1
|
Yildiz M, Altaf MT, Baloch FS, Koçak M, Sadık G, Kuzğun C, Nadeem MA, Ali F, Bedir M, Tunçtürk M. Assessment of genetic diversity among 131 safflower (Carthamus tinctorius L.) accessions using peroxidase gene polymorphism (POGP) markers. Mol Biol Rep 2022; 49:6531-6539. [PMID: 35665441 DOI: 10.1007/s11033-022-07485-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Safflower (Carthamus tinctorius L.) is an old oilseed crop with a 1.4 GB genome size and its flowers are used for food coloring, dyes and pharmaceutical industries. It was domesticated from its putative wild ancestor Carthamus palestinus about forty-five hundred years ago in the fertile crescent region.The current study was aimed to determine the genetic diversity, population structure and to check the applicability of iPBS-retrotransposons markers. METHODS AND RESULTS Eleven POGP primers yielded 70 bands of which 61 were highly polymorphic with 87.14% polymorphism. A great level of genetic variation was examined with higher values of overall gene diversity (0.27), genetic distance (0.53), number of effective alleles (1.46), Shannon's information index (0.41) and polymorphism information contents (0.71). Analysis of molecular variance revealed high genetic variation with 79% within the population. The STRUCTURE, PCoA and Neighbor-joining analysis separated the safflower germplasm into 2 major populations and 1 un-classified population. The accessions which were from Asian countries i.e., China, Afghanistan, Turkey, Iran and Pakistan were genetically similar and clustered together in both populations A and B. The maximum genetic distance was measured 0.88 between Pakistan 26 x Pakistan 24. CONCLUSION Findings of this research such as maximum diversity indices, higher PIC values showed the effectiveness and utility of POGP markers for the evaluation of genetic relationships among safflower accessions. The results of this study also showed that POGP markers are less effective compared to ISSRs, iPBS-retrotransposons and DArTSeq markers. AMOVA showed high genetic variation (79%) within a population and maximum genetic distance was found between the accessions Pakistan 26- Pakistan 24 and may be suggested as candidate parents for future breeding activities of safflower. The accessions from the fertile crescent region were clustered together and proved the origin of safflower domestication. This study highlights genetic variation among safflower germplasm and could be helpfull for parental selection and planning for future breeding programs.
Collapse
Affiliation(s)
- Mehtap Yildiz
- Department of Agricultural Biotechnology, Faculty of Agriculture, Van Yuzuncu Yil University, 65080, Van, Turkey.
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey.
| | - Metin Koçak
- Department of Agricultural Biotechnology, Faculty of Agriculture, Van Yuzuncu Yil University, 65080, Van, Turkey
| | - Gökhan Sadık
- Department of Agricultural Biotechnology, Faculty of Agriculture, Van Yuzuncu Yil University, 65080, Van, Turkey
| | - Cansu Kuzğun
- Department of Agricultural Biotechnology, Faculty of Agriculture, Van Yuzuncu Yil University, 65080, Van, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Fawad Ali
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Murat Tunçtürk
- Department of Field Crops, Faculty of Agriculture, Van Yuzuncu Yil University, 65080, Van, Turkey
| |
Collapse
|
2
|
Zhao H, Li Y, Petkowski J, Kant S, Hayden MJ, Daetwyler HD. Genomic prediction and genomic heritability of grain yield and its related traits in a safflower genebank collection. THE PLANT GENOME 2021; 14:e20064. [PMID: 33140563 DOI: 10.1002/tpg2.20064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 05/28/2023]
Abstract
Safflower, a minor oilseed crop, is gaining increased attention for food and industrial uses. Safflower genebank collections are an important genetic resource for crop enhancement and future breeding programs. In this study, we investigated the population structure of a safflower collection sourced from the Australian Grain Genebank and assessed the potential of genomic prediction (GP) to evaluate grain yield and related traits using single and multi-site models. Prediction accuracies (PA) of genomic best linear unbiased prediction (GBLUP) from single site models ranged from 0.21 to 0.86 for all traits examined and were consistent with estimated genomic heritability (h2 ), which varied from low to moderate across traits. We generally observed a low level of genome × environment interactions (g × E). Multi-site g × E GBLUP models only improved PA for accessions with at least some phenotypes in the training set. We observed that relaxing quality filtering parameters for genotype-by-sequencing (GBS), such as missing genotype call rate, did not affect PA but upwardly biased h2 estimation. Our results indicate that GP is feasible in safflower evaluation and is potentially a cost-effective tool to facilitate fast introgression of desired safflower trait variation from genebank germplasm into breeding lines.
Collapse
Affiliation(s)
- Huanhuan Zhao
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3400, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Yongjun Li
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Joanna Petkowski
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3400, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Melbourne, VIC, Australia
| | - Matthew J Hayden
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Hans D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| |
Collapse
|
3
|
Hassani SMR, Talebi R, Pourdad SS, Naji AM, Fayaz F. Morphological description, genetic diversity and population structure of safflower ( Carthamus tinctorius L.) mini core collection using SRAP and SSR markers. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1818620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
| | - Reza Talebi
- Department of Agronomy and Plant Breeding, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran
| | - Sayyed Saeid Pourdad
- Dryland Agricultural Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Kermanshah, Iran
| | - Amir Mohammad Naji
- Department of Plant Breeding, College of Agriculture, Shahed University, Tehran, Iran
| | - Farzad Fayaz
- Department of Agronomy and Plant Breeding, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran
| |
Collapse
|
4
|
Golkar P, Mokhtari N. Molecular diversity assessment of a world collection of safflower genotypes by SRAP and SCoT molecular markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:1261-1271. [PMID: 30425439 PMCID: PMC6214440 DOI: 10.1007/s12298-018-0545-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/06/2018] [Accepted: 05/02/2018] [Indexed: 05/05/2023]
Abstract
Safflower (Carthamus tinctorius L.) is considered as an oil crop that is rich in medicinal and industrial properties. In this study, the genetic diversity of safflower was assessed using 12 polymorphic sequence-related amplified polymorphism (SRAPs) and 11 polymorphic start codon targeted (SCoT) markers in 100 genotypes of safflower gathered from different geographical regions of the world. The 23 primers generated a total of 227 polymorphism fragments with a mean of 68.2% within the range of 3 (SCoT 31 and SCoT 35) to 13 (SCoT 35) bands per primer. Polymorphism per primer ranged between 100% (in Me4-Em1) and 18.1% (in SCoT19), with an average of 36.76%. The polymorphism information contents of the SRAP and SCoT markers were 0.35 and 0.30, respectively, indicating that SRAP markers were more effective than SCoT markers for assessing the degree of genetic diversity of the safflower. The results of the analysis of molecular variance showed a significant difference across cultivated safflower genotypes possessing a high intra-population variation. The examined accessions were categorized into five clusters based on similarity centers: the Middle East containing Iran, Iraq, Turkey, and Tajikistan; the Far East, including India, Pakistan, and Korea; Europe; the American continent; and Africa, including Egypt, Sudan and Libya. The present study shows the effectiveness of employing the mixture of SRAP and SCoT markers in the identification of safflower genetic diversity that would be useful for conservation and population genetics of safflower improvement in further studies.
Collapse
Affiliation(s)
- Pooran Golkar
- Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, 84156 83111 Iran
| | - Niloofar Mokhtari
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156 83111 Iran
| |
Collapse
|