Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane

Hui Zhang; Pingping Lin; Yanming Liu; Chaohua Huang; Guoqiang Huang; Hongtao Jiang; Liangnian Xu; Muqing Zhang; Zuhu Deng; Xinwang Zhao

doi:10.3390/genes13081477

Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane

Genes (Basel). 2022 Aug 19;13(8):1477. doi: 10.3390/genes13081477.

Authors

Hui Zhang¹, Pingping Lin¹, Yanming Liu¹, Chaohua Huang¹, Guoqiang Huang¹, Hongtao Jiang¹, Liangnian Xu¹, Muqing Zhang², Zuhu Deng¹, Xinwang Zhao^{1

2}

Affiliations

¹ National Engineering Research Center for Sugarcane, Key Laboratory of Sugarcane Biology and Genetic, Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
² Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530005, China.

Abstract

A genetic diversity analysis and identification of plant germplasms and varieties are important and necessary for plant breeding. Deoxyribonucleotide (DNA) fingerprints based on genomic molecular markers play an important role in accurate germplasm identification. In this study, Specific-Locus Amplified Fragment Sequencing (SLAF-seq) was conducted for a sugarcane population with 103 cultivated and wild accessions. In total, 105,325 genomic single nucleotide polymorphisms (SNPs) were called successfully to analyze population components and genetic diversity. The genetic diversity of the population was complex and clustered into two major subpopulations. A principal component analysis (PCA) showed that these accessions could not be completely classified based on geographical origin. After filtration, screening, and comparison, 192 uniformly-distributed SNP loci were selected for the 32 chromosomes of sugarcane. An SNP complex genotyping detection system was established using the SNaPshot typing method and used for the precise genotyping and identification of 180 sugarcane germplasm samples. According to the stability and polymorphism of the SNPs, 32 high-quality SNP markers were obtained and successfully used to construct the first SNP fingerprinting and quick response codes (QR codes) for sugarcane. The results provide new insights for genotyping, classifying, and identifying germplasm and resources for sugarcane breeding.

Keywords: DNA fingerprinting; SNP; genetic diversity; sugarcane; variety identification.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Fingerprinting
Genetics, Population
Plant Breeding
Polymorphism, Single Nucleotide / genetics
Saccharum* / genetics

Grants and funding

This research was financially supported in part by grants from the Central Government-guided Local Science and Technology Development Projects of Chian (2021L3009), the Independent research Project of the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (SKLCUSA-a201912), the Special Project for Modern Agriculture Technology of China (CARS-170106), Young and Middle-aged Teachers Education Research Project of Fujian Education Department (JAT200091), and the Innovation Fund of Fujian Agriculture and Forestry University (KFA20082A, KHF210001, KFA17626A, KFA19134A).