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Naqvi SAH, Abbas A, Farhan M, Kiran R, Hassan Z, Mehmood Y, Ali A, Ahmed N, Hassan MZ, Alrefaei AF, Ölmez F, Yang SH, Baloch FS. Unveiling the Genetic Tapestry: Exploring Rhizoctonia solani AG-3 Anastomosis Groups in Potato Crops across Borders. Plants (Basel) 2024; 13:715. [PMID: 38475561 DOI: 10.3390/plants13050715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
The current study was carried out to screen 10 isolates (ARS-01-ARS-10) of Rhizoctonia. solani from potato tubers cv. Kuroda, which were collected from various potato fields in Multan, Pakistan. The isolates were found to be morphologically identical, as the hyphae exhibit the production of branches at right angles and acute angles often accompanied by septum near the emerging branches. Anastomosis grouping showed that these isolates belonged to AG-3. A pathogenicity test was performed against the susceptible Kuroda variety and among the isolates, ARS-05 exhibited the highest mean severity score of approximately 5.43, followed by ARS-09, which showed a mean severity score of about 3.67, indicating a moderate level of severity. On the lower end of the severity scale, isolates ARS-06 and ARS-07 displayed mean severity scores of approximately 0.53 and 0.57, respectively, suggesting minimal symptom severity. These mean severity scores offer insights into the varying degrees of symptom expression among the different isolates of R. solani under examination. PCoA indicates that the severe isolate causing black scurf on the Kuroda variety was AG-3. A comprehensive analysis of the distribution, genetic variability, and phylogenetic relationships of R. solani anastomosis groups (AGs) related to potato crops across diverse geographic regions was also performed to examine AG prevalence in various countries. AG-3 was identified as the most widespread group, prevalent in Sweden, China, and the USA. AG-5 showed prominence in Sweden and the USA, while AG-2-1 exhibited prevalence in China and Japan. The phylogenetic analysis unveiled two different clades: Clade I comprising AG-3 and Clade II encompassing AG-2, AG-4, and AG-5, further subdivided into three subclades. Although AGs clustered together regardless of origin, their genetic diversity revealed complex evolutionary patterns. The findings pave the way for region-specific disease management strategies to combat R. solani's impact on potato crops.
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Affiliation(s)
- Syed Atif Hasan Naqvi
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Aqleem Abbas
- Department of Agriculture and Food Technology, Karakoram International University, Gilgit Baltistan, Gilgit 15100, Pakistan
| | - Muhammad Farhan
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Rafia Kiran
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Zeshan Hassan
- College of Agriculture, University of Layyah, Layyah 31200, Pakistan
| | - Yasir Mehmood
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Amjad Ali
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Niaz Ahmed
- Department of Soil Science, Bahauddin Zakariya University, Multan 60800, Pakistan
| | | | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Fatih Ölmez
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Seung-Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, Yenişehir, Mersin 33343, Türkiye
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Ashraf H, Ghouri F, Baloch FS, Nadeem MA, Fu X, Shahid MQ. Hybrid Rice Production: A Worldwide Review of Floral Traits and Breeding Technology, with Special Emphasis on China. Plants (Basel) 2024; 13:578. [PMID: 38475425 DOI: 10.3390/plants13050578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/26/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024]
Abstract
Rice is an important diet source for the majority of the world's population, and meeting the growing need for rice requires significant improvements at the production level. Hybrid rice production has been a significant breakthrough in this regard, and the floral traits play a major role in the development of hybrid rice. In grass species, rice has structural units called florets and spikelets and contains different floret organs such as lemma, palea, style length, anther, and stigma exsertion. These floral organs are crucial in enhancing rice production and uplifting rice cultivation at a broader level. Recent advances in breeding techniques also provide knowledge about different floral organs and how they can be improved by using biotechnological techniques for better production of rice. The rice flower holds immense significance and is the primary focal point for researchers working on rice molecular biology. Furthermore, the unique genetics of rice play a significant role in maintaining its floral structure. However, to improve rice varieties further, we need to identify the genomic regions through mapping of QTLs (quantitative trait loci) or by using GWAS (genome-wide association studies) and their validation should be performed by developing user-friendly molecular markers, such as Kompetitive allele-specific PCR (KASP). This review outlines the role of different floral traits and the benefits of using modern biotechnological approaches to improve hybrid rice production. It focuses on how floral traits are interrelated and their possible contribution to hybrid rice production to satisfy future rice demand. We discuss the significance of different floral traits, techniques, and breeding approaches in hybrid rice production. We provide a historical perspective of hybrid rice production and its current status and outline the challenges and opportunities in this field.
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Affiliation(s)
- Humera Ashraf
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin 33100, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Xuelin Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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Yilmaz H, Özer G, Baloch FS, Çiftçi V, Chung YS, Sun HJ. Genome-Wide Identification and Expression Analysis of MTP (Metal Ion Transport Proteins) Genes in the Common Bean. Plants (Basel) 2023; 12:3218. [PMID: 37765382 PMCID: PMC10535811 DOI: 10.3390/plants12183218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
MTP/CDF carriers, called metal ion transport proteins, act as substrates for the transmission of micronutrients such as iron (Fe), zinc (Zn), and manganese (Mn) to membrane carriers in plants. In this study, genome-wide analysis of the MTP gene family in the common bean genome, expression analysis of the PvMTP4, PvMTP5, and PvMTP12 genes after Fe and Zn treatments, and the effects of Fe and Zn applications on iron and zinc content were investigated. This study used common bean genotypes assumed to have high or low Fe and Zn accumulation ability. PvMTP genes were defined as containing conserved catalytic domains with molecular weights and protein lengths ranging from 41.35 to 91.05 kDa and from 369 to 813 amino acids (aa), respectively. As a result of the phylogenetic analysis, three main clusters containing seven subgroups were formed. In this study, the first characterization of the MTP gene family of beans was performed, and the responses of three different PvMTP genes in the Zn-CDF group to Fe and Zn applications were revealed. The obtained findings are thought to constitute pioneering resources for future research on common bean biofortification studies, plant breeding related to Fe and Zn, and the functional characterization of the MTP gene family.
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Affiliation(s)
- Hilal Yilmaz
- Plant and Animal Production Program, Izmit Vocational School, Kocaeli University, Kocaeli 41285, Türkiye;
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu 14030, Türkiye;
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu 14030, Türkiye;
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu 14030, Türkiye;
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju 63243, Republic of Korea;
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 63243, Republic of Korea;
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Abbas A, Ali A, Hussain A, Ali A, Alrefaei AF, Naqvi SAH, Rao MJ, Mubeen I, Farooq T, Ölmez F, Baloch FS. Assessment of Genetic Variability and Evolutionary Relationships of Rhizoctonia solani Inherent in Legume Crops. Plants (Basel) 2023; 12:2515. [PMID: 37447079 DOI: 10.3390/plants12132515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]
Abstract
Rhizoctonia solani is one of the most common soil-borne fungal pathogens of legume crops worldwide. We collected rDNA-ITS sequences from NCBI GenBank, and the aim of this study was to examine the genetic diversity and phylogenetic relationships of various R. solani anastomosis groups (AGs) that are commonly associated with grain legumes (such as soybean, common bean, pea, peanut, cowpea, and chickpea) and forage legumes (including alfalfa and clover). Soybean is recognized as a host for multiple AGs, with AG-1 and AG-2 being extensively investigated. This is evidenced by the higher representation of sequences associated with these AGs in the NCBI GenBank. Other AGs documented in soybean include AG-4, AG-7, AG-11, AG-5, AG-6, and AG-9. Moreover, AG-4 has been extensively studied concerning its occurrence in chickpea, pea, peanut, and alfalfa. Research on the common bean has been primarily focused on AG-2, AG-4, and AG-1. Similarly, AG-1 has been the subject of extensive investigation in clover and cowpea. Collectively, AG-1, AG-2, and AG-4 have consistently been identified and studied across these diverse legume crops. The phylogenetic analysis of R. solani isolates across different legumes indicates that the distinct clades or subclades formed by the isolates correspond to their specific anastomosis groups (AGs) and subgroups, rather than being determined by their host legume crop. Additionally, there is a high degree of sequence similarity among isolates within the same clade or subclade. Principal coordinate analysis (PCoA) further supports this finding, as isolates belonging to the same AGs and/or subgroups cluster together, irrespective of their host legume. Therefore, the observed clustering of R. solani AGs and subgroups without a direct association with the host legume crop provides additional support for the concept of AGs in understanding the genetic relationships and evolution of R. solani.
