Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)
Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleo...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2021-06-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/11593.pdf |
| _version_ | 1797420795810545664 |
|---|---|
| author | Vipin Tomar Guriqbal Singh Dhillon Daljit Singh Ravi Prakash Singh Jesse Poland Arun Kumar Joshi Budhi Sagar Tiwari Uttam Kumar |
| author_facet | Vipin Tomar Guriqbal Singh Dhillon Daljit Singh Ravi Prakash Singh Jesse Poland Arun Kumar Joshi Budhi Sagar Tiwari Uttam Kumar |
| author_sort | Vipin Tomar |
| collection | DOAJ |
| description | Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs. |
| first_indexed | 2024-03-09T07:06:38Z |
| format | Article |
| id | doaj.art-c8e07f4694bd458d82ce1aae6f4cd886 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:06:38Z |
| publishDate | 2021-06-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-c8e07f4694bd458d82ce1aae6f4cd8862023-12-03T09:30:26ZengPeerJ Inc.PeerJ2167-83592021-06-019e1159310.7717/peerj.11593Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)Vipin Tomar0Guriqbal Singh Dhillon1Daljit Singh2Ravi Prakash Singh3Jesse Poland4Arun Kumar Joshi5Budhi Sagar Tiwari6Uttam Kumar7Borlaug Institute for South Asia, New Delhi, Delhi, IndiaDepartment of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, IndiaThe Climate Corporation, Bayer Crop Science, Creve Coeur, MO, USAGlobal Wheat Program, International Maize and Wheat Improvement Centre, Texcoco, MexicoDepartment of Plant Pathology, Kansas State University, Manhattan, KS, United States of AmericaBorlaug Institute for South Asia, New Delhi, Delhi, IndiaDepartment of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, Gandhinagar, Gujarat, IndiaBorlaug Institute for South Asia, New Delhi, Delhi, IndiaGenetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.https://peerj.com/articles/11593.pdfWheatGenotyping-by-sequencing (GBS) SNPGenetic diversityPopulation structureAnalysis of molecular variance (AMOVA) |
| spellingShingle | Vipin Tomar Guriqbal Singh Dhillon Daljit Singh Ravi Prakash Singh Jesse Poland Arun Kumar Joshi Budhi Sagar Tiwari Uttam Kumar Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.) PeerJ Wheat Genotyping-by-sequencing (GBS) SNP Genetic diversity Population structure Analysis of molecular variance (AMOVA) |
| title | Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.) |
| title_full | Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.) |
| title_fullStr | Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.) |
| title_full_unstemmed | Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.) |
| title_short | Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.) |
| title_sort | elucidating snp based genetic diversity and population structure of advanced breeding lines of bread wheat triticum aestivum l |
| topic | Wheat Genotyping-by-sequencing (GBS) SNP Genetic diversity Population structure Analysis of molecular variance (AMOVA) |
| url | https://peerj.com/articles/11593.pdf |
| work_keys_str_mv | AT vipintomar elucidatingsnpbasedgeneticdiversityandpopulationstructureofadvancedbreedinglinesofbreadwheattriticumaestivuml AT guriqbalsinghdhillon elucidatingsnpbasedgeneticdiversityandpopulationstructureofadvancedbreedinglinesofbreadwheattriticumaestivuml AT daljitsingh elucidatingsnpbasedgeneticdiversityandpopulationstructureofadvancedbreedinglinesofbreadwheattriticumaestivuml AT raviprakashsingh elucidatingsnpbasedgeneticdiversityandpopulationstructureofadvancedbreedinglinesofbreadwheattriticumaestivuml AT jessepoland elucidatingsnpbasedgeneticdiversityandpopulationstructureofadvancedbreedinglinesofbreadwheattriticumaestivuml AT arunkumarjoshi elucidatingsnpbasedgeneticdiversityandpopulationstructureofadvancedbreedinglinesofbreadwheattriticumaestivuml AT budhisagartiwari elucidatingsnpbasedgeneticdiversityandpopulationstructureofadvancedbreedinglinesofbreadwheattriticumaestivuml AT uttamkumar elucidatingsnpbasedgeneticdiversityandpopulationstructureofadvancedbreedinglinesofbreadwheattriticumaestivuml |