1
|
Elias M, Chere D, Lule D, Serba D, Tirfessa A, Gelmesa D, Tesso T, Bantte K, Menamo TM. Multi-locus genome-wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm. Plant Genome 2024:e20436. [PMID: 38361379 DOI: 10.1002/tpg2.20436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/17/2024]
Abstract
The identification of genomic regions underlying the root system architecture (RSA) is vital for improving crop abiotic stress tolerance. To improve sorghum (Sorghum bicolor L. Moench) for environmental stress tolerance, information on genetic variability and genomic regions linked to RSA traits is paramount. The aim of this study was, therefore, to investigate common quantitative trait nucleotides (QTNs) via multiple methodologies and identify genomic regions linked to RSA traits in a panel of 274 Ethiopian sorghum accessions. Multi-locus genome-wide association study was conducted using 265,944 high-quality single nucleotide polymorphism markers. Considering the QTN detected by at least three different methods, a total of 17 reliable QTNs were found to be significantly associated with root angle, number, length, and dry weight. Four QTNs were detected on chromosome SBI-05, followed by SBI-01 and SBI-02 with three QTNs each. Among the 17 QTNs, 11 are colocated with previously identified root traits quantitative trait loci and the remaining six are genome regions with novel genes. A total of 118 genes are colocated with these up- and down-streams of the QTNs. Moreover, five QTNs were found intragenic. These QTNs are S5_8994835 (number of nodal roots), S10_55702393 (number of nodal roots), S1_56872999 (nodal root angle), S9_1212069 (nodal root angle), and S5_5667192 (root dry weight) intragenic regions of Sobic.005G073101, Sobic.010G198000, Sobic.001G273000, Sobic.009G013600, and Sobic.005G054700, respectively. Particularly, Sobic.005G073101, Sobic.010G198000, and Sobic.009G013600 were found responsible for the plant growth hormone-induced RSA. These genes may regulate root development in the seedling stage. Further analysis on these genes might be important to explore the genetic structure of RSA of sorghum.
Collapse
Affiliation(s)
- Masarat Elias
- School of Plant Science, Haramaya University, Dire Dawa, Ethiopia
| | - Diriba Chere
- Department of Agronomy, Kansas State University, Manhattan, Kansas, USA
| | - Dagnachew Lule
- Ethiopia Agricultural Transformation Institute, Addis Ababa, Ethiopia
| | - Desalegn Serba
- United States Department of Agriculture, Agricultural Research Service, U.S. Arid Land Agricultural Research Center, Maricopa, Arizona, USA
| | - Alemu Tirfessa
- Ethiopian Institute of Agricultural Research (EIAR), Melkassa Agricultural Research Center, Adama, Ethiopia
| | - Dandena Gelmesa
- School of Plant Science, Haramaya University, Dire Dawa, Ethiopia
| | - Tesfaye Tesso
- Department of Agronomy, Kansas State University, Manhattan, Kansas, USA
| | - Kassahun Bantte
- Department of Plant Science and Horticulture, Jimma University, Jimma, Ethiopia
| | - Temesgen M Menamo
- Department of Plant Science and Horticulture, Jimma University, Jimma, Ethiopia
| |
Collapse
|
2
|
Devos KM, Qi P, Bahri BA, Gimode DM, Jenike K, Manthi SJ, Lule D, Lux T, Martinez-Bello L, Pendergast TH, Plott C, Saha D, Sidhu GS, Sreedasyam A, Wang X, Wang H, Wright H, Zhao J, Deshpande S, de Villiers S, Dida MM, Grimwood J, Jenkins J, Lovell J, Mayer KFX, Mneney EE, Ojulong HF, Schatz MC, Schmutz J, Song B, Tesfaye K, Odeny DA. Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nat Commun 2023; 14:3694. [PMID: 37344528 DOI: 10.1038/s41467-023-38915-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/19/2023] [Indexed: 06/23/2023] Open
Abstract
Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.
