Genetic dissection of thousand-seed weight in linseed (Linum usitatissimum L.) using multi-locus genome-wide association study
Flaxseed/linseed is an important oilseed crop having applications in the food, nutraceutical, and paint industry. Seed weight is one of the most crucial determinants of seed yield in linseed. Here, quantitative trait nucleotides (QTNs) associated with thousand-seed weight (TSW) have been identified...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-06-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1166728/full |
| _version_ | 1797813641407365120 |
|---|---|
| author | Ankit Saroha Sunil S. Gomashe Vikender Kaur Deepa Pal Shraddha Ujjainwal J. Aravind Mamta Singh S. Rajkumar Kuldeep Singh Ashok Kumar Dhammaprakash Pandhari Wankhede |
| author_facet | Ankit Saroha Sunil S. Gomashe Vikender Kaur Deepa Pal Shraddha Ujjainwal J. Aravind Mamta Singh S. Rajkumar Kuldeep Singh Ashok Kumar Dhammaprakash Pandhari Wankhede |
| author_sort | Ankit Saroha |
| collection | DOAJ |
| description | Flaxseed/linseed is an important oilseed crop having applications in the food, nutraceutical, and paint industry. Seed weight is one of the most crucial determinants of seed yield in linseed. Here, quantitative trait nucleotides (QTNs) associated with thousand-seed weight (TSW) have been identified using multi-locus genome-wide association study (ML-GWAS). Field evaluation was carried out in five environments in multi-year-location trials. SNP genotyping information of the AM panel of 131 accessions comprising 68,925 SNPs was employed for ML-GWAS. From the six ML-GWAS methods employed, five methods helped identify a total of 84 unique significant QTNs for TSW. QTNs identified in ≥ 2 methods/environments were designated as stable QTNs. Accordingly, 30 stable QTNs have been identified for TSW accounting up to 38.65% trait variation. Alleles with positive effect on trait were analyzed for 12 strong QTNs with r2 ≥ 10.00%, which showed significant association of specific alleles with higher trait value in three or more environments. A total of 23 candidate genes have been identified for TSW, which included B3 domain-containing transcription factor, SUMO-activating enzyme, protein SCARECROW, shaggy-related protein kinase/BIN2, ANTIAUXIN-RESISTANT 3, RING-type E3 ubiquitin transferase E4, auxin response factors, WRKY transcription factor, and CBS domain-containing protein. In silico expression analysis of candidate genes was performed to validate their possible role in different stages of seed development process. The results from this study provide significant insight and elevate our understanding on genetic architecture of TSW trait in linseed. |
| first_indexed | 2024-03-13T07:54:45Z |
| format | Article |
| id | doaj.art-139658cb4ff84b9aae51f885ca95103e |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-13T07:54:45Z |
| publishDate | 2023-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-139658cb4ff84b9aae51f885ca95103e2023-06-02T05:48:52ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-06-011410.3389/fpls.2023.11667281166728Genetic dissection of thousand-seed weight in linseed (Linum usitatissimum L.) using multi-locus genome-wide association studyAnkit Saroha0Sunil S. Gomashe1Vikender Kaur2Deepa Pal3Shraddha Ujjainwal4J. Aravind5Mamta Singh6S. Rajkumar7Kuldeep Singh8Ashok Kumar9Dhammaprakash Pandhari Wankhede10Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaICAR-National Bureau of Plant Genetic Resources, Regional Station Akola, Maharashtra, IndiaDivision of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaICAR-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaFlaxseed/linseed is an important oilseed crop having applications in the food, nutraceutical, and paint industry. Seed weight is one of the most crucial determinants of seed yield in linseed. Here, quantitative trait nucleotides (QTNs) associated with thousand-seed weight (TSW) have been identified using multi-locus genome-wide association study (ML-GWAS). Field evaluation was carried out in five environments in multi-year-location trials. SNP genotyping information of the AM panel of 131 accessions comprising 68,925 SNPs was