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Affiliation(s)
- Aqleem Abbas
- Department of Agriculture and Food Technology, Karakoram International University (KIU), Gilgit 15100, Pakistan
| | - Amjad Ali
- Department of Agriculture and Food Technology, Karakoram International University (KIU), Gilgit 15100, Pakistan
| | - Azhar Hussain
- Department of Agriculture and Food Technology, Karakoram International University (KIU), Gilgit 15100, Pakistan
| | - Amjad Ali
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Syed Atif Hasan Naqvi
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Muhammad Junaid Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530021, China
| | - Iqra Mubeen
- State Key Laboratory of Rice Biology, and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tahir Farooq
- Plant Protection Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, China
| | - Fatih Ölmez
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Faheem Shehzad Baloch
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
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Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
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Baran N, Shimira F, Nadeem MA, Altaf MT, Andirman M, Baloch FS, Gültekin Temiz M. Exploring the genetic diversity and population structure of upland cotton germplasm by iPBS-retrotransposons markers. Mol Biol Rep 2023; 50:4799-4811. [PMID: 37031323 DOI: 10.1007/s11033-023-08399-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/22/2023] [Indexed: 04/10/2023]
Abstract
BACKGROUND Upland cotton is one of the utmost significant strategic fiber crops, and play a vital role in the global textile industry. METHODS AND RESULTS A total of 128 genotypes comprised Gossypium hirsutum L, Gossypium barbadense L., and pure lines were used to examine genetic diversity using iPBS-retrotransposon markers system. Eleven highly polymorphic primers yielded 287 bands and 99.65% polymorphism was recorded. The mean polymorphism information content was estimated at 0.297 and the average diversity indices for the effective number of alleles, Shannon's information index, and overall gene diversity were 1.481, 0.443, and 0.265, respectively. The analysis of molecular variance (AMOVA) revealed that 69% of the genetic variation was within the population. A model-based STRUCTURE algorithm divided the entire germplasm into four populations and one un-classified population, the genotypes G42 (originating in Egypt) and G128 (originating in the United States), showed the highest genetic distance (0.996) so these genotypes could be suggested for breeding programs as parental lines. CONCLUSIONS This is the first investigation using an iPBS-retrotransposon marker system to examine the genetic diversity and population structure of upland cotton germplasm. The rich diversity found in upland cotton germplasm could be exploited as a genetic resource when developing breeding programs and could also help with efforts to breed cotton around the world. These findings also show the applicability and effectiveness of iPBS-retrotransposons for the molecular characterization of cotton germplasm.
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Affiliation(s)
- Nurettin Baran
- Faculty of Applied Sciences, Department of Plant Production and Technologies, Mus Alparslan University, Mus, Turkey
| | - Flavien Shimira
- Department of Horticulture, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Mehtap Andirman
- Department of Plant and Animal Production, Organic Agriculture Program Batman, Batman University Sason Vocational School, Batman, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey.
| | - Mefhar Gültekin Temiz
- Faculty of Agriculture, Department of Field Crops, Dicle University, Diyarbakır, Turkey
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Ali A, Umar UUD, Naqvi SAH, Shakeel MT, Tahir MN, Khan MF, Altaf MT, Ölmez F, Dababat AA, Haq ZU, Nadeem MA, Hatipoğlu R, Baloch FS, Chung YS. Molecular characterization of divergent isolates of Citrus bent leaf viroid (CBLVd) from citrus cultivars of Punjab, Pakistan. Front Genet 2023; 13:1104635. [PMID: 36712883 PMCID: PMC9878587 DOI: 10.3389/fgene.2022.1104635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Citrus viroid infection is emerging as a serious threat because of its efficient systemic movement within the host plant and its quick spread due to contaminated pruning tools. A survey was conducted to investigate the primary distribution and molecular characterization of Citrus bent leaf viroid (CBLVd) and its variants in different citrus cultivars. A total of 154 symptomatic citrus samples were collected and detected by RT‒PCR with newly designed specific primers with the incidence of 36.33%. During biological indexing study on Etrog citron, expressions of reduced leaf size, yellowing with a light green pattern, and bending were observed. Amplified products were sequenced and analyzed using a nucleotide BLAST search, which showed 98% homology with other CBLVd isolates. The results of the phylogenetic tree analysis showed the presence of two main groups (A and B), with the predominant variants of CBLVd, i.e., CVd-I-LSS (Citrus viroid Low Sequence Similarity) sequences, clustering in subgroup A1 along with newly detected CVd-I-LSS from Palestinian sweet lime (Citrus limettioides), which has been identified as a new host of CVd-I-LSS in Pakistan. Further analysis of the sequences in subgroup A1 showed that the variant of CVd-I-LSS infecting citrus cultivars had a close relationship with isolates reported from China, Japan, and Iran, which may have resulted from the exchange of planting material. This study also unveiled the variability in nucleotide sequences of CBLVd, which made it unable to be detected by old primers. The results of this study indicate that the widespread presence of divergent variants of CBLVd is a major concern for the citrus industry in Pakistan and other countries where virulent isolates of CBLVd are prevalent. These findings suggest the need for future research on effective management and quarantine measures to stop the spread of CBLVd.
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Affiliation(s)
- Amjad Ali
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan,Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | - Ummad ud Din Umar
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan,*Correspondence: Ummad ud Din Umar, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Syed Atif Hasan Naqvi
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan
| | | | - Muhammad Nouman Tahir
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera GhaziKhan, Punjab, Pakistan
| | - Muhammad Fahad Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera GhaziKhan, Punjab, Pakistan
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | - Fatih Ölmez
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | | | - Zia ul Haq
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, Kirsehir Ahi Evran Universitesi, Kirsehir, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey,*Correspondence: Ummad ud Din Umar, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yong Suk Chung
- Department of Field Crops, Faculty of Agriculture, Kirsehir Ahi Evran Universitesi, Kirsehir, Turkey,*Correspondence: Ummad ud Din Umar, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
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Çelik A, Emiralioğlu O, Yeken MZ, Çiftçi V, Özer G, Kim Y, Baloch FS, Chung YS. A novel study on bean common mosaic virus accumulation shows disease resistance at the initial stage of infection in Phaseolus vulgaris. Front Genet 2023; 14:1136794. [PMID: 37021006 PMCID: PMC10067576 DOI: 10.3389/fgene.2023.1136794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Accurate and early diagnosis of bean common mosaic virus (BCMV) in Phaseolus vulgaris tissues is critical since the pathogen can spread easily and have long-term detrimental effects on bean production. The use of resistant varieties is a key factor in the management activities of BCMV. The study reported here describes the development and application of a novel SYBR Green-based quantitative real-time PCR (qRT-PCR) assay targeting the coat protein gene to determine the host sensitivity to the specific NL-4 strain of BCMV. The technique showed high specificity, validated by melting curve analysis, without cross-reaction. Further, the symptoms development of twenty advanced common bean genotypes after mechanical BCMV-NL-4 infection was evaluated and compared. The results showed that common bean genotypes exhibit varying levels of host susceptibility to this BCMV strain. The YLV-14 and BRS-22 genotypes were determined as the most resistant and susceptible genotypes, respectively, in terms of aggressiveness of symptoms. The accumulation of BCMV was analyzed in the resistant and susceptible genotypes 3, 6, and 9 days following the inoculation by the newly developed qRT-PCR. The mean cycle threshold (Ct) values showed that the viral titer was significantly lower in YLV-14, which was evident in both root and leaf 3 days after the inoculation. The qRT-PCR thus facilitated an accurate, specific, and feasible assessment of BCMV accumulation in bean tissues even in low virus titers, allowing novel clues in selecting resistant genotypes in the early stages of infection, which is critical for disease management. To the best of our knowledge, this is the first study of a successfully performed qRT-PCR to estimate BCMV quantification.
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Affiliation(s)
- Ali Çelik
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Orkun Emiralioğlu
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yoonha Kim
- Laboratory of Crop Production, Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
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Ali A, Altaf MT, Nadeem MA, Karaköy T, Shah AN, Azeem H, Baloch FS, Baran N, Hussain T, Duangpan S, Aasim M, Boo KH, Abdelsalam NR, Hasan ME, Chung YS. Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes. Front Plant Sci 2022; 13:952759. [PMID: 36247536 PMCID: PMC9554552 DOI: 10.3389/fpls.2022.952759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.
