Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome

• Published in: BMC plant biology Vol. 20; no. 1; p. 245
• Main Authors: Liu, Na, Cheng, Fangyun
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 02.06.2020; BioMed Central; BMC
• Subjects: Agricultural production; Analysis; Association analysis; Association mapping; Biodiversity; Chromosome Mapping; Crop yield; Crops; Cultivars; DNA binding proteins; EST-SSR markers; Expressed Sequence Tags; Gene expression; Gene families; Gene mapping; Genes; Genes, Plant - genetics; Genes, Plant - physiology; Genetic diversity; Genetic Markers - genetics; Genome-Wide Association Study; Genomes; Genotyping; Herbal medicine; High-Throughput Nucleotide Sequencing; Linkage disequilibrium; Loci; Mapping; Markers; Medicinal plants; Microsatellite Repeats - genetics; Next-generation sequencing; Oilseeds; Ornamental plants; Paeonia - genetics; Paeonia - growth & development; Paeonia rockii; Phenotypic variations; Plant Proteins - genetics; Plant Proteins - physiology; Population; Quantitative Trait Loci - genetics; Quantitative Trait, Heritable; Seeds; Subpopulations; Transcription factors; Transcription Factors - genetics; Transcription Factors - physiology; Trees; Wheat; Woody plants; Yield traits; China; Association mapping; Transcription factors; Yield traits; Paeonia rockii; EST-SSR markers
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-020-02449-6

Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS). The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%). Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.