Collapse
Affiliation(s)
- Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Bochra A Bahri
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Pathology, University of Georgia, Griffin, GA, 30223, USA
| | - Davis M Gimode
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
| | - Katharine Jenike
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Samuel J Manthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
| | - Dagnachew Lule
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
- Ethiopian Agricultural Transformation Agency, Addis Ababa, Bole, Ethiopia
| | - Thomas Lux
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Liliam Martinez-Bello
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- UR Ventures, University of Rochester, Rochester, NY, 14627, USA
| | - Thomas H Pendergast
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Dipnarayan Saha
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- ICAR-Central Research Institute for Jute and Allied Fibers, Kolkata, West Bengal, 700120, India
| | - Gurjot S Sidhu
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hao Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hallie Wright
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Jianxin Zhao
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Santosh Deshpande
- ICRISAT, Patancheru, 502 324, T.S., India
- Hytech Seed India Pvt. Ltd., Ravalkol Village, Medcahl-Malkajgiri Dist-, 501 401, Hubballi, T.S, India
| | - Santie de Villiers
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, 80108, Kenya
- Pwani University Biosciences Research Center (PUBReC), Kilifi, 80108, Kenya
| | - Mathews M Dida
- Department of Crop and Soil Science, Maseno University, P.O. 333, Maseno, Kenya
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - John Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Emmarold E Mneney
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar Es Salaam, Tanzania
- Biotechnology Society of Tanzania, P.O. Box 10257, Dar es Salaam, Tanzania
| | - Henry F Ojulong
- ICRISAT, Matopos Research Station, P.O. Box 776, Bulawayo, Zimbabwe
| | - Michael C Schatz
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bo Song
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
| |
Collapse
|
3
|
Mengistu G, Shimelis H, Assefa E, Lule D. Genome-wide association analysis of anthracnose resistance in sorghum [Sorghum bicolor (L.) Moench]. PLoS One 2021; 16:e0261461. [PMID: 34929013 PMCID: PMC8687563 DOI: 10.1371/journal.pone.0261461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/27/2021] [Accepted: 12/02/2021] [Indexed: 11/18/2022] Open
Abstract
In warm-humid ago-ecologies of the world, sorghum [Sorghum bicolor (L.) Moench] production is severely affected by anthracnose disease caused by Colletotrichum sublineolum Henn. New sources of anthracnose resistance should be identified to introgress novel genes into susceptible varieties in resistance breeding programs. The objective of this study was to determine genome-wide association of Diversity Arrays Technology Sequencing (DArTseq) based single nucleotide polymorphisms (SNP) markers and anthracnose resistance genes in diverse sorghum populations for resistance breeding. Three hundred sixty-six sorghum populations were assessed for anthracnose resistance in three seasons in western Ethiopia using artificial inoculation. Data on anthracnose severity and the relative area under the disease progress curve were computed. Furthermore, the test populations were genotyped using SNP markers with DArTseq protocol. Population structure analysis and genome-wide association mapping were undertaken based on 11,643 SNPs with <10% missing data. The evaluated population was grouped into eight distinct genetic clusters. A total of eight significant (P < 0.001) marker-trait associations (MTAs) were detected, explaining 4.86–15.9% of the phenotypic variation for anthracnose resistance. Out of which the four markers were above the cutoff point. The significant MTAs in the assessed sorghum population are useful for marker-assisted selection (MAS) in anthracnose resistance breeding programs and for gene and quantitative trait loci (QTL) mapping.
Collapse
Affiliation(s)
- Girma Mengistu
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Oromia Agricultural Research Institute, Addis Ababa, Ethiopia
- * E-mail:
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Ermias Assefa
- Ethiopian Biotechnology Institute, Bioinformatics and Genomics Research Directorate (BGRD), Addis Ababa, Ethiopia
| | - Dagnachew Lule
- Oromia Agricultural Research Institute, Addis Ababa, Ethiopia
| |
Collapse
|
4
|
Mekonnen T, Sneller CH, Haileselassie T, Ziyomo C, Abeyo BG, Goodwin SB, Lule D, Tesfaye K. Genome-Wide Association Study Reveals Novel Genetic Loci for Quantitative Resistance to Septoria Tritici Blotch in Wheat ( Triticum aestivum L.). Front Plant Sci 2021; 12:671323. [PMID: 34630445 PMCID: PMC8500178 DOI: 10.3389/fpls.2021.671323] [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] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Septoria tritici blotch, caused by the fungus Zymoseptoria titici, poses serious and persistent challenges to wheat cultivation in Ethiopia and worldwide. Deploying resistant cultivars is a major component of controlling septoria tritici blotch (STB). Thus, the objective of this study was to elucidate the genomic architecture of STB resistance in an association panel of 178 bread wheat genotypes. The association panel was phenotyped for STB resistance, phenology, yield, and yield-related traits in three locations for 2 years. The panel was also genotyped for single nucleotide polymorphism (SNP) markers using the genotyping-by-sequencing (GBS) method, and a total of 7,776 polymorphic SNPs were used in the subsequent analyses. Marker-trait associations were also computed using a genome association and prediction integrated tool (GAPIT). The study then found that the broad-sense heritability for STB resistance ranged from 0.58 to 0.97 and 0.72 to 0.81 at the individual and across-environment levels, respectively, indicating the presence of STB resistance alleles in the association panel. Population structure and principal component analyses detected two sub-groups with greater degrees of admixture. A linkage disequilibrium (LD) analysis in 338,125 marker pairs also detected the existence of significant (p ≤ 0.01) linkage in 27.6% of the marker pairs. Specifically, in all chromosomes, the LD between SNPs declined within 2.26-105.62 Mbp, with an overall mean of 31.44 Mbp. Furthermore, the association analysis identified 53 loci that were significantly (false discovery rate, FDR, <0.05) associated with STB resistance, further pointing to 33 putative quantitative trait loci (QTLs). Most of these shared similar chromosomes with already published Septoria resistance genes, which were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A,3 B, 3D, 4A, 5A, 5B, 6A, 7A, 7B, and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D, and 6B appeared to be novel. Dissecting the detected loci on IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions that are involved in plant defense responses. These putative QTLs explained 2.7-13.2% of the total phenotypic variation. Seven of the QTLs (R 2 = 2.7-10.8%) for STB resistance also co-localized with marker-trait associations (MTAs) for agronomic traits. Overall, this analysis reported on putative QTLs for adult plant resistance to STB and some important agronomic traits. The reported and novel QTLs have been identified previously, indicating the potential to improve STB resistance by pyramiding QTLs by marker-assisted selection.
