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Leaf shape is an important trait that influences the utilization rate of light, and affects quality and yield of pea ( Pisum sativum ). In the present study, a joint method of high-density genetic mapping using specific locus amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) was applied to rapidly detect loci with leaf shape traits. A total of 7,146 polymorphic SLAFs containing 12,213 SNP markers were employed to construct a high-density genetic map for pea. We conducted quantitative trait locus (QTL) mapping on an F 2  population to identify QTLs associated with leaf shape traits. Moreover, SLAF-BSA was conducted on the same F 2  population to identify the single nucleotide polymorphism (SNP) markers linked to leaf shape in pea. Two QTLs (qLeaf_or-1, qLeaf_or-2) were mapped on linkage group 7 (LG7) for pea leaf shape. Through alignment of SLAF markers with  Cicer arietinum, Medicago truncatula , and  Glycine max , the pea LGs were assigned to their corresponding homologous chromosomal groups. The comparative genetic analysis showed that pea is more closely related to  M. truncatula . Based on the sequencing results of two pools with different leaf shape, 179 associated markers were obtained after association analysis. The joint analysis of SLAF-seq and BSA showed that the QTLs obtained from mapping on a high-density genetic map are convincing due to the closely associated map region with the BSA results, which provided more potential markers related to leaf shape. Thus, the identified QTLs could be used in marker-assisted selection for pea breeding in the future. Our study revealed that joint analysis of QTL mapping on a high-density genetic map and BSA-seq is a cost-effective and accurate method to reveal genetic architecture of target traits in plant species without a reference genome.

QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing