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

Wenjin Su; Lianjun Wang; Jian Lei; Shasha Chai; Yi Liu; Yuanyuan Yang; Xinsun Yang; Chunhai Jiao

doi:10.1371/journal.pone.0172066

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

PLoS One. 2017 Feb 10;12(2):e0172066. doi: 10.1371/journal.pone.0172066. eCollection 2017.

Authors

Wenjin Su^{1

2}, Lianjun Wang¹, Jian Lei¹, Shasha Chai¹, Yi Liu³, Yuanyuan Yang¹, Xinsun Yang¹, Chunhai Jiao⁴

Affiliations

¹ Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China.
² Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China.
³ College of Agriculture, Yangtze University, Jingzhou, China.
⁴ Hubei Academy of Agricultural Sciences, Wuhan, China.

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.

MeSH terms

Gene Frequency
Genome, Plant
Ipomoea batatas / classification
Ipomoea batatas / genetics*
Phylogeny*
Polymorphism, Genetic*
Seed Bank / standards

Grants and funding

This work was supported by Hubei Engineering and Technology Research Center of Sweet Potato, Introduction and Utilization of Sweet Potato Germplasm Resources from America (2013-Z61), Science and Technology Innovation Center of Hubei Academy of Agricultural Sciences (2007-620-001-03), China Agriculture Research System (CARS-11-C-15), Characteristic Discipline of Hubei Academy of Agricultural Sciences (2015TSXK06), National Natural Science Foundation of China Grant (31301377), Innovation and Application of Major Crops Germplasm Resources Introduced from Africa and Southeast Asia (2016ABA087). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.