Abstract
Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for the discovery of large-scale de novo genotyping of single nucleotide polymorphism (SNP) markers. In the present research, in order to facilitate genome-guided breeding in potato, this strategy was used to develop a large number of SNP markers and construct a high-density genetic linkage map for tetraploid potato. The genomic DNA extracted from 106 F1 individuals derived from a cross between two tetraploid potato varieties YSP-4 × MIN-021 and their parents was used for high-throughput sequencing and SLAF library construction. A total of 556.71 Gb data, which contained 2269.98 million pair-end reads, were obtained after preprocessing. According to bioinformatics analysis, a total of 838,604 SLAF labels were developed, with an average sequencing depth of 26.14-fold for parents and 15.36-fold for offspring of each SLAF, respectively. In total, 113,473 polymorphic SLAFs were obtained, from which 7638 SLAFs were successfully classified into four segregation patterns. After filtering, a total of 7329 SNP markers were detected for genetic map construction. The final integrated linkage map of tetraploid potato included 3001 SNP markers on 12 linkage groups, and covered 1415.88 cM, with an average distance of 0.47 cM between adjacent markers. To our knowledge, the integrated map described herein has the best coverage of the potato genome and the highest marker density for tetraploid potato. This work provides a foundation for further quantitative trait loci (QTL) location, map-based gene cloning of important traits and marker-assisted selection (MAS) of potato.
Highlights
Potato, Solanum tuberosum L., is the fourth most important food crop in the world behind maize, wheat, and rice, with a total production of more than 388 million tons in 2017 [1]
Of all the high-quality data, 48,849,737 reads were from the male parent MIN-21, 41,510,213 reads were from the female parent YSP-4, and the average 90,562,465 reads were from 106 offspring of the F1 mapping population (Table 1)
The results showed that SLAF-seq was an effective tool to rapid develop large-scale single nucleotide polymorphism (SNP) markers, which met the requirements for high-density genetic map construction of tetraploid potato
Summary
Solanum tuberosum L., is the fourth most important food crop in the world behind maize, wheat, and rice, with a total production of more than 388 million tons in 2017 [1]. Cultivated potato is a highly heterozygous outcrossing autotetraploid (2n = 4x = 48), which causes complexities in genetic or genomic studies, and provides many challenges for breeding. A high-density genetic linkage map can provide a large amount of information that facilitates map-based cloning, QTL identification, and comparative genomic researches, establishing a general tool for marker-assisted selection breeding (MAS). Over the past two decades, multiple linkage maps have been constructed for potato (both diploid and autotetraploid potato) for the purpose of better understanding the potato genome, facilitating map-based cloning, and developing markers for MAS [6,7,8,9,10,11]. Gebhardt et al (1991) [6] reported the first potato map in the world, including 135 restriction fragment length polymorphism (RFLP) molecular markers and defining
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