Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing

Suzhen Niu; Hisashi Koiwa; Qinfei Song; Dahe Qiao; Juan Chen; Degang Zhao; Zhengwu Chen; Ying Wang; Tianyuan Zhang

doi:10.7717/peerj.8572

Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing

PeerJ. 2020 Mar 13:8:e8572. doi: 10.7717/peerj.8572. eCollection 2020.

Authors

Suzhen Niu^{1

2}, Hisashi Koiwa³, Qinfei Song², Dahe Qiao¹, Juan Chen¹, Degang Zhao¹, Zhengwu Chen¹, Ying Wang⁴, Tianyuan Zhang⁴

Affiliations

¹ Guiyang Station for DUS Testing Center of New Plant Varteties (MOA) / Institute of Tea, Guizhou Academy of Agricultural Sciences, Guiyang, China.
² The Key Laboratory of Plant Resources Conservation and Germplasm Innovationin Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering / College of Tea Science, Guizhou University, Guiyang, China.
³ Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Molecular and Environmental Plant Sciences Program, Texas A&M University, College Station, Texas, USA.
⁴ Wuhan Benagen Tech Solutions Company Limited, Wuhan, China.

Abstract

An accurate depiction of the genetic relationship, the development of core collection, and genome-wide association analysis (GWAS) are key for the effective exploitation and utilization of genetic resources. Here, genotyping-by-sequencing (GBS) was used to characterize 415 tea accessions mostly collected from the Guizhou region in China. A total of 30,282 high-quality SNPs was used to estimate the genetic relationships, develop core collections, and perform GWAS. We suggest 198 and 148 accessions to represent the core set and mini-core set, which consist of 47% and 37% of the whole collection, respectively, and contain 93-95% of the total SNPs. Furthermore, the frequencies of all alleles and genotypes in the whole set were very well retained in the core set and mini-core set. The 415 accessions were clustered into 14 groups and the core and the mini-core collections contain accessions from each group, species, cultivation status and growth habit. By analyzing the significant SNP markers associated with multiple traits, nine SNPs were found to be significantly associated with four leaf size traits, namely MLL, MLW, MLA and MLSI (P < 1.655E-06). This study characterized the genetic distance and relationship of tea collections, suggested the core collections, and established an efficient GWAS analysis of GBS result.

Keywords: Core Collections; GBS; GWAS; Leaf Size; Tea Plant.

Grants and funding

This work was supported by the National Science Foundation of China (31560222), the Science and Technology Plan Project of Guizhou province (20172558, 20172557, 20175788, 20191404), the USDA-NIFA SCRI grant (2017-51181-26834), the Guizhou Top Level Innovation Talents Cultivation Project (20164003), the Talent Base for Germplasm Resources Utilization and Innovation of Characteristic Plant in Guizhou (RCJD2018-14) and the Genetically Breeding Major Project of the Ministry of Agriculture of China (2016ZX08010-003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.