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Affiliation(s)
- Amjad Ali
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Hajra Azeem
- Department of Plant Pathology, Faculty of Agricultural Sciences & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Nurettin Baran
- Bitkisel Uretim ve Teknolojileri Bolumu, Uygulamali Bilimler Faku Itesi, Mus Alparslan Universitesi, Mus, Turkey
| | - Tajamul Hussain
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Saowapa Duangpan
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Kyung-Hwan Boo
- Subtropical/Tropical Organism Gene Bank, Department of Biotechnology, College of Applied Life Science, Jeju National University, Jeju, South Korea
| | - Nader R. Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Mohamed E. Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, South Korea
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10
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Aasim M, Katirci R, Baloch FS, Mustafa Z, Bakhsh A, Nadeem MA, Ali SA, Hatipoğlu R, Çiftçi V, Habyarimana E, Karaköy T, Chung YS. Innovation in the Breeding of Common Bean Through a Combined Approach of in vitro Regeneration and Machine Learning Algorithms. Front Genet 2022; 13:897696. [PMID: 36092939 PMCID: PMC9451102 DOI: 10.3389/fgene.2022.897696] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Common bean is considered a recalcitrant crop for in vitro regeneration and needs a repeatable and efficient in vitro regeneration protocol for its improvement through biotechnological approaches. In this study, the establishment of efficient and reproducible in vitro regeneration followed by predicting and optimizing through machine learning (ML) models, such as artificial neural network algorithms, was performed. Mature embryos of common bean were pretreated with 5, 10, and 20 mg/L benzylaminopurine (BAP) for 20 days followed by isolation of plumular apice for in vitro regeneration and cultured on a post-treatment medium containing 0.25, 0.50, 1.0, and 1.50 mg/L BAP for 8 weeks. Plumular apice explants pretreated with 20 mg/L BAP exerted a negative impact and resulted in minimum shoot regeneration frequency and shoot count, but produced longer shoots. All output variables (shoot regeneration frequency, shoot counts, and shoot length) increased significantly with the enhancement of BAP concentration in the post-treatment medium. Interaction of the pretreatment × post-treatment medium revealed the need for a specific combination for inducing a high shoot regeneration frequency. Higher shoot count and shoot length were achieved from the interaction of 5 mg/L BAP × 1.00 mg/L BAP followed by 10 mg/L BAP × 1.50 mg/L BAP and 20 mg/L BAP × 1.50 mg/L BAP. The evaluation of data through ML models revealed that R2 values ranged from 0.32 to 0.58 (regeneration), 0.01 to 0.22 (shoot counts), and 0.18 to 0.48 (shoot length). On the other hand, the mean squared error values ranged from 0.0596 to 0.0965 for shoot regeneration, 0.0327 to 0.0412 for shoot count, and 0.0258 to 0.0404 for shoot length from all ML models. Among the utilized models, the multilayer perceptron model provided a better prediction and optimization for all output variables, compared to other models. The achieved results can be employed for the prediction and optimization of plant tissue culture protocols used for biotechnological approaches in a breeding program of common beans.
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Affiliation(s)
- Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Ramazan Katirci
- Department of Metallurgical and Materials Engineering, Faculty of Engineering and Natural Sciences, Sivas University of Science and Technology, Sivas, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
- *Correspondence: Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Zemran Mustafa
- Department of Plant Production and Technologies, Faculty of Agricultural Science and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Allah Bakhsh
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Seyid Amjad Ali
- Department of Information Systems and Technologies, Bilkent University, Ankara, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, South Korea
- *Correspondence: Faheem Shehzad Baloch, ; Yong Suk Chung,
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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12
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Naeem M, Abbas A, Ul-Allah S, Malik W, Baloch FS. Comparative genetic, biochemical and physiological analysis of sodium and chlorine in wheat. Mol Biol Rep 2022; 49:9715-9724. [PMID: 35513633 DOI: 10.1007/s11033-022-07453-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 04/05/2022] [Indexed: 11/29/2022]
Abstract
Plant with a great diversity shows several responses towards the biotic and abiotic stresses. Among these abiotic stresses, salinity is the main damaging factor as it reduces the yield of wheat plant with moderate salt tolerance. For its survival, plant undergoes through some genetic, biochemical and physiological changes to tackle the stress. This review mainly describes the conditions where various ions present in the soil, especially sodium and chlorine, enter into the plant and the genes or proteins involved with survival mechanism against the damage in plants. Salt stress causes alteration in enzymatic activity and Photosynthesis, oxidative stress, damage of cellular structure and components and ionic imbalance. Ion toxicity stress occur due to accumulation of excessive sodium ion and chloride ion. Transcriptional factors TaPIMP, TaSRG and TaMYBsdu 1 play key role in gene expression mechanism to overcome the stress. High affinity potassium transporter gene family is responsible for salt tolerance in wheat plant. HKT1;4 and HKT1;5 genes are responsible for Na exclusion in Triticum monococcum. Forty QTLs were found with the marker assisted selection in bread wheat for salinity tolerance and some morphological traits, 5 QTLs were related to sodium ion exclusion. In bread wheat, salt stress tolerance mechanism is mainly an exclusion of Na+ ions but also include K+ ion concentration. The salinity tolerant germplasm MW#293 provides an opportunity for the development of future salinity tolerant bread wheat.
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Affiliation(s)
- Muhammad Naeem
- Department of Plant Breeding and Genetics, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.
| | - Arshad Abbas
- Department of Plant Breeding and Genetics, Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Sami Ul-Allah
- College of Agriculture, Bahadur Sub Campus Layyah, Bahauddin Zakariya University, Multan, Pakistan
| | - Waqas Malik
- Department of Plant Breeding and Genetics, Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey.
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Baloch FS, Nadeem MA, Sönmez F, Habyarimana E, Mustafa Z, Karaköy T, Cömertpay G, Alsaleh A, Çiftçi V, Sun S, Chung G, Chung YS. Magnesium- a Forgotten Element: Phenotypic Variation and Genome Wide Association Study in Turkish Common Bean Germplasm. Front Genet 2022; 13:848663. [PMID: 35586571 PMCID: PMC9108430 DOI: 10.3389/fgene.2022.848663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022] Open
Abstract
Magnesium (Mg) is the fourth most abundant element in the human body and plays the role of cofactor for more than 300 enzymatic reactions. In plants, Mg is involved in various key physiological and biochemical processes like growth, development, photophosphorylation, chlorophyll formation, protein synthesis, and resistance to biotic and abiotic stresses. Keeping in view the importance of this element, the present investigation aimed to explore the Mg contents diversity in the seeds of Turkish common bean germplasm and to identify the genomic regions associated with this element. A total of 183 common bean accessions collected from 19 provinces of Turkey were used as plant material. Field experiments were conducted according to an augmented block design during 2018 in two provinces of Turkey, and six commercial cultivars were used as a control group. Analysis of variance depicted that Mg concentration among common bean accessions was statistically significant (p < 0.05) within each environment, however genotype × environment interaction was non-significant. A moderate level (0.60) of heritability was found in this study. Overall mean Mg contents for both environments varied from 0.33 for Nigde-Dermasyon to 1.52 mg kg−1 for Nigde-Derinkuyu landraces, while gross mean Mg contents were 0.92 mg kg−1. At the province level, landraces from Bolu were rich while the landraces from Bitlis were poor in seed Mg contents respectively. The cluster constellation plot divided the studied germplasm into two populations on the basis of their Mg contents. Marker-trait association was performed using a mixed linear model (Q + K) with a total of 7,900 DArTseq markers. A total of six markers present on various chromosomes (two at Pv01, and one marker at each chromosome i.e., Pv03, Pv07, Pv08, Pv11) showed statistically significant association for seed Mg contents. Among these identified markers, the DArT-3367607 marker present on chromosome Pv03 contributed to maximum phenotypic variation (7.5%). Additionally, this marker was found within a narrow region of previously reported markers. We are confident that the results of this study will contribute significantly to start common bean breeding activities using marker assisted selection regarding improved Mg contents.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
- *Correspondence: Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Ferit Sönmez
- Department of Seed Science and Technology, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Zemran Mustafa
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Turkey
| | - Ahmad Alsaleh
- Molecular Genetic Laboratory, Science and Technology Application and Research Center, Institute for Hemp Research, Yozgat Bozok University, Yozgat, Turkey
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, Chonnam, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, South Korea
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, South Korea
- *Correspondence: Faheem Shehzad Baloch, ; Yong Suk Chung,
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14
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Baloch FS, Guizado SJV, Altaf MT, Yüce I, Çilesiz Y, Bedir M, Nadeem MA, Hatipoglu R, Gómez JCC. Applicability of inter-primer binding site iPBS- retrotransposon marker system for the assessment of genetic diversity and population structure of Peruvian rosewood (Aniba rosaeodora Ducke) germplasm. Mol Biol Rep 2022; 49:2553-2564. [PMID: 35023008 DOI: 10.1007/s11033-021-07056-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/02/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Rosewood (Aniba rosaeodora Ducke), which has a great demand due to its essential oil globally, is an evergreen tree of the Amazon forests. Rosewood natural stands have been depleted through deforestation and the destruction of habitat. Currently, rosewood is included in the ICUN red list of endangered species. METHODS AND RESULTS The 11 highly polymorphic primers amplified total 305 bands of which 301 (98.69%) were polymorphic. The number of effective alleles (Ne), Shannon's information index (I), overall gene diversity (Ht), gene diversity (h), and polymorphism information content (PIC) were (1.562), (0.505), (0.330), (0.337) and (0.343), respectively. These diversity indices explored high genetic diversity in rosewood germplasm. Among studied germplasm, the Santa Marta population was found most diverse by reflecting higher values of diversity indices while the Zungarococha population was found least diverse. The analysis of molecular variance (AMOVA) revealed that 79% of the genetic variation was within the populations. The STRUCTURE algorithm, unweighted pair group with arithmetic mean (UPGMA), and principal coordinate's analysis (PCoA) separated all germplasms into different population groups according to their geographic locations. Santa Marta population was found more diverse by reflecting higher values of diversity indices. The maximum genetic distance (0.868) was found between the Huajoya-10 and Nanay-3. In this investigation, iPBS- retrotransposon marker system was used to explore the genetic diversity of Peruvian rosewood germplasm. CONCLUSIONS The results in this study such as higher genetic diversity indices, AMOVA (79%) within population and PIC value (0.343) showed the utility and reproducibility of iPBS-retrotransposons in this species successfully. The STRUCTURE algorithm separated the germplasms into six population groups according to their geographic locations. These results have valuable information for the conservation, management strategies and future breeding activities of rosewood.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey.
