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Ali F, Arif MAR, Ali A, Nadeem MA, Aksoy E, Bakhsh A, Khan SU, Kurt C, Tekdal D, Ilyas MK, Hameed A, Chung YS, Baloch FS. Genome-wide association studies identifies genetic loci related to fatty acid and branched-chain amino acid metabolism and histone modifications under varying nitrogen treatments in safflower ( Carthamus tinctorius). FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23310. [PMID: 38683936 DOI: 10.1071/fp23310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
Effective identification and usage of genetic variation are prerequisites for developing nutrient-efficient cultivars. A collection of 94 safflower (Carthamus tinctorius ) genotypes (G) was investigated for important morphological and photosynthetic traits at four nitrogen (N) treatments. We found significant variation for all the studied traits except chlorophyll b (chl b ) among safflower genotypes, nitrogen treatments and G×N interaction. The examined traits showed a 2.82-50.00% increase in response to N application. Biological yield (BY) reflected a significantly positive correlation with fresh shoot weight (FSW), root length (RL), fresh root weight (FRW) and number of leaves (NOL), while a significantly positive correlation was also observed among carotenoids (C), chlorophyll a (chl a ), chl b and total chlorophyll content (CT) under all treatments. Superior genotypes with respect to plant height (PH), FSW, NOL, RL, FRW and BY were clustered into Group 3, while genotypes with better mean performance regarding chl a , chl b C and CT were clustered into Group 2 as observed in principal component analysis. The identified eight best-performing genotypes could be useful to develop improved nitrogen efficient cultivars. Genome-wide association analysis resulted in 32 marker-trait associations (MTAs) under four treatments. Markers namely DArT-45481731 , DArT-17812864 , DArT-15670279 and DArT-45482737 were found consistent. Protein-protein interaction networks of loci associated with MTAs were related to fatty acid and branched-chain amino acid metabolism and histone modifications.
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Affiliation(s)
- Fawad Ali
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry Hainan University, Sanya 572025, Hai-nan, China; and Department of Botany, University of Baltistan Skardu, Gilgil Baltistan, 16100, Pakistan
| | - Mian A R Arif
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Arif Ali
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad A Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Turkey
| | - Emre Aksoy
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shahid U Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China; and Women Medical and Dental College, Khyber Medical University, Peshawar, KPK, 22020, Pakistan
| | - Cemal Kurt
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Dilek Tekdal
- Faculty of Science, Department of Biotechnology, Mersin University, 33343, Yenisehir, Mersin, Turkey
| | - Muhammad K Ilyas
- National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Amjad Hameed
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Yong S Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju 63243, Republic of Korea
| | - Faheem S Baloch
- Faculty of Science, Department of Biotechnology, Mersin University, 33343, Yenisehir, Mersin, Turkey
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Tomlekova N, Idziak-Helmcke D, Franke P, Rojek-Jelonek M, Kwasniewska J. Phaseolus vulgaris mutants reveal variation in the nuclear genome. FRONTIERS IN PLANT SCIENCE 2024; 14:1308830. [PMID: 38239224 PMCID: PMC10794375 DOI: 10.3389/fpls.2023.1308830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/08/2023] [Indexed: 01/22/2024]
Abstract
Phaseolus vulgaris L. (common bean) is an essential source of proteins in the human diet worldwide. Bean breeding programs to increase genetic diversity based on induced mutagenesis have a long tradition in Bulgaria. Common bean varieties with high productivity, wide environmental adaptability, good nutritional properties, and improved disease resistance have been successfully developed. In this study, we aimed to investigate selected nuclear genome features, such as the genome size, the number and chromosomal distribution of 5S and 35S rDNA loci by using the fluorescence in situ hybridization (FISH), as well as the level of DNA damage in some local Bulgarian accessions and mutants of P. vulgaris. Flow cytometry analyses revealed no significant differences in genome size between analyzed lines except for one of the analyzed mutants, M19. The value of genome size 2C DNA is about 1.37 pg2C -1 for all lines, whereas it is 1.42 pg2C-1 for M19. The chromosome number remains the same (2n=22) for all analyzed lines. Results of FISH analyses showed that the number of 5S rDNA was stable among accessions and mutant lines (four loci), while the number of 35S rDNA loci was shown as highly polymorphic, varying between ten and sixteen, and displaying differences in the size and location of 35S rDNA loci between analyzed genotypes. The cell cycle profile was different for the analyzed genotypes. The results revealed that wide variation in genome organization and size as well as DNA damage characterizes the analyzed genetic resources of the common bean.
