Association study of SNP locus for color related traits in herbaceous peony (Paeonia lactiflora Pall.) using SLAF-seq
Paeonia lactiflora Pall. (P. lactiflora) is a famous ornamental plant with showy and colorful flowers that has been domesticated in China for 4,000 years. However, the genetic basis of phenotypic variation and genealogical relationships in P. lactiflora population is poorly understood due to limited...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-12-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1032449/full |
| _version_ | 1811190517909684224 |
|---|---|
| author | Genzhong Liu Ying Li Xia Sun Xianfeng Guo Nannan Jiang Yifu Fang Junqiang Chen Zhilong Bao Fangfang Ma |
| author_facet | Genzhong Liu Ying Li Xia Sun Xianfeng Guo Nannan Jiang Yifu Fang Junqiang Chen Zhilong Bao Fangfang Ma |
| author_sort | Genzhong Liu |
| collection | DOAJ |
| description | Paeonia lactiflora Pall. (P. lactiflora) is a famous ornamental plant with showy and colorful flowers that has been domesticated in China for 4,000 years. However, the genetic basis of phenotypic variation and genealogical relationships in P. lactiflora population is poorly understood due to limited genetic information, which brings about bottlenecks in the application of effective and efficient breeding strategies. Understanding the genetic basis of color-related traits is essential for improving flower color by marker-assisted selection (MAS). In this study, a high throughput sequencing of 99 diploid P. lactiflora accessions via specific-locus amplified fragment sequencing (SLAF-seq) technology was performed. In total, 4,383,645 SLAF tags were developed from 99 P. lactiflora accessions with an average sequencing depth of 20.81 for each SLAF tag. A total of 2,954,574 single nucleotide polymorphisms (SNPs) were identified from all SLAF tags. The population structure and phylogenetic analysis showed that P. lactiflora population used in this study could be divided into six divergent groups. Through association study using Mixed linear model (MLM), we further identified 40 SNPs that were significantly positively associated with petal color. Moreover, a derived cleaved amplified polymorphism (dCAPS) marker that was designed based on the SLAF tag 270512F co-segregated with flower colors in P. lactiflora population. Taken together, our results provide valuable insights into the application of MAS in P. lactiflora breeding programs. |
| first_indexed | 2024-04-11T14:52:33Z |
| format | Article |
| id | doaj.art-2bedf3447988496a93c742c6f67e4b0b |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T14:52:33Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-2bedf3447988496a93c742c6f67e4b0b2022-12-22T04:17:23ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-12-011310.3389/fpls.2022.10324491032449Association study of SNP locus for color related traits in herbaceous peony (Paeonia lactiflora Pall.) using SLAF-seqGenzhong Liu0Ying Li1Xia Sun2Xianfeng Guo3Nannan Jiang4Yifu Fang5Junqiang Chen6Zhilong Bao7Fangfang Ma8State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, ChinaState Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, ChinaState Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, ChinaCollege of Forestry, Shandong Agricultural University, Tai-An, Shandong, ChinaInstitute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, ChinaInstitute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, ChinaInstitute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, ChinaState Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, ChinaState Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, ChinaPaeonia lactiflora Pall. (P. lactiflora) is a famous ornamental plant with showy and colorful flowers that has been domesticated in China for 4,000 years. However, the genetic basis of phenotypic variation and genealogical relationships in P. lactiflora population is poorly understood due to limited genetic information, which brings about bottlenecks in the application of effective and efficient breeding strategies. Understanding the genetic basis of color-related traits is essential for improving flower color by marker-assisted selection (MAS). In this study, a high throughput sequencing of 99 diploid P. lactiflora accessions via specific-locus amplified fragment sequencing (SLAF-seq) technology was performed. In total, 4,383,645 SLAF tags were developed from 99 P. lactiflora accessions with an average sequencing depth of 20.81 for each SLAF tag. A total of 2,954,574 single nucleotide polymorphisms (SNPs) were identified from all SLAF tags. The population structure and phylogenetic analysis showed that P. lactiflora population used in this study could be divided into six divergent groups. Through association study using Mixed linear model (MLM), we further identified 40 SNPs that were significantly positively associated with petal color. Moreover, a derived cleaved amplified polymorphism (dCAPS) marker that was designed based on the SLAF tag 270512F co-segregated with flower colors in P. lactiflora population. Taken together, our results provide valuable insights into the application of MAS in P. lactiflora breeding programs.https://www.frontiersin.org/articles/10.3389/fpls.2022.1032449/fullPaeonia lactiflora Pall.SLAF-seqassociation studypopulation structureDCAPSmarker-assisted selection |
| spellingShingle | Genzhong Liu Ying Li Xia Sun Xianfeng Guo Nannan Jiang Yifu Fang Junqiang Chen Zhilong Bao Fangfang Ma Association study of SNP locus for color related traits in herbaceous peony (Paeonia lactiflora Pall.) using SLAF-seq Frontiers in Plant Science Paeonia lactiflora Pall. SLAF-seq association study population structure DCAPS marker-assisted selection |
| title | Association study of SNP locus for color related traits in herbaceous peony (Paeonia lactiflora Pall.) using SLAF-seq |
| title_full | Association study of SNP locus for color related traits in herbaceous peony (Paeonia lactiflora Pall.) using SLAF-seq |
| title_fullStr | Association study of SNP locus for color related traits in herbaceous peony (Paeonia lactiflora Pall.) using SLAF-seq |
| title_full_unstemmed | Association study of SNP locus for color related traits in herbaceous peony (Paeonia lactiflora Pall.) using SLAF-seq |
| title_short | Association study of SNP locus for color related traits in herbaceous peony (Paeonia lactiflora Pall.) using SLAF-seq |
| title_sort | association study of snp locus for color related traits in herbaceous peony paeonia lactiflora pall using slaf seq |
| topic | Paeonia lactiflora Pall. SLAF-seq association study population structure DCAPS marker-assisted selection |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1032449/full |
| work_keys_str_mv | AT genzhongliu associationstudyofsnplocusforcolorrelatedtraitsinherbaceouspeonypaeonialactiflorapallusingslafseq AT yingli associationstudyofsnplocusforcolorrelatedtraitsinherbaceouspeonypaeonialactiflorapallusingslafseq AT xiasun associationstudyofsnplocusforcolorrelatedtraitsinherbaceouspeonypaeonialactiflorapallusingslafseq AT xianfengguo associationstudyofsnplocusforcolorrelatedtraitsinherbaceouspeonypaeonialactiflorapallusingslafseq AT nannanjiang associationstudyofsnplocusforcolorrelatedtraitsinherbaceouspeonypaeonialactiflorapallusingslafseq AT yifufang associationstudyofsnplocusforcolorrelatedtraitsinherbaceouspeonypaeonialactiflorapallusingslafseq AT junqiangchen associationstudyofsnplocusforcolorrelatedtraitsinherbaceouspeonypaeonialactiflorapallusingslafseq AT zhilongbao associationstudyofsnplocusforcolorrelatedtraitsinherbaceouspeonypaeonialactiflorapallusingslafseq AT fangfangma associationstudyofsnplocusforcolorrelatedtraitsinherbaceouspeonypaeonialactiflorapallusingslafseq |