| | - Stalin Juan Vasquez Guizado
- Specialized Unit of Biotechnology, Research Center of Natural Resources of the Amazon, National University of the Peruvian Amazon, Iquitos, 1600, Peru
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Ilker Yüce
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Yeter Çilesiz
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Rustu Hatipoglu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, 01380, Adana, Turkey
| | - Juan Carlos Castro Gómez
- Specialized Unit of Biotechnology, Research Center of Natural Resources of the Amazon, National University of the Peruvian Amazon, Iquitos, 1600, Peru
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15
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Bashir SS, Hussain A, Hussain SJ, Wani OA, Zahid Nabi S, Dar NA, Baloch FS, Mansoor S. Plant drought stress tolerance: understanding its physiological, biochemical and molecular mechanisms. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2021.2020161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Sheikh Shanawaz Bashir
- Department of Botany, School of Chemical and Life Science, Jamia Hamdard University, New Delhi, India
| | - Anjuman Hussain
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Sofi Javed Hussain
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Owais Ali Wani
- Department of Soil Science, FoA, Wadura, Sopore, Sher-e-Kashmir University of Agricultural Sciences & Technology Shalimar Kashmir, Srinagar, Jammu and Kashmir, India
| | - Sheikh Zahid Nabi
- Division of Biochemistry, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Niyaz A. Dar
- ARSSSS Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology, Shalimar Kashmir, Srinagar, Jammu and Kashmir, India
| | - Faheem Shehzad Baloch
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Sheikh Mansoor
- Division of Biochemistry, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
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16
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Ahad A, Aslam R, Gul A, Amir R, Munir F, Batool TS, Ilyas M, Sarwar M, Nadeem MA, Baloch FS, Fiaz S, Zia MAB. Genome-wide analysis of bZIP, BBR, and BZR transcription factors in Triticum aestivum. PLoS One 2021; 16:e0259404. [PMID: 34847173 PMCID: PMC8631640 DOI: 10.1371/journal.pone.0259404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
Transcription factors are regulatory proteins known to modulate gene expression. These are the critical component of signaling pathways and help in mitigating various developmental and stress responses. Among them, bZIP, BBR, and BZR transcription factor families are well known to play a crucial role in regulating growth, development, and defense responses. However, limited data is available on these transcription factors in Triticum aestivum. In this study, bZIP, BBR, and BZR sequences from Brachypodium distachyon, Oryza sativa, Oryza barthii, Oryza brachyantha, T. aestivum, Triticum urartu, Sorghum bicolor, Zea mays were retrieved, and dendrograms were constructed to analyze the evolutionary relatedness among them. The sequences clustered into one group indicated a degree of evolutionary correlation highlighting the common lineage of cereal grains. This analysis also exhibited that these genes were highly conserved among studied monocots emphasizing their common ancestry. Furthermore, these transcription factor genes were evaluated for envisaging conserved motifs, gene structure, and subcellular localization in T. aestivum. This comprehensive computational analysis has provided an insight into transcription factor evolution that can also be useful in developing approaches for future functional characterization of these genes in T. aestivum. Furthermore, the data generated can be beneficial in future for genetic manipulation of economically important plants.
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Affiliation(s)
- Arzoo Ahad
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Roohi Aslam
- NUTECH School of Applied Sciences and Humanities, National University of Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Tuba Sharf Batool
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Mahnoor Ilyas
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Sarwar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Hyber Pakhtunkhwa, Pakistan
| | - Muhammad Abu Bakar Zia
- College of Agriculture, Bahauddin Zakariya University, Bahadur sub–Campus Layyah, Punjab, Pakistan
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Kashtwari M, Mansoor S, Wani AA, Najar MA, Deshmukh RK, Baloch FS, Abidi I, Zargar SM. Random mutagenesis in vegetatively propagated crops: opportunities, challenges and genome editing prospects. Mol Biol Rep 2021; 49:5729-5749. [PMID: 34427889 DOI: 10.1007/s11033-021-06650-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/15/2021] [Indexed: 12/23/2022]
Abstract
In order to meet the growing human food and nutrition demand a perpetual process of crop improvement is idealized. It has seen changing trends and varying concepts throughout human history; from simple selection to complex gene-editing. Among these techniques, random mutagenesis has been shown to be a promising technology to achieve desirable genetic gain with less time and minimal efforts. Over the decade, several hundred varieties have been released through random mutagenesis, but the production is falling behind the demand. Several food crops like banana, potato, cassava, sweet potato, apple, citrus, and others are vegetatively propagated. Since such crops are not propagated through seed, genetic improvement through classical breeding is impractical for them. Besides, in the case of polyploids, accomplishment of allelic homozygosity requires a considerable land area, extensive fieldwork with huge manpower, and hefty funding for an extended period of time. Apart from induction, mapping of induced genes to facilitate the knowledge of biological processes has been performed only in a few selected facultative vegetative crops like banana and cassava which can form a segregating population. During the last few decades, there has been a shift in the techniques used for crop improvement. With the introduction of the robust technologies like meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) more and more crops are being subjected to gene editing. However, more work needs to be done in case of vegetatively propagated crops.
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Affiliation(s)
- Mahpara Kashtwari
- Cytogenetics and Molecular Biology Laboratory, Department of Botany, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190006, India
| | - Sheikh Mansoor
- Division of Biochemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology, FBSc, Jammu, Jammu and Kashmir, 180009, India
| | - Aijaz A Wani
- Cytogenetics and Molecular Biology Laboratory, Department of Botany, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190006, India.
| | - Mushtaq Ahmad Najar
- Cytogenetics and Molecular Biology Laboratory, Department of Botany, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190006, India
| | - Rupesh K Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140308, India
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Ishfaq Abidi
- Directorate of Research, Sher-e-Kashmir University of Agricultural Sciences and Technology, Shalimar, Jammu and Kashmir, 190025, India
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Shalimar, Jammu and Kashmir, 190025, India.
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Shimira F, Boyaci HF, Çilesiz Y, Nadeem MA, Baloch FS, Taşkin H. Exploring the genetic diversity and population structure of scarlet eggplant germplasm from Rwanda through iPBS-retrotransposon markers. Mol Biol Rep 2021; 48:6323-6333. [PMID: 34383245 DOI: 10.1007/s11033-021-06626-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Scarlet eggplant (Solanum aethiopicum gr. gilo) is a part of African indigenous vegetables and acknowledged as a source of variations in the breeding of Brinjal. Since its genetic diversity is still largely unexplored, therefore genetic diversity and population structure of this plant were investigated in this study. METHODS AND RESULTS Scarlet eggplant germplasm made of fifty-two accessions originated from two districts of Rwanda was assessed by employing the iPBS-retrotransposon markers system. Twelve most polymorphic primers were employed for molecular characterization and they yielded 329 total bands whereupon 85.03% were polymorphic. The recorded mean polymorphism information content was 0.363 and other diversity indices such as; mean the effective number of alleles, mean Shannon's information index and gene diversity with the following values; 1.298, 0.300 and 0.187 respectively. A superior level of diversity was noticed among accessions from Musanze district. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) gathered scarlet germplasm in a divergence manner to their collection district. Analysis of molecular variance (AMOVA) displayed that the utmost variations (81%) in scarlet eggplant germplasm are resulting in differences within populations. CONCLUSIONS The extensive diversity of scarlet eggplant in Rwanda might be used to form the base and genetic resource of an exhaustive breeding program of this economically important African indigenous vegetable. For instance, accessions MZE53 and GKE11 might be proposed as parent candidates due to their high relative genetic distance (0.6781).