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Affiliation(s)
- Nasya Tomlekova
- Laboratory of Molecular Biology, Department of Breeding, Marisa Vegetable Crops Research Institute, Plovdiv, Agricultural Academy, Sofia, Bulgaria
| | - Dominika Idziak-Helmcke
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paula Franke
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Magdalena Rojek-Jelonek
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Jolanta Kwasniewska
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Ugwuanyi S, Udengwu OS, Snowdon RJ, Obermeier C. Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean. FRONTIERS IN PLANT SCIENCE 2022; 13:1014282. [PMID: 36438107 PMCID: PMC9685177 DOI: 10.3389/fpls.2022.1014282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Phaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition around the world. However, the genetic basis of most important traits in common bean remains unknown. This study aimed at identifying QTL and candidate gene models underlying twenty-six agronomically important traits in common bean. For this, we assembled and phenotyped a diversity panel of 200 P. vulgaris genotypes in the greenhouse, comprising determinate bushy, determinate climbing and indeterminate climbing beans. The panel included dry beans and snap beans from different breeding programmes, elite lines and landraces from around the world with a major focus on accessions of African, European and South American origin. The panel was genotyped using a cost-conscious targeted genotyping-by-sequencing (GBS) platform to take advantage of highly polymorphic SNPs detected in previous studies and in diverse germplasm. The detected single nucleotide polymorphisms (SNPs) were applied in marker-trait analysis and revealed sixty-two quantitative trait loci (QTL) significantly associated with sixteen traits. Gene model identification via a similarity-based approach implicated major candidate gene models underlying the QTL associated with ten traits including, flowering, yield, seed quality, pod and seed characteristics. Our study revealed six QTL for pod shattering including three new QTL potentially useful for breeding. However, the panel was evaluated in a single greenhouse environment and the findings should be corroborated by evaluations across different field environments. Some of the detected QTL and a number of candidate gene models only elucidate the understanding of the genetic nature of these traits and provide the basis for further studies. Finally, the study showed the possibility of using a limited number of SNPs in performing marker-trait association in common bean by applying a highly scalable targeted GBS approach. This targeted GBS approach is a cost-efficient strategy for assessment of the genetic basis of complex traits and can enable geneticists and breeders to identify novel loci and targets for marker-assisted breeding more efficiently.
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Affiliation(s)
- Samson Ugwuanyi
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
- Department of Plant Science and Biotechnology, University of Nigeria, Nsukka, Nigeria
| | - Obi Sergius Udengwu
- Department of Plant Science and Biotechnology, University of Nigeria, Nsukka, Nigeria
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
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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] [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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Park M, Darwish AG, Elhag RI, Tsolova V, Soliman KFA, El-Sharkawy I. A multi-locus genome-wide association study reveals the genetics underlying muscadine antioxidant in berry skin. FRONTIERS IN PLANT SCIENCE 2022; 13:969301. [PMID: 35991419 PMCID: PMC9386419 DOI: 10.3389/fpls.2022.969301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Muscadine berries display enhanced nutraceutical value due to the accumulation of distinctive phytochemical constituents with great potential antioxidant activity. Such nutritional and health merits are not only restricted to muscadine, but muscadine berries accumulate higher amounts of bioactive polyphenolics compared with other grape species. For the genetic study of the antioxidant trait in muscadine, a multi-locus genome-wide association study (GWAS) with 350 muscadine genotypes and 1,283 RNase H2 enzyme-dependent amplicon sequencing (rhAmpSeq) markers was performed. Phenotyping was conducted with several antioxidant-related traits, including total phenolic content (TPC), total flavonoid content (TFC), 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity, and FRAP antioxidant assay in muscadine berry skin. The correlation coefficient analysis revealed that the TPC, and DPPH/FRAP activities were significantly correlated. Through the GWAS analysis, 12 QTNs were identified from the four traits, of which six were pleiotropic QTNs. Two pleiotropic QTNs, chr2_14464718 and chr4_16491374, were commonly identified from the TPC and DPPH/FRAP activities. Co-located genes with the two pleiotropic QTNs were isolated, and two candidate genes were identified with transcriptome analysis. UDP-glycosyltransferase and 4-hydroxy-4-methyl-2-oxoglutarate aldolase were the candidate genes that are positively and negatively correlated to the quantitative property of traits, respectively. These results are the first genetic evidence of the quantitative property of antioxidants in muscadine and provide genetic resources for breeding antioxidant-rich cultivars for both Muscadinia and Euvitis species.
