Abstract
Germplasm resource collection and utilization are important in forestry species breeding. High-through sequencing technologies have been playing increasing roles in forestry breeding. In this study, specific-locus amplified fragment sequencing (SLAF-seq) was employed to analyze 149 masson pine (Pinus massoniana) accessions collected from Guangdong in China. A large number of 471,660 SNPs in the total collection were identified from 599,164 polymorphic SLAF tags. Population structure analysis showed that 149 masson pines could not be obviously divided into subpopulations. Two core sets, containing 29 masson pine accessions for increasing resin and wood yield respectively, were obtained from the total collection. Phenotypic analyses of five traits showed abundant variations, 25 suggestive and 9 significant SNPs were associated with the resin-yielding capacity (RYC’) and volume of wood (VW) using EMMAX and FaST-LMM; 22 suggestive and 11 significant SNPs were associated with RYC’ and VW using mrMLM and FASTmrMLM. Moreover, a large number of associated SNPs were detected in trait HT, DBH, RW and RYC using mrMLM, FASTmrMLM, FASTmrEMMA and ISIS EM-BLASSO. The core germplasm sets would be a valuable resource for masson pine improvement and breeding. In addition, the associated SNP markers would be meaningful for masson pine resource selection.
Highlights
Masson pine (Pinus massoniana) is a native species that grows throughout central and southern China
A total of 599,164 polymorphic SLAF tags containing 2,774,976 Single nucleotide polymorphisms (SNPs) were developed for the 149 samples that were used for further analysis
After filtering out the invalid SNPs, 471,660 SNPs were remained among the 149 masson pine accessions
Summary
Masson pine (Pinus massoniana) is a native species that grows throughout central and southern China. A new strategy for de novo SNP discovery and genotyping of large populations, referred to as specific-locus amplified fragment sequencing (SLAF-seq), has been employed[19]. We could identify a polymorphic specific SNP locus from all of the accessions through software alignment This high-resolution method has been tested on many organisms, including crape myrtle[20], cucumber[21], rapeseed[22], sesame[23] and soybean[24]. To better understand the genetic relationship and the genetic architecture of wood and resin yield traits of the P. massoniana accessions in Guangdong province, we conduct a genome-wide SNP discovery based on the SLAF-seq method. The results would be of great value for masson pine selection and breeding
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