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Affiliation(s)
- Flavien Shimira
- Department of Horticulture, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Hatice Filiz Boyaci
- Department of Vegetable Crops and Ornamentals, Bati Akdeniz Agricultural Research Institute, Antalya, Turkey
| | - Yeter Çilesiz
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey.
| | - Hatıra Taşkin
- Department of Horticulture, Faculty of Agriculture, Cukurova University, Adana, Turkey
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Nadeem MA, Habyarimana E, Karaköy T, Baloch FS. Genetic dissection of days to flowering via genome-wide association studies in Turkish common bean germplasm. Physiol Mol Biol Plants 2021; 27:1609-1622. [PMID: 34366600 PMCID: PMC8295450 DOI: 10.1007/s12298-021-01029-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Common bean is a nutrient-dense legume crop serving as a source of food for millions of people. Characterization of unexplored common bean germplasm to unlock the phenotypic and genetic variations is still needed to explore the breeding potential of this crop. The current study aimed to dissect the genetic basis having association for days to flowering (DF). A total of 188 common bean accessions collected from 19 provinces of Turkey were used as plant material under five environments and two locations. Analysis of variance (ANOVA) revealed that genotypes and genotype by environment interaction have significant effects on DF. A total of 10 most stable accessions were evaluated from stability analysis. Overall maximum (75) and minimum (54) DF were observed for Hakkari-51 and Mus-46 accessions, respectively. The implemented constellation plot divided studied germplasm according to their DF and growth habit. A total of 7900 DArTseq markers were used for association analysis. Mixed linear model using the Q + K Model resulted a total of 18 DArTseq markers from five environments. DArT-8668385 marker identified in Bolu during 2016 was also associated with DF in Sivas during 2017. Combined data of five years resulted a total of four markers (DArT-22346534, DArT-3369768, DArT-3374613, and DArT-3370801) having significant association ( p < 0.01 ) for DF. DArT-22346534 present on Pv 08 accounted a maximum of 9.89% variation to the studied trait. A total of four putative candidate genes were predicted from sequences reflecting homology to identified four DArTseq markers. We envisage that exploitation of identified DArTseq markers will hopefully beneficial for the development of new common bean varieties having better adaptation ability to changing climatic conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01029-8.
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Affiliation(s)
- Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140 Sivas, Turkey
| | - Ephrem Habyarimana
- CREA Research Center for Cereal and Industrial Crops, 40128 Bologna, Italy
| | - Tolga Karaköy
- 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
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Nadeem MA, Yeken MZ, Shahid MQ, Habyarimana E, Yılmaz H, Alsaleh A, Hatipoğlu R, Çilesiz Y, Khawar KM, Ludidi N, Ercişli S, Aasim M, Karaköy T, Baloch FS. Common bean as a potential crop for future food security: an overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1920462] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant İzzet Baysal University, Bolu, Turkey
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, PR China
| | | | - Hilal Yılmaz
- Department of Plant and Animal Production, Izmit Vocational School, Kocaeli University, Kocaeli, Turkey
| | - Ahmad Alsaleh
- Department of Food and Agriculture, Insitutue of Hemp Research, Yozgat Bozok University, 66200, Yozgat, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, Adana, Turkey
| | - Yeter Çilesiz
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Khalid Mahmood Khawar
- Department of Field Crops, Faculty of Agriculture, Ankara University, Ankara, Turkey
| | - Ndiko Ludidi
- Department of Biotechnology and DSI-NRF Center of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
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Kurt C, Demirbas A, Nawaz MA, Chung G, Baloch FS, Altunay N. Determination of Se content of 78 sesame accessions with different geographical origin. J Food Compost Anal 2020. [DOI: 10.1016/j.jfca.2020.103621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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Nawaz MA, Azeem F, Zakharenko AM, Lin X, Atif RM, Baloch FS, Chan TF, Chung G, Ham J, Sun S, Golokhvast KS. In-silico Exploration of Channel Type and Efflux Silicon Transporters and Silicification Proteins in 80 Sequenced Viridiplantae Genomes. Plants (Basel) 2020; 9:plants9111612. [PMID: 33233677 PMCID: PMC7709012 DOI: 10.3390/plants9111612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/29/2022]
Abstract
Silicon (Si) accumulation protects plants from biotic and abiotic stresses. It is transported and distributed within the plant body through a cooperative system of channel type (e.g., OsLsi1) and efflux (Lsi2s e.g., OsLsi2) Si transporters (SITs) that belong to Noduline-26 like intrinsic protein family of aquaporins and an uncharacterized anion transporter family, respectively. Si is deposited in plant tissues as phytoliths and the process is known as biosilicification but the knowledge about the proteins involved in this process is limited. In the present study, we explored channel type SITs and Lsi2s, and siliplant1 protein (Slp1) in 80 green plant species. We found 80 channel type SITs and 133 Lsi2s. The channel type SITs characterized by the presence of two NPA motifs, GSGR or STAR selectivity filter, and 108 amino acids between two NPA motifs were absent from Chlorophytes, while Streptophytes evolved two different types of channel type SITs with different selectivity filters. Both channel type SITs and Lsi2s evolved two types of gene structures each, however, Lsi2s are ancient and were also found in Chlorophyta. Homologs of Slp1 (225) were present in almost all Streptophytes regardless of their Si accumulation capacity. In Si accumulator plant species, the Slp1s were characterized by the presence of H, D-rich domain, P, K, E-rich domain, and P, T, Y-rich domain, while moderate Si accumulators lacked H, D-rich domain and P, T, Y-rich domains. The digital expression analysis and coexpression networks highlighted the role of channel type and Lsi2s, and how Slp1 homologs were ameliorating plants’ ability to withstand different stresses by co-expressing with genes related to structural integrity and signaling. Together, the in-silico exploration made in this study increases our knowledge of the process of biosilicification in plants.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Laboratory of Bio-Economics and Biotechnology, Department of Bio-Economics and Food Safety, School of Economics and Management, Far Eastern Federal University, 690950 Vladivostok, Russia;
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan;
| | | | - Xiao Lin
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong SAR, Hong Kong 999077, China; (X.L.); (T.-F.C.)
| | - Rana Muhammad Atif
- US-Pakistan Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Turkey;
| | - Ting-Fung Chan
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong SAR, Hong Kong 999077, China; (X.L.); (T.-F.C.)
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
| | - Junghee Ham
- Department of Health Policy and Management, Wonkwang University, Iksan, Jeonbuk 54538, Korea;
| | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
- Correspondence: (S.S.); (K.S.G.)
| | - Kirill S. Golokhvast
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 42, 44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia;
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, 690950 Vladivostok, Russia
- Pacific Geographical Institute, FEB RAS, 7 Radio street, 690014 Vladivostok, Russia
- Correspondence: (S.S.); (K.S.G.)
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23
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Wang Y, Shahid MQ, Ghouri F, Baloch FS. De Novo Assembly and Annotation of the Juvenile Tuber Transcriptome of a Gastrodia elata Hybrid by RNA Sequencing: Detection of SSR Markers. Biochem Genet 2020; 58:914-934. [DOI: 10.1007/s10528-020-09983-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 06/25/2020] [Indexed: 02/08/2023]
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Wang Y, Nie F, Shahid MQ, Baloch FS. Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset. BMC Plant Biol 2020; 20:250. [PMID: 32493212 PMCID: PMC7268529 DOI: 10.1186/s12870-020-02461-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/24/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species. RESULTS We identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves' transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including "Terpenoid backbone biosynthesis", "Valine, leucine and isoleucine biosynthesis", "Butanoate metabolism", "C5-Branched dibasic acid metabolism" "Pantothenate and CoA biosynthesis". We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species. CONCLUSION Some important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.