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Affiliation(s)
- Minkyu Park
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Ahmed G. Darwish
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
- Department of Biochemistry, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Rashid I. Elhag
- College of Science and Technology, Florida A&M University, Tallahassee, FL, United States
| | - Violeta Tsolova
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Karam F. A. Soliman
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Islam El-Sharkawy
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
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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] [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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Tapia G, Méndez J, Inostroza L, Lozano C. Water Shortage Affects Vegetative and Reproductive Stages of Common Bean ( Phaseolus vulgaris) Chilean Landraces, Differentially Impacting Grain Yield Components. PLANTS (BASEL, SWITZERLAND) 2022; 11:749. [PMID: 35336629 PMCID: PMC8948600 DOI: 10.3390/plants11060749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Water availability for agricultural use is currently a global problem that worsens with climate change in several regions of the world. Among grain legumes, common bean (Phaseolus vulgaris) is the most cultivated in the worldwide. The Chilean germplasm of common bean is characterized by tolerance to water stress. Here, we analyzed a selection of nine ancient Chilean landraces in regard to their drought tolerance, simulating optimal (OW) and restricted watering (RW) in a Mediterranean environment. Phenological, growth, and yield traits were recorded, and correlation analysis was performed. Accordingly, leaf temperature and osmotic potential were higher under RW, while the leaf chlorophyll content decreased in all landraces. Physiological maturity days and seed-filling days were lower in RW than in OW. This similarly occurred with the grain yield. The % yield reduction was negatively correlated with the % pod reduction and the relative rate of leaf expansion (RLAE) reduction. However, the 100-seed weight value was not significantly modified by water treatment (p > 0.05). For instance, landraces that preferred to fill the grain with a lower rate of leaf expansion showed a lower loss in grain yield under drought conditions. These results suggest that the resource partitioning between growing leaves, flowers, and developing pods in Chilean landraces is variable, affecting the common bean drought tolerance.
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NADEEM MA. Türk Bakla Genetik Kaynaklarının Tohum Mineral İçeriği için Fenotipik Çeşitliliğin Araştırılması. ULUSLARARASI TARIM VE YABAN HAYATI BILIMLERI DERGISI 2021. [DOI: 10.24180/ijaws.949496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Amalova A, Abugalieva S, Babkenov A, Babkenova S, Turuspekov Y. Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan. PeerJ 2021; 9:e11857. [PMID: 34395089 PMCID: PMC8323601 DOI: 10.7717/peerj.11857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/05/2021] [Indexed: 12/13/2022] Open
Abstract
Background Bread wheat is the most important cereal in Kazakhstan, where it is grown on over 12 million hectares. One of the major constraints affecting wheat grain yield is drought due to the limited water supply. Hence, the development of drought-resistant cultivars is critical for ensuring food security in this country. Therefore, identifying quantitative trait loci (QTLs) associated with drought tolerance as an essential step in modern breeding activities, which rely on a marker-assisted selection approach. Methods A collection of 179 spring wheat accessions was tested under irrigated and rainfed conditions in Northern Kazakhstan over three years (2018, 2019, and 2020), during which data was collected on nine traits: heading date (HD), seed maturity date (SMD), plant height (PH), peduncle length (PL), number of productive spikes (NPS), spike length (SL), number of kernels per spike (NKS), thousand kernel weight (TKW), and kernels yield per m2 (YM2). The collection was genotyped using a 20,000 (20K) Illumina iSelect SNP array, and 8,662 polymorphic SNP markers were selected for a genome-wide association study (GWAS) to identify QTLs for targeted agronomic traits. Results Out of the total of 237 discovered QTLs, 50 were identified as being stable QTLs for irrigated and rainfed conditions in the Akmola region, Northern Kazakhstan; the identified QTLs were associated with all the studied traits except PH. The results indicate that nine QTLs for HD and 11 QTLs for SMD are presumably novel genetic factors identified in the irrigated and rainfed conditions of Northern Kazakhstan. The identified SNP markers of the QTLs for targeted traits in rainfed conditions can be applied to develop new competitive spring wheat cultivars in arid zones using a marker-assisted selection approach.
