Volume 14, Issue 44 (12-2022)
jcb 2022, 14(44): 46-55 |
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Ghanavati M, Houshmand S, Albrecht S, Otto L. (2022). Genome Wide Assosiation Study (GWAS) in some Chamomile Genotypes (Matricaria chamomilla L.) using Morphological, Phenological Traits. jcb. 14(44), 46-55. doi:10.52547/jcb.14.44.46
URL: http://jcb.sanru.ac.ir/article-1-1357-en.html
URL: http://jcb.sanru.ac.ir/article-1-1357-en.html
Department of Agriculture, Payame Noor University, Tehran, Iran
Abstract: (1608 Views)
Extended Abstract
Introduction and Objective: German chamomile is one of the most widely used medicinal plants in the world, and large amounts of its essential oil are used every year in the pharmaceutical, cosmetic, health, and food industries.
Medicinal plants have many applications in the treatment of humans, among which chamomile is one of the most valuable and widely used medicinal plants in the world. One of the most important breeding programs is the recognition of genetic diversity for the initial evaluation of plant masses. For this purpose, a study of genetic diversity and classification of experimental chamomile ecotypes was designed and implemented.
Material and methods: 46 native and foreign ecotypes of chamomile were evaluated in a randomized complete block design with four replications in the research farm of German Pharmaplant. Some of these ecotypes were collected from their natural growing areas and some were chamomile cultivars. For this purpose, some morphological, phenological and were evaluated. GWAS technique was used to investigate the relationship between markers and studied traits. In GWAS, Manhattan analysis and QQ plot diagram based on MLM and FarmCPU models were used to identify SNPs related to different morphological and biochemical traits.
Results: The results of Manhattan analysis and their validation with QQ plot diagram based on MLM and FarmCPU models led to the identification of SNPs related to the following traits in chamomile: Flowering time, intensity of plot green color, leaf surface state (smoothness and roughness), density of foliage part, branching style of sub-branches, type of lower branches of the plant, homogeneity of plot plants, plant height, presence or absence of large flower, flower diameter, plot flower number, number of days to flowering, plant fresh weight, plant dry weight, relative amount of stem anthocyanin, oil content, matricin, alpha-bisabolol, bisabolol oxide A, and bisabolone oxide to alpha-bisabolol ratio. The following markers were identified in this study: SNP with locus_161754-71 and log -Pvalue=10.35354 as the most relevant marker for flowering time trait, SNP with locus_136992-38 and log -Pvalue=6.5950 as the most relevant marker for green color of plot, SNP with locus_31850-95 and log -Pvalue=5.92567 as the most relevant marker for leaf surface (fine and rough) of plot, SNP with locus_136992-38 and log -Pvalue=6.5950 as the most relevant marker for density of the foliage part of plot, SNP with locus_35488-32 and log -Pvalue=8.0247 as the most relevant marker for status of sub-branches of plot, SNP with locus_139800-67 and log -Pvalue=8.438303 as the most relevant marker for status of lower branches of the plant, SNP with locus_135707-30 and log -Pvalue=11.4573 as the most relevant marker for height of plant, , SNP with locus_2494-70 and log -Pvalue=5.8867 as the most relevant marker for the flower diameter, Overall, we discovered the genetic structure in the chamomile ecotypes by using GBS and also identifed SNPs associated with some morpho-physiological. Therefore, the SNP markers identified in this GWAS study can be used for marker-assisted selection in chamomile breeding programs.
Conclusion: The SNP markers identified in this GWAS study, especially those with a higher economic aspect, can be used for marker-assisted selection in German chamomile breeding programs.
Introduction and Objective: German chamomile is one of the most widely used medicinal plants in the world, and large amounts of its essential oil are used every year in the pharmaceutical, cosmetic, health, and food industries.
Medicinal plants have many applications in the treatment of humans, among which chamomile is one of the most valuable and widely used medicinal plants in the world. One of the most important breeding programs is the recognition of genetic diversity for the initial evaluation of plant masses. For this purpose, a study of genetic diversity and classification of experimental chamomile ecotypes was designed and implemented.
Material and methods: 46 native and foreign ecotypes of chamomile were evaluated in a randomized complete block design with four replications in the research farm of German Pharmaplant. Some of these ecotypes were collected from their natural growing areas and some were chamomile cultivars. For this purpose, some morphological, phenological and were evaluated. GWAS technique was used to investigate the relationship between markers and studied traits. In GWAS, Manhattan analysis and QQ plot diagram based on MLM and FarmCPU models were used to identify SNPs related to different morphological and biochemical traits.
Results: The results of Manhattan analysis and their validation with QQ plot diagram based on MLM and FarmCPU models led to the identification of SNPs related to the following traits in chamomile: Flowering time, intensity of plot green color, leaf surface state (smoothness and roughness), density of foliage part, branching style of sub-branches, type of lower branches of the plant, homogeneity of plot plants, plant height, presence or absence of large flower, flower diameter, plot flower number, number of days to flowering, plant fresh weight, plant dry weight, relative amount of stem anthocyanin, oil content, matricin, alpha-bisabolol, bisabolol oxide A, and bisabolone oxide to alpha-bisabolol ratio. The following markers were identified in this study: SNP with locus_161754-71 and log -Pvalue=10.35354 as the most relevant marker for flowering time trait, SNP with locus_136992-38 and log -Pvalue=6.5950 as the most relevant marker for green color of plot, SNP with locus_31850-95 and log -Pvalue=5.92567 as the most relevant marker for leaf surface (fine and rough) of plot, SNP with locus_136992-38 and log -Pvalue=6.5950 as the most relevant marker for density of the foliage part of plot, SNP with locus_35488-32 and log -Pvalue=8.0247 as the most relevant marker for status of sub-branches of plot, SNP with locus_139800-67 and log -Pvalue=8.438303 as the most relevant marker for status of lower branches of the plant, SNP with locus_135707-30 and log -Pvalue=11.4573 as the most relevant marker for height of plant, , SNP with locus_2494-70 and log -Pvalue=5.8867 as the most relevant marker for the flower diameter, Overall, we discovered the genetic structure in the chamomile ecotypes by using GBS and also identifed SNPs associated with some morpho-physiological. Therefore, the SNP markers identified in this GWAS study can be used for marker-assisted selection in chamomile breeding programs.
Conclusion: The SNP markers identified in this GWAS study, especially those with a higher economic aspect, can be used for marker-assisted selection in German chamomile breeding programs.
Type of Study: Research |
Subject:
اصلاح نباتات مولكولي
Received: 2022/03/7 | Revised: 2023/02/22 | Accepted: 2022/05/17 | Published: 2023/01/1
Received: 2022/03/7 | Revised: 2023/02/22 | Accepted: 2022/05/17 | Published: 2023/01/1
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