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Affiliation(s)
- Yunsheng Wang
- College of Health and Life Science, Kaili University, Kaili City, 556011 Guizhou Province China
| | - Fei Nie
- Biological institute of Guizhou Province, Guiyang City, 556000 Guizhou Province China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong Province China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
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Ali F, Nadeem MA, Barut M, Habyarimana E, Chaudhary HJ, Khalil IH, Alsaleh A, Hatipoğlu R, Karaköy T, Kurt C, Aasim M, Sameeullah M, Ludidi N, Yang SH, Chung G, Baloch FS. Genetic Diversity, Population Structure and Marker-Trait Association for 100-Seed Weight in International Safflower Panel Using SilicoDArT Marker Information. Plants (Basel) 2020; 9:E652. [PMID: 32455816 PMCID: PMC7284372 DOI: 10.3390/plants9050652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023]
Abstract
Safflower is an important oilseed crop mainly grown in the arid and semi-arid regions of the world. The aim of this study was to explore phenotypic and genetic diversity, population structure, and marker-trait association for 100-seed weight in 94 safflower accessions originating from 26 countries using silicoDArT markers. Analysis of variance revealed statistically significant genotypic effects (p < 0.01), while Turkey samples resulted in higher 100-seed weight compared to Pakistan samples. A Constellation plot divided the studied germplasm into two populations on the basis of their 100-seed weight. Various mean genetic diversity parameters including observed number of alleles (1.99), effective number of alleles (1.54), Shannon's information index (0.48), expected heterozygosity (0.32), and unbiased expected heterozygosity (0.32) for the entire population exhibited sufficient genetic diversity using 12232 silicoDArT markers. Analysis of molecular variance (AMOVA) revealed that most of the variations (91%) in world safflower panel are due to differences within country groups. A model-based structure grouped the 94 safflower accessions into populations A, B, C and an admixture population upon membership coefficient. Neighbor joining analysis grouped the safflower accessions into two populations (A and B). Principal coordinate analysis (PCoA) also clustered the safflower accessions on the basis of geographical origin. Three accessions; Egypt-5, Egypt-2, and India-2 revealed the highest genetic distance and hence might be recommended as candidate parental lines for safflower breeding programs. The mixed linear model i.e., the Q + K model, demonstrated that two DArTseq markers (DArT-45483051 and DArT-15672391) had significant association (p < 0.01) for 100-seed weight. We envisage that identified DArTseq markers associated with 100-seed weight will be helpful to develop high-yielding cultivars of safflower through marker-assisted breeding in the near future.
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Affiliation(s)
- Fawad Ali
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (F.A.); (H.J.C.)
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140 Sivas, Turkey; (M.A.N.); (T.K.); (M.A.)
| | - Muzaffer Barut
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
- Department of Field Crops, Faculty of Agriculture, Çukurova University, 1000 Adana, Turkey; (R.H.); (C.K.)
| | - Ephrem Habyarimana
- CREA Research Center for Cereal and Industrial Crops, 40128 Bologna, Italy;
| | - Hassan Javed Chaudhary
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (F.A.); (H.J.C.)
| | - Iftikhar Hussain Khalil
- Department of Plant Breeding and Genetics, The University of Agriculture, Peshawar 25130, Pakistan;
| | - Ahmad Alsaleh
- Science and Technology Application and Research Center (BİLTEM), Yozgat Bozok University, 66900 Yozgat, Turkey;
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, Çukurova University, 1000 Adana, Turkey; (R.H.); (C.K.)
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140 Sivas, Turkey; (M.A.N.); (T.K.); (M.A.)
| | - Cemal Kurt
- Department of Field Crops, Faculty of Agriculture, Çukurova University, 1000 Adana, Turkey; (R.H.); (C.K.)
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140 Sivas, Turkey; (M.A.N.); (T.K.); (M.A.)
| | - Muhammad Sameeullah
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
| | - Ndiko Ludidi
- Department of Biotechnology and Center of Excellence in Food Security, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa;
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
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Habyarimana E, De Franceschi P, Ercisli S, Baloch FS, Dall’Agata M. Genome-Wide Association Study for Biomass Related Traits in a Panel of Sorghum bicolor and S. bicolor × S. halepense Populations. Front Plant Sci 2020; 11:551305. [PMID: 33281836 PMCID: PMC7688983 DOI: 10.3389/fpls.2020.551305] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 10/26/2020] [Indexed: 05/08/2023]
Abstract
The efficient use of sorghum as a renewable energy source requires high biomass yields and reduced agricultural inputs. Hybridization of Sorghum bicolor with wild Sorghum halepense can help meet both requirements, generating high-yielding and environment friendly perennial sorghum cultivars. Selection efficiency, however, needs to be improved to exploit the genetic potential of the derived recombinant lines and remove weedy and other wild traits. In this work, we present the results from a Genome-Wide Association Study conducted on a diversity panel made up of S. bicolor and an advanced population derived from S. bicolor × S. halepense multi-parent crosses. The objective was to identify genetic loci controlling biomass yield and biomass-relevant traits for breeding purposes. Plants were phenotyped during four consecutive years for dry biomass yield, dry mass fraction of fresh material, plant height and plant maturity. A genotyping-by-sequencing approach was implemented to obtain 92,383 high quality SNP markers used in this work. Significant marker-trait associations were uncovered across eight of the ten sorghum chromosomes, with two main hotspots near the end of chromosomes 7 and 9, in proximity of dwarfing genes Dw1 and Dw3. No significant marker was found on chromosomes 2 and 4. A large number of significant marker loci associated with biomass yield and biomass-relevant traits showed minor effects on respective plant characteristics, with the exception of seven loci on chromosomes 3, 8, and 9 that explained 5.2-7.8% of phenotypic variability in dry mass yield, dry mass fraction of fresh material, and maturity, and a major effect (R 2 = 16.2%) locus on chromosome 1 for dry mass fraction of fresh material which co-localized with a zinc-finger homeodomain protein possibly involved in the expression of the D (Dry stalk) locus. These markers and marker haplotypes identified in this work are expected to boost marker-assisted selection in sorghum breeding.
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Affiliation(s)
- Ephrem Habyarimana
- CREA Research Center for Cereal and Industrial Crops, Bologna, Italy
- *Correspondence: Ephrem Habyarimana,
| | | | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
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Wang Y, Shahid MQ, Ghouri F, Ercişli S, Baloch FS. Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome. 3 Biotech 2019; 9:292. [PMID: 31321198 DOI: 10.1007/s13205-019-1823-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 06/23/2019] [Indexed: 01/28/2023] Open
Abstract
Tianma (Gastrodia elata Blume) has unique biological characteristics and high medicinal value. The wild resource of G. elata is being overutilized and should be conserved as it is already included in the list of endangered species in China. The population size of cultivated G. elata is small because of domestication bottleneck. Therefore, it is of utmost importance to evolve high-quality varieties and conserve wild resources of G. elata. In this study, we sequenced tuber transcriptomes of three major cultivated sub-species of Gastrodia elata, namely G. elata BI. f. elata, G. elata Bl. f. glauca S. Chow, and G. elata Bl. f. Viridis, and obtained about 7.8G clean data. The assembled high-quality reads of three sub-species were clustered into 56,884 unigenes. Of these, 31,224 (54.89%), 25,733 (45.24%), 22,629 (39.78%), and 11,856 (20.84%) unigenes were annotated by Nr, Swiss-Port, Eukaryotic Ortholog Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Here, a total of 3766 EST-SSRs and 128,921 SNPs were identified from the unigenes. The results not only offer huge number of genes that were responsible for the growth, development, and metabolism of bioactive components, but also a large number of molecular markers were detected for future studies on the conservation genetics and molecular breeding of G. elata.
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Wang Y, Shahid MQ, Ghouri F, Ercişli S, Baloch FS, Nie F. Transcriptome analysis and annotation: SNPs identified from single copy annotated unigenes of three polyploid blueberry crops. PLoS One 2019; 14:e0216299. [PMID: 31034501 PMCID: PMC6488077 DOI: 10.1371/journal.pone.0216299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/17/2019] [Indexed: 02/03/2023] Open
Abstract
Blueberry is a kind of new rising popular perennial fruit with high healthful quality. It is of utmost importance to develop new blueberry varieties for different climatic zones to satisfy the demand of people in the world. Molecular marker assisted breeding is believed to be an ideal method for the development of new blueberry varieties for its shorter breeding cycle than the conventional breeding. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) markers are widely used molecular tools for marker assisted breeding, which could be detected at large scale by the transcriptome sequencing. Here, we sequenced the leaves transcriptome of 19 rabbiteye (Vaccinium ashei Reade), 13 southern highbush (Vaccinium. corymbosum L × native southern Vaccinium Spp) and 22 cultivars of northern highbush blueberry (Vaccinium corymbosum L) by using next generation sequencing technologies. A total of 80.825 Gb clean data with an average of about 12.525 million reads per cultivar were obtained. We assembled 58,968, 55,973 and 53,887 unigenes by using the clean data from rabbiteye, southern highbush and northern highbush blueberry cultivars, respectively. Among these unigenes, 3599, 3495 and 3513 unigenes were detected as candidate resistance genes in three blueberry crops. Moreover, we identified more than 8756, 9020, and 9198 SSR markers from these unigenes, and 7665, 4861, 13,063 SNPs from the annotated single copy unigenes, respectively. The results will be helpful for the molecular genetics and association analysis of blueberry and the basic molecular information of pest and disease resistance of blueberry, and would also offer huge number of molecular tools for the marker assisted breeding to produce blueberry cultivars with different adaptive characteristics.
