Construction of a high-density genetic map and mapping of QTLs for soybean (Glycine max) agronomic and seed quality traits by specific length amplified fragment sequencing

Abstract

BackgroundSoybean is not only an important oil crop, but also an important source of edible protein and industrial raw material. Yield-traits and quality-traits are increasingly attracting the attention of breeders. Therefore, fine mapping the QTLs associated with yield-traits and quality-traits of soybean would be helpful for soybean breeders. In the present study, a high-density linkage map was constructed to identify the QTLs for the yield-traits and quality-traits, using specific length amplified fragment sequencing (SLAF-seq).ResultsSLAF-seq was performed to screen SLAF markers with 149 F8:11 individuals from a cross between a semi wild soybean, ‘Huapidou’, and a cultivated soybean, ‘Qihuang26’, which generated 400.91 M paired-end reads. In total, 53,132 polymorphic SLAF markers were obtained. The genetic linkage map was constructed by 5111 SLAF markers with segregation type of aa×bb. The final map, containing 20 linkage groups (LGs), was 2909.46 cM in length with an average distance of 0.57 cM between adjacent markers. The average coverage for each SLAF marker on the map was 81.26-fold in the male parent, 45.79-fold in the female parent, and 19.84-fold average in each F8:11 individual. According to the high-density map, 35 QTLs for plant height (PH), 100-seeds weight (SW), oil content in seeds (Oil) and protein content in seeds (Protein) were found to be distributed on 17 chromosomes, and 14 novel QTLs were identified for the first time. The physical distance of 11 QTLs was shorter than 100 Kb, suggesting a direct opportunity to find candidate genes. Furthermore, three pairs of epistatic QTLs associated with Protein involving 6 loci on 5 chromosomes were identified. Moreover, 13, 14, 7 and 9 genes, which showed tissue-specific expression patterns, might be associated with PH, SW, Oil and Protein, respectively.ConclusionsWith SLAF-sequencing, some novel QTLs and important QTLs for both yield-related and quality traits were identified based on a new, high-density linkage map. Moreover, 43 genes with tissue-specific expression patterns were regarded as potential genes in further study. Our findings might be beneficial to molecular marker-assisted breeding, and could provide detailed information for accurate QTL localization.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5035-9) contains supplementary material, which is available to authorized users.

High-Resolution Mapping in Two RIL Populations Refines Major “QTL Hotspot” Regions for Seed Size and Shape in Soybean (Glycine max L.)

“…QTL mapping is a practical approach and has been frequently employed for the detection of QTLs/genes underlying the quantitative traits in crop plants. However, the efficiency and accuracy of QTL mappings are influenced, mainly by parental diversity and marker density [26]. The quality of genetic maps has a significant impact on the accuracy of QTL detection, and, consequently, increasing marker density can intensify the resolution of QTL mapping [37].…”

“…Hence, it is vital to identify and validate QTLs in multiple backgrounds and environments for their potential use in marker-assisted breeding (MAB). Lastly, the earlier studies mostly focused on the identification of main-effect QTLs for seed size/shape in soybean; however, minimal efforts have been made to understand complex genetic interaction effects, such as epistasis and environment effects [24][25][26].…”

Construction of a SNP-Based Genetic Map Using SLAF-Seq and QTL Analysis of Morphological Traits in Eggplant

“…Specific length amplified fragment (SLAF) sequencing (SLAF-seq) is an improved reduced representation library (RRL) sequencing strategy that brings down the cost through genome reduction. SLAF-seq has been proved an effective method for de novo SNP discovery and high-throughput genotyping and has wide applications in genetic map construction in sesame , kiwifruit (Huang et al, 2013), soybean (Qi et al, 2014;Zhang et al, 2018), cucumber (Wei et al, 2014;Zhu et al, 2016), peanut (Hu et al, 2018), sweet osmanthus (He et al, 2017), and cotton (Zhang et al, 2016;Ali et al, 2018). In the present study, we developed an interspecific F 2 population containing 121 individuals from a cross between an eggplant cultivar and the wild relative S. linnaeanum.…”

Quantitative trait loci analysis of seed oil content and composition of wild and cultivated soybean

“…20 (qOil_20) using 3343 polymorphic SNPs (3 K-SNP) [25]. Specific-locus amplified fragment sequencing (SLAF-seq) technology has been used to construct high-density genetic maps, constituting an efficient method for large-scale de novo SNP discovery and genotyping in soybean [31,32]. Li et al (2017) detected 26 stable QTLs for five fatty acids using 3541 SLAF markers with an average distance of 0.72 cM [31].…”

“…Li et al (2017) detected 26 stable QTLs for five fatty acids using 3541 SLAF markers with an average distance of 0.72 cM [31]. Zhang et al (2018) created a high-density genetic map containing 8597 SNP loci with an average distance of 0.57 cM, from which two QTLs, qOil10-1 and qOil10-2, for oil content were mapped [32]. In addition, some genes associated with soybean seed oil content and composition have been discovered through genome-wide association studies (GWAS) by SNP genotyping [30,[33][34][35][36][37][38].…”