Collapse
Affiliation(s)
- Tilahun Mekonnen
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Clay H. Sneller
- Biosciences Eastern and Central Africa (BecA), Nairobi, Kenya
| | | | - Cathrine Ziyomo
- Biosciences Eastern and Central Africa (BecA), Nairobi, Kenya
| | - Bekele G. Abeyo
- International Maize and Wheat Improvement Center- CIMMYT (Ethiopia), Addis Ababa, Ethiopia
| | - Stephen B. Goodwin
- United States Department of Agriculture (USDA)-Agricultural Research Service, West Lafayette, IN, United States
| | - Dagnachew Lule
- Oromia Agricultural Research Institute (OARI), Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute (EBTi), Addis Ababa, Ethiopia
| |
Collapse
|
5
|
Girma G, Nida H, Tirfessa A, Lule D, Bejiga T, Seyoum A, Mekonen M, Nega A, Dessalegn K, Birhanu C, Bekele A, Gebreyohannes A, Ayana G, Tesso T, Ejeta G, Mengiste T. A comprehensive phenotypic and genomic characterization of Ethiopian sorghum germplasm defines core collection and reveals rich genetic potential in adaptive traits. Plant Genome 2020; 13:e20055. [PMID: 33217211 DOI: 10.1002/tpg2.20055] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
Understanding population genetic structure and diversity of a crop is essential in designing selection strategies in plant breeding. About 2010 Ethiopian sorghum accessions were phenotyped for different traits at multiple locations. A subset of the collection, 1628 accessions, predominantly landraces, some improved varieties, and inbred lines were genotyped by sequencing. Phenotypic data revealed association of important traits with different sorghum growing agro-climatic regions, high genetic diversity and the presence of rare natural variation in the Ethiopian sorghum germplasm. Subsequent genotypic analysis determined optimum number of sub-populations, distinct cluster groups and ancestries of each sorghum accessions. To improve utilization of germplasm, a core subset of 387 lines were selected following posteriori grouping of genotypes based on cluster groups obtained through GBS analysis followed by stratified random sampling using quantitative traits. In order to evaluate how well this new sorghum and millet innovation lab (SMIL) collection from Ethiopia is represented within the largest world sorghum collection at United States Department of Agriculture - National Plant Germplasm System (USDA-NPGS) and the sorghum association panel (SAP), comparisons were conducted based on SNP data. The SMIL collection displayed high genetic diversity with some redundancy with the USDA-NPGS germplasm but SAP showed clear distinction. Furthermore, genome-environment association analysis identified candidate genes associated with adaptation to abiotic factors, that will be important for exploitation of adaptive potential to different environments. In summary, our results described the diversity and relationship of sorghum collections, representativeness of developed core and provide novel insights into candidate genes associated to abiotic stress tolerance.
