title: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing.
abstract: Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is cultivated worldwide. However, no genome-wide assessment of the genetic diversity of sweet potato has been reported to date. In the present study, the population structure and genetic diversity of 197 sweet potato accessions most of which were from China were assessed using 62,363 SNPs. A model-based structure analysis divided the accessions into three groups: group 1, group 2 and group 3. The genetic relationships among the accessions were evaluated using a phylogenetic tree, which clustered all the accessions into three major groups. A principal component analysis (PCA) showed that the accessions were distributed according to their population structure. The mean genetic distance among accessions ranged from 0.290 for group 1 to 0.311 for group 3, and the mean polymorphic information content (PIC) ranged from 0.232 for group 1 to 0.251 for group 3. The mean minor allele frequency (MAF) ranged from 0.207 for group 1 to 0.222 for group 3. Analysis of molecular variance (AMOVA) showed that the maximum diversity was within accessions (89.569%). Using CoreHunter software, a core set of 39 accessions was obtained, which accounted for approximately 19.8% of the total collection. The core germplasm set of sweet potato developed will be a valuable resource for future sweet potato improvement strategies.
authors.affiliation: Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China.|Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China.
authors.forename: Wenjin
authors.identifier: http://orcid.org/0000-0001-5983-1341
authors.initials: W
authors.lastname: Su
authors.affiliation: Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Lianjun
authors.initials: L
authors.lastname: Wang
authors.affiliation: Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Lei
authors.affiliation: Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Shasha
authors.initials: S
authors.lastname: Chai
authors.affiliation: College of Agriculture, Yangtze University, Jingzhou, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Xinsun
authors.initials: X
authors.lastname: Yang
authors.affiliation: Hubei Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Chunhai
authors.initials: C
authors.lastname: Jiao
mesh_terms: D005787:Gene Frequency; D018745:Genome, Plant; D027723:Ipomoea batatas / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D011110:Polymorphism, Genetic; D000068098:Seed Bank / Q000592:standards