High-density SNP-based QTL mapping and candidate gene screening for yield-related blade length and width in Saccharina japonica (Laminariales, Phaeophyta)

Xiuliang Wang,Zhihang Chen,Delin Duan,Jie Zhang,Qiuying Li,Shun Liu

doi:10.1038/s41598-018-32015-y

Abstract

Saccharina japonica is one of the most important marine crops in China, Japan and Korea. Candidate genes associated with blade length and blade width have not yet been reported. Here, based on SLAF-seq, the 7627 resulting SNP loci were selected for genetic linkage mapping to 31 linkage groups with an average spacing of 0.69 cM, and QTL analyses were performed to map the blade length and blade width phenotypes of S. japonica. In total, 12 QTLs contributing to blade length and 10 to width were detected. Some QTL intervals were detected for both blade length and width. Additive alleles for increasing blade length and width in S. japonica came from both parents. After the QTL interval regions were comparatively mapped to the current reference genome of S. japonica (MEHQ00000000), 14 Tic20 (translocon on the inner envelope membrane of chloroplast) genes and three peptidase genes were identified. RT-qPCR analysis showed that the transcription levels of four Tic20 genes were different not only in the two parent sporophytes but also at different cultivation times within one parent. The SNP markers closely associated with blade length and width could be used to improve the selection efficiency of S. japonica breeding.

Highlights

A total of 5.6 million tons of S. japonica was produced worldwide in 2012, mainly in China[7]
In the two quantitative trait locus (QTL) mapping studies of S. japonica to date, several QTLs have been mapped for kelp blade length and width, raw weight and base shape[20,22]
SNP markers are di-allelic and represent the smallest type of genetic variation in genomes; they have been extensively applied for genetic diversity detection, genetic linkage map construction, QTL mapping, and GWAS23

Summary

Introduction

A total of 5.6 million tons (wet weight) of S. japonica was produced worldwide in 2012, mainly in China[7]. Attempts have been made to use molecular markers to construct genetic linkage map and perform quantitative trait locus (QTL) mapping for S. japonica[18,19,20,21,22]. To improve QTL mapping efficiency for S. japonica, high-density genetic linkage maps are desirable, and these are best constructed using SNP markers. We conducted QTL mapping for S. japonica’s blade length and width based on a high-density genetic linkage map constructed with SNP markers that we developed using SLAF-seq. Our aim is to combine the collinearity of the high-density genetic linkage map with the reference genome to identify candidate genes for the yield-related blade length and width traits of S. japonica

Objectives

Methods

Results