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Affiliation(s)
- Yunsheng Wang
- College of Life and Health Science, Kaili University, Kaili City, Guizhou Province, China
- * E-mail: (YW); (FN)
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
| | - Fei Nie
- Biological Institute of Guizhou Province, Guiyang City, Guizhou Province, China
- * E-mail: (YW); (FN)
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Huang TQ, Shahid MQ, Baloch FS, Lin SQ, Yang XH. Effects of trimethylamine oxide (TMAO) and loading duration on the shoot tip cryopreservation of loquat ( Eriobotrya japonica). Turk J Biol 2019; 42:224-230. [PMID: 30814884 DOI: 10.3906/biy-1712-51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Two cryoprotectant solutions, including trimethylamine oxide (TMAO) and dimethyl sulfoxide (DMSO), and several loading durations were used to evaluate the cryopreservation of the shoot tip of Eriobotrya plants. The best results for regrowth (59.91%) were obtained from 10% TMAO compared to 10% DMSO as cryoprotectant, although nonsignificant differences were found for survival between the two cryoprotectants. We detected pronounced effects of loading duration on survival and regrowth rates of shoot tips. The maximum regrowth (56.36%) was observed at 9 h of loading duration. The cryoprotectants and loading durations greatly affected the regrowth of Eriobotrya shoot tips, and TMAO could be introduced as a nontoxic and efficient cryoprotectant. These results could lay a foundation for the cryopreservation of Eriobotrya.
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Affiliation(s)
- Tian-Qi Huang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture , Guangzhou , P.R. China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University , Guangzhou , P.R. China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University , Guangzhou , P.R. China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agriculture and Natural Sciences, Abant İzzet Baysal University , Bolu , Turkey
| | - Shun-Quan Lin
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture , Guangzhou , P.R. China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University , Guangzhou , P.R. China
| | - Xiang-Hui Yang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture , Guangzhou , P.R. China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University , Guangzhou , P.R. China
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Nadeem MA, Habyarimana E, Çiftçi V, Nawaz MA, Karaköy T, Comertpay G, Shahid MQ, Hatipoğlu R, Yeken MZ, Ali F, Ercişli S, Chung G, Baloch FS. Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information. PLoS One 2018; 13:e0205363. [PMID: 30308006 PMCID: PMC6181364 DOI: 10.1371/journal.pone.0205363] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/20/2018] [Indexed: 12/31/2022] Open
Abstract
Turkey presents a great diversity of common bean landraces in farmers' fields. We collected 183 common bean accessions from 19 different Turkish geographic regions and 5 scarlet runner bean accessions to investigate their genetic diversity and population structure using phenotypic information (growth habit, and seed weight, flower color, bracteole shape and size, pod shape and leaf shape and color), geographic provenance and 12,557 silicoDArT markers. A total of 24.14% markers were found novel. For the entire population (188 accessions), the expected heterozygosity was 0.078 and overall gene diversity, Fst and Fis were 0.14, 0.55 and 1, respectively. Using marker information, model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 188 accessions into two main populations A (predominant) and B, and 5 unclassified genotypes, representing 3 meaningful heterotic groups for breeding purposes. Phenotypic information clearly distinguished these populations; population A and B, respectively, were bigger (>40g/100 seeds) and smaller (<40g/100 seeds) seed-sized. The unclassified population was pure and only contained climbing genotypes with 100 seed weight 2-3 times greater than populations A and B. Clustering was mainly based on A: seed weight, B: growth habit, C: geographical provinces and D: flower color. Mean kinship was generally low, but population B was more diverse than population A. Overall, a useful level of gene and genotypic diversity was observed in this work and can be used by the scientific community in breeding efforts to develop superior common bean strains.
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Affiliation(s)
- Muhammad Azhar Nadeem
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Ephrem Habyarimana
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria–Centro di ricerca cerealicoltura e colture industriali, Bologna, Italy
| | - Vahdettin Çiftçi
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, Republic of Korea
| | - Tolga Karaköy
- Organic Agriculture Program, Vocational School of Sivas, University of Cumhuriyet, Sivas, Turkey
| | - Gonul Comertpay
- Eastern Mediterranean Agricultural Research Institute, Turkey
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio resources, South China Agricultural University, Guangzhou, China
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, Adana, Turkey
| | - Mehmet Zahit Yeken
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Fawad Ali
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, Republic of Korea
| | - Faheem Shehzad Baloch
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
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Nawaz MA, Lin X, Chan TF, Imtiaz M, Rehman HM, Ali MA, Baloch FS, Atif RM, Yang SH, Chung G. Characterization of Cellulose Synthase A (CESA) Gene Family in Eudicots. Biochem Genet 2018; 57:248-272. [PMID: 30267258 DOI: 10.1007/s10528-018-9888-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/20/2018] [Indexed: 12/30/2022]
Abstract
Cellulose synthase A (CESA) is a key enzyme involved in the complex process of plant cell wall biosynthesis, and it remains a productive subject for research. We employed systems biology approaches to explore structural diversity of eudicot CESAs by exon-intron organization, mode of duplication, synteny, and splice site analyses. Using a combined phylogenetics and comparative genomics approach coupled with co-expression networks we reconciled the evolution of cellulose synthase gene family in eudicots and found that the basic forms of CESA proteins are retained in angiosperms. Duplications have played an important role in expansion of CESA gene family members in eudicots. Co-expression networks showed that primary and secondary cell wall modules are duplicated in eudicots. We also identified 230 simple sequence repeat markers in 103 eudicot CESAs. The 13 identified conserved motifs in eudicots will provide a basis for gene identification and functional characterization in other plants. Furthermore, we characterized (in silico) eudicot CESAs against senescence and found that expression levels of CESAs decreased during leaf senescence.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Xiao Lin
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Ting-Fung Chan
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Muhammad Imtiaz
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510275, China
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, 14280, Bolu, Turkey
| | - Rana Muhammad Atif
- US-Pakistan Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
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Nadeem MA, Nawaz MA, Shahid MQ, Doğan Y, Comertpay G, Yıldız M, Hatipoğlu R, Ahmad F, Alsaleh A, Labhane N, Özkan H, Chung G, Baloch FS. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1400401] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Muhammad Azhar Nadeem
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, School of Engineering, Chonnam National University, Yeosu, Korea
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, P. R. China
| | - Yıldız Doğan
- Department of Field Crops, Eastern Mediterranean Agricultural Research Institute, Agricultural Ministry, Adana, Turkey
| | - Gonul Comertpay
- Department of Field Crops, Eastern Mediterranean Agricultural Research Institute, Agricultural Ministry, Adana, Turkey
| | - Mehtap Yıldız
- Department of Agricultural Biotechnology, Faculty of Agriculture, Yuzuncu Yıl University, Van, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Fiaz Ahmad
- Botany Division, Institute of Pure and Applied Biology, Bahauddin Zakariya University, Punjab, Pakistan
| | - Ahmad Alsaleh
- Molecular Genetics Laboratory, Science and Technology Application and Research Center, Bozok University, Yozgat, Turkey
| | - Nitin Labhane
- Department of Botany, Bhavan's College, University of Mumbai, Mumbai, India
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, School of Engineering, Chonnam National University, Yeosu, Korea
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
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Nawaz MA, Rehman HM, Imtiaz M, Baloch FS, Lee JD, Yang SH, Lee SI, Chung G. Systems Identification and Characterization of Cell Wall Reassembly and Degradation Related Genes in Glycine max (L.) Merill, a Bioenergy Legume. Sci Rep 2017; 7:10862. [PMID: 28883533 PMCID: PMC5589831 DOI: 10.1038/s41598-017-11495-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/24/2017] [Indexed: 12/22/2022] Open
Abstract
Soybean is a promising biomass resource for generation of second-generation biofuels. Despite the utility of soybean cellulosic biomass and post-processing residues in biofuel generation, there is no comprehensive information available on cell wall loosening and degradation related gene families. In order to achieve enhanced lignocellulosic biomass with softened cell walls and reduced recalcitrance, it is important to identify genes involved in cell wall polymer loosening and degrading. Comprehensive genome-wide analysis of gene families involved in cell wall modifications is an efficient stratagem to find new candidate genes for soybean breeding for expanding biofuel industry. We report the identification of 505 genes distributed among 12 gene families related to cell wall loosening and degradation. 1262 tandem duplication events contributed towards expansion and diversification of studied gene families. We identified 687 Simple Sequence Repeat markers and 5 miRNA families distributed on 316 and 10 genes, respectively. Publically available microarray datasets were used to explore expression potential of identified genes in soybean plant developmental stages, 68 anatomical parts, abiotic and biotic stresses. Co-expression networks revealed transcriptional coordination of different gene families involved in cell wall loosening and degradation process.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Muhammad Imtiaz
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510275, China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, 14280, Bolu, Turkey
| | - Jeong Dong Lee
- Division of Plant Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Soo In Lee
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), Jeonju, 54874, Republic of Korea.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
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Nawaz MA, Rehman HM, Baloch FS, Ijaz B, Ali MA, Khan IA, Lee JD, Chung G, Yang SH. Genome and transcriptome-wide analyses of cellulose synthase gene superfamily in soybean. J Plant Physiol 2017; 215:163-175. [PMID: 28704793 DOI: 10.1016/j.jplph.2017.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 05/28/2023]
Abstract
The plant cellulose synthase gene superfamily belongs to the category of type-2 glycosyltransferases, and is involved in cellulose and hemicellulose biosynthesis. These enzymes are vital for maintaining cell-wall structural integrity throughout plant life. Here, we identified 78 putative cellulose synthases (CS) in the soybean genome. Phylogenetic analysis against 40 reference Arabidopsis CS genes clustered soybean CSs into seven major groups (CESA, CSL A, B, C, D, E and G), located on 19 chromosomes (except chromosome 18). Soybean CS expansion occurred in 66 duplication events. Additionally, we identified 95 simple sequence repeat makers related to 44 CSs. We next performed digital expression analysis using publically available datasets to understand potential CS functions in soybean. We found that CSs were highly expressed during soybean seed development, a pattern confirmed with an Affymatrix soybean IVT array and validated with RNA-seq profiles. Within CS groups, CESAs had higher relative expression than CSLs. Soybean CS models were designed based on maximum average RPKM values. Gene co-expression networks were developed to explore which CSs could work together in soybean. Finally, RT-PCR analysis confirmed the expression of 15 selected CSs during all four seed developmental stages.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea
| | | | - Babar Ijaz
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan
| | - Iqrar Ahmad Khan
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Jeong Dong Lee
- Division of Plant Biosciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea.
