: J
authors.lastname: Hu
mesh_terms: D000483:Alleles; D018533:Biomass; D002681:China; D032461:Chromosomes, Plant; D017753:Ecosystem; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D005843:Geography; D018519:Meristem / Q000235:genetics; D018895:Microsatellite Repeats; D010802:Phylogeny; D018517:Plant Roots / Q000235:genetics; D011003:Ploidies; D032108:Salix / Q000235:genetics*; D059467:Transcriptome
chemical_list: D005819:Genetic Markers