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Affiliation(s)
- Akerke Amalova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Saule Abugalieva
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Adylkhan Babkenov
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Akmola Region, Kazakhstan
| | - Sandukash Babkenova
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Akmola Region, Kazakhstan
| | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.,Faculty of Agrobiology, Kazakh National Agrarian University, Almaty, Kazakhstan
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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. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 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] [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] [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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In-Depth Genetic Diversity and Population Structure of Endangered Peruvian Amazon Rosewood Germplasm Using Genotyping by Sequencing (GBS) Technology. FORESTS 2021. [DOI: 10.3390/f12020197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Research studies on conservative genetics of endangered plants are very important to establish the management plans for the conservation of biodiversity. Rosewood is an evergreen tree of the Amazon region and its essential oil has great acceptance in the medical and cosmetic industry. The present study aimed to explore the genetic diversity and population structure of 90 rosewood accessions collected from eight localities of Peruvian Amazon territory through DArTseq markers. A total of 7485 informative markers resulted from genotyping by sequencing (GBS) analysis were used for the molecular characterization of rosewood germplasm. Mean values of various calculated diversity parameters like observed number of alleles (1.962), the effective number of alleles (1.669), unbiased expected heterozygosity (0.411), and percent polymorphism (93.51%) over the entire germplasm showed the existence of a good level of genetic variations. Our results showed that the Mairiricay population was more diverse compared to the rest of the populations. Tamshiyacu-2 and Mairiricay-15 accessions were found genetically distinct accessions. The analysis of molecular variance (AMOVA) reflected maximum variations (75%) are due to differences within populations. The implemented clustering algorithms, i.e., STRUCTURE, neighbor-joining analysis and principal coordinate analysis (PCoA) separated the studied germplasm on the basis of their geographical locations. Diversity indices for STRUCTURE-based populations showed that subpopulation A is more diverse population than the rest of the populations, for such reason, individuals belonging to this subpopulation should be used for reintroduction or reinforcement plans of rosewood conservation. We envisage that molecular characterization of Peruvian rosewood germplasm with DArTseq markers will provide a platform for the conservation, management and restoration of endangered rosewood in upcoming years.
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Yildiz A, Hajyzadeh M, Ozbek K, Nadeem MA, Hunter D. Molecular characterisation of the oldest domesticated Turkish einkorn wheat landraces with simple sequence repeat (SSR) markers. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1970023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Ayse Yildiz
- The National Botanical Garden of Turkey, Rebublic of Turkey Ministry of Agriculture and Forestry, Üniversiteler Mah. Dumlupınar Boulevard, Ankara, Turkey
| | - Mortaza Hajyzadeh
- Department of Field Crops, Faculty of Agriculture, Şirnak University, Şirnak, Turkey
| | - Kursad Ozbek
- The National Botanical Garden of Turkey, Rebublic of Turkey Ministry of Agriculture and Forestry, Üniversiteler Mah. Dumlupınar Boulevard, Ankara, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Danny Hunter
- Alliance of Bioversity International and CIAT, Via di San Domenico, Rome, Italy
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Genetic Improvement of Cereals and Grain Legumes. Genes (Basel) 2020; 11:genes11111255. [PMID: 33113769 PMCID: PMC7692374 DOI: 10.3390/genes11111255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
The anticipated population growth by 2050 will be coupled with increased food demand. To achieve higher and sustainable food supplies in order to feed the global population by 2050, a 2.4% rise in the yield of major crops is required. The key to yield improvement is a better understanding of the genetic variation and identification of molecular markers, quantitative trait loci, genes, and pathways related to higher yields and increased tolerance to biotic and abiotic stresses. Advances in genetic technologies are enabling plant breeders and geneticists to breed crop plants with improved agronomic traits. This Special Issue is an effort to report the genetic improvements by adapting genomic techniques and genomic selection.
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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, SWITZERLAND) 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] [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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Zia MAB, Demirel U, Nadeem MA, Çaliskan ME. Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1003-1020. [PMID: 32377049 PMCID: PMC7196606 DOI: 10.1007/s12298-020-00785-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 02/01/2020] [Accepted: 02/21/2020] [Indexed: 05/22/2023]
Abstract
Potato is one of the most important food crops all over the world. Breeding activities for this crop are mainly aimed to improve the quality and yield of tuber. However, genetic architecture of various traits contributing to the quality and yield of potato are not yet completely understood. Genome wide association studies provides a broader way to identify the genomic regions associated with various traits. Panels of 237 tetraploid potato genotypes from different countries were grown for two consecutive years 2016 and 2017 at experimental research area of Potato research center Niğde, Turkey. A genome wide association study using SolCAP 12K array was performed for various morpho-agronomic traits. Structure algorithm and neighborhood joining analysis clearly divided all genotypes into 4 clusters on the basis of their origin. For the marker trait association, Mixed Linear Model in TASSEL was performed and 36 genomic regions were found for the traits under study. The mean r2 value was found to be 0.92 and mean significant LD was 47.5% in the populations. LD patterns reflected the breeding history of potato. The findings of present study provide a framework which could be useful for future potato breeding programs to enhance the production and to reduce the challenges in the coming years to feed world's population.
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Affiliation(s)
- Muhammad Abu Bakar Zia
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
- College of Agriculture, Bolu Abant Izzet Baysal University, Bahadur Sub Campus Layyah, Pakistan
| | - Ufuk Demirel
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
| | - Muhammad Azhar Nadeem
- Department of Field Crops, Faculty of Agricultural and Natural Science, Bahauddin Zakariya University, 14000 Bolu, Turkey
| | - Mehmet Emin Çaliskan
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
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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. FRONTIERS IN PLANT SCIENCE 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] [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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