Collapse
Affiliation(s)
- Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Habte Nida
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Alemu Tirfessa
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Dagnachew Lule
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
| | - Tamirat Bejiga
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Amare Seyoum
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Moges Mekonen
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Amare Nega
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Kebede Dessalegn
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
| | - Chemeda Birhanu
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
| | | | - Adane Gebreyohannes
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Getachew Ayana
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Tesfaye Tesso
- Department of Agronomy, Kansas State University, 3007 Throckmorton PSC 1712 Claflin Road, Manhattan, KS, 66506, USA
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
6
|
Kassubek J, Müller H, Del Tredici K, Lule D, Weishaupt J, Ludolph A. P19 A tract of interest-based DTI study for in-vivo-staging in ALS patients with C9orf72 mutation. Clin Neurophysiol 2020. [DOI: 10.1016/j.clinph.2019.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
7
|
Gorges M, Schmidt D, Kunz M, Knehr A, Lule D, Pinkhardt E, Weishaupt J, Ludolph A, Kassubek J. FV 29 Executive eye movement impairment in presymptomatic amyotrophic lateral sclerosis mutation carriers. Clin Neurophysiol 2019. [DOI: 10.1016/j.clinph.2019.04.638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
8
|
Girma G, Nida H, Seyoum A, Mekonen M, Nega A, Lule D, Dessalegn K, Bekele A, Gebreyohannes A, Adeyanju A, Tirfessa A, Ayana G, Taddese T, Mekbib F, Belete K, Tesso T, Ejeta G, Mengiste T. A Large-Scale Genome-Wide Association Analyses of Ethiopian Sorghum Landrace Collection Reveal Loci Associated With Important Traits. Front Plant Sci 2019; 10:691. [PMID: 31191590 PMCID: PMC6549537 DOI: 10.3389/fpls.2019.00691] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/08/2019] [Indexed: 05/20/2023]
Abstract
The eastern Africa region, Ethiopia and its surroundings, is considered as the center of origin and diversity for sorghum, and has contributed to global sorghum genetic improvement. The germplasm from this region harbors enormous genetic variation for various traits but little is known regarding the genetic architecture of most traits. Here, 1425 Ethiopian landrace accessions were phenotyped under field conditions for presence or absence of awns, panicle compactness and shape, panicle exsertion, pericarp color, glume cover, plant height and smut resistance under diverse environmental conditions in Ethiopia. In addition, F1 hybrids obtained from a subset of 1341 accessions crossed to an A1 cytoplasmic male sterile line, ATx623, were scored for fertility/sterility reactions. Subsequently, genotyping-by-sequencing generated a total of 879,407 SNPs from which 72,190 robust SNP markers were selected after stringent quality control (QC). Pairwise distance-based hierarchical clustering identified 11 distinct groups. Of the genotypes assigned to either one of the 11 sub-populations, 65% had high ancestry membership coefficient with the likelihood of more than 0.60 and the remaining 35% represented highly admixed accessions. A genome-wide association study (GWAS) identified loci and SNPs associated with aforementioned traits. GWAS based on compressed mixed linear model (CMLM) identified SNPs with significant association (FDR ≤ 0.05) to the different traits studied. The percentage of total phenotypic variation explained with significant SNPs across traits ranged from 2 to 43%. Candidate genes showing significant association with different traits were identified. The sorghum bHLH transcription factor, ABORTED MICROSPORES was identified as a strong candidate gene conditioning male fertility. Notably, sorghum CLAVATA1 receptor like kinase, known for regulation of plant growth, and the ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR gene RAP2-7, known to suppress transition to flowering, were significantly associated with plant height. In addition, the YELLOW SEED1 like MYB transcription factor and TANNIN1 showed strong association with pericarp color validating previous observations. Overall, the genetic architecture of natural variation representing the complex Ethiopian sorghum germplasm was established. The study contributes to the characterization of genes and alleles controlling agronomic traits, and will serve as a source of markers for molecular breeding.
Collapse
Affiliation(s)
- Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Habte Nida
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Amare Seyoum
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Moges Mekonen
- Chiro Agricultural Research Center, Ethiopian Institute of Agricultural Research, Chiro, Ethiopia
| | - Amare Nega
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Dagnachew Lule
- Bako Agricultural Research Center, Oromia Agricultural Research Institute, Bako, Ethiopia
| | - Kebede Dessalegn
- Bako Agricultural Research Center, Oromia Agricultural Research Institute, Bako, Ethiopia
| | - Alemnesh Bekele
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Adane Gebreyohannes
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Adedayo Adeyanju
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Alemu Tirfessa
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Getachew Ayana
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Taye Taddese
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Firew Mekbib
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Ketema Belete
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Tesfaye Tesso
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
- *Correspondence: Gebisa Ejeta,
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Tesfaye Mengiste,
| |
Collapse
|
9
|
Kassubek J, Müller H, Del Tredici K, Lule D, Pinkhardt E, Braak H, Ludolph A. FV 1 In vivo staging in ALS – A mono-centric cross-sectional and longitudinal DTI-based study. Clin Neurophysiol 2017. [DOI: 10.1016/j.clinph.2017.06.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
10
|
Kassubek J, Lule D, Riecker A, Ludolph A, Unrath A, Müller H. Multiparametric MRI analysis of patients with amyotrophic lateral sclerosis compared to controls. Neuroimage 2009. [DOI: 10.1016/s1053-8119(09)71220-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|