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea.
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Baloch FS, Alsaleh A, Shahid MQ, Çiftçi V, E. Sáenz de Miera L, Aasim M, Nadeem MA, Aktaş H, Özkan H, Hatipoğlu R. A Whole Genome DArTseq and SNP Analysis for Genetic Diversity Assessment in Durum Wheat from Central Fertile Crescent. PLoS One 2017; 12:e0167821. [PMID: 28099442 PMCID: PMC5242537 DOI: 10.1371/journal.pone.0167821] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 11/21/2016] [Indexed: 11/18/2022] Open
Abstract
Until now, little attention has been paid to the geographic distribution and evaluation of genetic diversity of durum wheat from the Central Fertile Crescent (modern-day Turkey and Syria). Turkey and Syria are considered as primary centers of wheat diversity, and thousands of locally adapted wheat landraces are still present in the farmers' small fields. We planned this study to evaluate the genetic diversity of durum wheat landraces from the Central Fertile Crescent by genotyping based on DArTseq and SNP analysis. A total of 39,568 DArTseq and 20,661 SNP markers were used to characterize the genetic characteristic of 91 durum wheat land races. Clustering based on Neighbor joining analysis, principal coordinate as well as Bayesian model implemented in structure, clearly showed that the grouping pattern is not associated with the geographical distribution of the durum wheat due to the mixing of the Turkish and Syrian landraces. Significant correlation between DArTseq and SNP markers was observed in the Mantel test. However, we detected a non-significant relationship between geographical coordinates and DArTseq (r = -0.085) and SNP (r = -0.039) loci. These results showed that unconscious farmer selection and lack of the commercial varieties might have resulted in the exchange of genetic material and this was apparent in the genetic structure of durum wheat in Turkey and Syria. The genomic characterization presented here is an essential step towards a future exploitation of the available durum wheat genetic resources in genomic and breeding programs. The results of this study have also depicted a clear insight about the genetic diversity of wheat accessions from the Central Fertile Crescent.
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Affiliation(s)
- Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant İzzet Baysal University, Bolu, Turkey
- * E-mail: (FSB); (MQS)
| | - Ahmad Alsaleh
- Department of Biotechnology, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- * E-mail: (FSB); (MQS)
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant İzzet Baysal University, Bolu, Turkey
| | | | - Muhammad Aasim
- Department of Biotechnology, Faculty Science, Necmettin Erbakan University, Konya, Turkey
| | - Muhammad Azhar Nadeem
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant İzzet Baysal University, Bolu, Turkey
| | - Husnu Aktaş
- Artuklu University Vocational Higher School of Kızıltepe, Mardin, Turkey
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
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Özer G, Bayraktar H, Baloch FS. iPBS retrotransposons ‘A Universal Retrotransposons’ now in molecular phylogeny of fungal pathogens. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Shaaf S, Sharma R, Baloch FS, Badaeva ED, Knüpffer H, Kilian B, Özkan H. The grain Hardness locus characterized in a diverse wheat panel (Triticum aestivum L.) adapted to the central part of the Fertile Crescent: genetic diversity, haplotype structure, and phylogeny. Mol Genet Genomics 2016; 291:1259-75. [DOI: 10.1007/s00438-016-1180-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 02/03/2016] [Indexed: 12/27/2022]
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Cömertpay G, Baloch FS, Derya M, Andeden EE, Alsaleh A, Sürek H, Özkan H. Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data. Genet Mol Res 2016; 15:gmr7158. [PMID: 26909982 DOI: 10.4238/gmr.15017158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Effective breeding programs based on genetic diversity are needed to broaden the genetic basis of rice (Oryza sativa L.) in Turkey. In this study, 81 commercial varieties from seven countries were studied in order to estimate the genomic relationships among them using nine inter-primer binding site (iPBS)-retrotransposon and 17 simple-sequence repeat (SSR) markers. A total of 59 alleles for the SSR markers and 96 bands for the iPBS-retrotransposon markers were detected, with an average of 3.47 and 10.6 per locus, respectively. Each of the varieties could be unequivocally identified by the SSR and iPBS-retrotransposon profiles. The iPBS-retrotransposon- and SSR-based clustering were identical and closely mirrored each other, with a significantly high correlation (r = 0.73). A neighbor-joining cluster based on the combined SSR and iPBS-retrotransposon data divided the rice varieties into three clusters. The population structure was determined using the STRUCTURE software, and three populations (K = 3) were identified among the varieties studied, showing that the diversity harbored by Turkish rice varieties is low. The results indicate that iPBS-retrotransposon markers are a very powerful technique to determine the genetic diversity of rice varieties.
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Affiliation(s)
- G Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Doğankent, Adana, Turkey
| | - F S Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant Izzet Baysal University, Bolu, Turkey
| | - M Derya
- Department of Biotechnology, University of Çukurova, Adana, Turkey
| | - E E Andeden
- Department of Biotechnology, University of Çukurova, Adana, Turkey
| | - A Alsaleh
- Department of Biotechnology, University of Çukurova, Adana, Turkey
| | - H Sürek
- Thrace Agricultural Research Institute, Edirne, Turkey
| | - H Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
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Wang Y, Shahid MQ, Ghouri F, Baloch FS, Wang Y, Huang H. Evaluation of the geographical pattern of genetic diversity of Glycine soja and Glycine max based on four single copy nuclear gene loci: For conservation of soybean germplasm. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Yıldız M, Koçak M, Baloch FS. Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment. Genet Mol Res 2015; 14:10588-602. [PMID: 26400290 DOI: 10.4238/2015.september.8.20] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Lack of requisite genetic variation in Turkish okra has necessitated the use of different types of markers for estimating the genetic diversity and identifying the source of variation. Transposable elements, present abundantly in plant genomes, generate genomic diversity through their replication and are thus an excellent source of molecular markers. We hypothesized that inter-primer binding site (iPBS)-retrotransposons could be the source of variation because of their genome plasticity nature. In the present study, genetic diversity of 66 okra landraces was analyzed using iPBS-retrotransposon markers. iPBS-retrotransposons detected 88 bands with 40.2% polymorphism and an average of 6.8 bands per primer. Gene diversity and Shannon's information index ranged from 0.01 to 0.13 and 0.02 to 0.21 for iPBS-retrotransposons and from 0.06 to 0.46 and 0.14 to 0.65 for simple sequence repeat (SSR) markers, respectively. Polymorphism information content value for retrotransposons varied between 0.12 and 0.99, while that for SSR was from 0.52 to 0.81. Neighbor joining analysis based on retrotransposons and SSRs divided all the accessions into four clusters; however, SSR markers were more efficient in clustering the landraces based on their origin. Using the STRUCTURE software for determining population structure, and two populations (at the number of hypothetical subpopulations, K = 2) were identified among the landraces. Low genetic diversity in Turkish okra highlights the need for the introduction of plants from countries with greater genetic diversity for these crops. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in okra.
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Affiliation(s)
- M Yıldız
- Department of Agricultural Biotechnology, Faculty of Agriculture, Yuzuncu Yil University, Van, Turkey
| | - M Koçak
- Department of Agricultural Biotechnology, Faculty of Agriculture, Yuzuncu Yil University, Van, Turkey
| | - F S Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant İzzet Baysal University, Bolu, Turkey
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Baloch FS, Alsaleh A, de Miera LES, Hatipoğlu R, Çiftçi V, Karaköy T, Yıldız M, Özkan H. DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.06.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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