employed for ML-GWAS. From the six ML-GWAS methods employed, five methods helped identify a total of 84 unique significant QTNs for TSW. QTNs identified in ≥ 2 methods/environments were designated as stable QTNs. Accordingly, 30 stable QTNs have been identified for TSW accounting up to 38.65% trait variation. Alleles with positive effect on trait were analyzed for 12 strong QTNs with r2 ≥ 10.00%, which showed significant association of specific alleles with higher trait value in three or more environments. A total of 23 candidate genes have been identified for TSW, which included B3 domain-containing transcription factor, SUMO-activating enzyme, protein SCARECROW, shaggy-related protein kinase/BIN2, ANTIAUXIN-RESISTANT 3, RING-type E3 ubiquitin transferase E4, auxin response factors, WRKY transcription factor, and CBS domain-containing protein. In silico expression analysis of candidate genes was performed to validate their possible role in different stages of seed development process. The results from this study provide significant insight and elevate our understanding on genetic architecture of TSW trait in linseed.https://www.frontiersin.org/articles/10.3389/fpls.2023.1166728/fulllinseedflaxseedseed weightgenome-wide association studiesquantitative trait nucleotidescandidate genes |
| spellingShingle | Ankit Saroha Sunil S. Gomashe Vikender Kaur Deepa Pal Shraddha Ujjainwal J. Aravind Mamta Singh S. Rajkumar Kuldeep Singh Ashok Kumar Dhammaprakash Pandhari Wankhede Genetic dissection of thousand-seed weight in linseed (Linum usitatissimum L.) using multi-locus genome-wide association study Frontiers in Plant Science linseed flaxseed seed weight genome-wide association studies quantitative trait nucleotides candidate genes |
| title | Genetic dissection of thousand-seed weight in linseed (Linum usitatissimum L.) using multi-locus genome-wide association study |
| title_full | Genetic dissection of thousand-seed weight in linseed (Linum usitatissimum L.) using multi-locus genome-wide association study |
| title_fullStr | Genetic dissection of thousand-seed weight in linseed (Linum usitatissimum L.) using multi-locus genome-wide association study |
| title_full_unstemmed | Genetic dissection of thousand-seed weight in linseed (Linum usitatissimum L.) using multi-locus genome-wide association study |
| title_short | Genetic dissection of thousand-seed weight in linseed (Linum usitatissimum L.) using multi-locus genome-wide association study |
| title_sort | genetic dissection of thousand seed weight in linseed linum usitatissimum l using multi locus genome wide association study |
| topic | linseed flaxseed seed weight genome-wide association studies quantitative trait nucleotides candidate genes |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1166728/full |
| work_keys_str_mv | AT ankitsaroha geneticdissectionofthousandseedweightinlinseedlinumusitatissimumlusingmultilocusgenomewideassociationstudy AT sunilsgomashe geneticdissectionofthousandseedweightinlinseedlinumusitatissimumlusingmultilocusgenomewideassociationstudy AT vikenderkaur geneticdissectionofthousandseedweightinlinseedlinumusitatissimumlusingmultilocusgenomewideassociationstudy AT deepapal geneticdissectionofthousandseedweightinlinseedlinumusitatissimumlusingmultilocusgenomewideassociationstudy AT shraddhaujjainwal geneticdissectionofthousandseedweightinlinseedlinumusitatissimumlusingmultilocusgenomewideassociationstudy AT jaravind geneticdissectionofthousandseedweightinlinseedlinumusitatissimumlusingmultilocusgenomewideassociationstudy AT mamtasingh geneticdissectionofthousandseedweightinlinseedlinumusitatissimumlusingmultilocusgenomewideassociationstudy AT srajkumar geneticdissectionofthousandseedweightinlinseedlinumusitatissimumlusingmultilocusgenomewideassociationstudy AT kuldeepsingh geneticdissectionofthousandseedweightinlinseedlinumusitatissimumlusingmultilocusgenomewideassociationstudy AT ashokkumar geneticdissectionofthousandseedweightinlinseedlinumusitatissimumlusingmultilocusgenomewideassociationstudy AT dhammaprakashpandhariwankhede geneticdissectionofthousandseedweightinlinseedlinumusitatissimumlusingmultilocusgenomewideassociationstudy |