1
|
Sehgal D, Rathan ND, Özdemir F, Keser M, Akin B, Dababat AA, Koc E, Dreisigacker S, Morgounov A. Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm. Sci Rep 2024; 14:8431. [PMID: 38600135 PMCID: PMC11006659 DOI: 10.1038/s41598-024-57469-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
A panel comprising of 84 Turkish winter wheat landraces (LR) and 73 modern varieties (MV) was analyzed with genome wide association study (GWAS) to identify genes/genomic regions associated with increased yield under favorable and drought conditions. In addition, selective sweep analysis was conducted to detect signatures of selection in the winter wheat genome driving the differentiation between LR and MV, to gather an understanding of genomic regions linked to adaptation and yield improvement. The panel was genotyped with 25 K wheat SNP array and phenotyped for agronomic traits for two growing seasons (2018 and 2019) in Konya, Turkey. Year 2018 was treated as drought environment due to very low precipitation prior to heading whereas year 2019 was considered as a favorable season. GWAS conducted with SNPs and haplotype blocks using mixed linear model identified 18 genomic regions in the vicinities of known genes i.e., TaERF3-3A, TaERF3-3B, DEP1-5A, FRIZZY PANICLE-2D, TaSnRK23-1A, TaAGL6-A, TaARF12-2A, TaARF12-2B, WAPO1, TaSPL16-7D, TaTGW6-A1, KAT-2B, TaOGT1, TaSPL21-6B, TaSBEIb, trs1/WFZP-A, TaCwi-A1-2A and TaPIN1-7A associated with grain yield (GY) and yield related traits. Haplotype-based GWAS identified five haplotype blocks (H1A-42, H2A-71, H4A-48, H7B-123 and H7B-124), with the favorable haplotypes showing a yield increase of > 700 kg/ha in the drought season. SNP-based GWAS, detected only one larger effect genomic region on chromosome 7B, in common with haplotype-based GWAS. On an average, the percentage variation (PV) explained by haplotypes was 8.0% higher than PV explained by SNPs for all the investigated traits. Selective sweep analysis detected 39 signatures of selection between LR and MV of which 15 were within proximity of known functional genes controlling flowering (PRR-A1, PPR-D1, TaHd1-6B), GY and GY components (TaSus2-2B, TaGS2-B1, AG1-1A/WAG1-1A, DUO-A1, DUO-B1, AG2-3A/WAG2-3A, TaLAX1, TaSnRK210-4A, FBP, TaLAX1, TaPIL1 and AP3-1-7A/WPA3-7A) and 10 regions underlying various transcription factors and regulatory genes. The study outcomes contribute to utilization of LR in breeding winter wheat.
Collapse
Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mex-Veracruz, El Batan, CP 56237, Veracruz, Mexico.
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK.
| | | | - Fatih Özdemir
- Bahri Dagdas International Agricultural Research Institute, Konya, Turkey
| | - Mesut Keser
- International Center for Agricultural Research in Dry Areas (ICARDA), Ankara, Turkey
| | - Beyhan Akin
- International Maize and Wheat Improvement Center (CIMMYT), Ankara, Turkey
| | | | - Emrah Koc
- International Maize and Wheat Improvement Center (CIMMYT), Ankara, Turkey
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mex-Veracruz, El Batan, CP 56237, Veracruz, Mexico
| | - Alexey Morgounov
- Scientific Production Center of Grain, Shortandy, Astana reg., 010000, Kazakhstan.
| |
Collapse
|
2
|
Li S, Cao Y, Wang C, Yan C, Sun X, Zhang L, Wang W, Song S. Genome-wide association mapping for yield-related traits in soybean (Glycine max) under well-watered and drought-stressed conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1265574. [PMID: 37877078 PMCID: PMC10593458 DOI: 10.3389/fpls.2023.1265574] [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: 07/23/2023] [Accepted: 09/18/2023] [Indexed: 10/26/2023]
Abstract
Soybean (Glycine max) productivity is significantly reduced by drought stress. Breeders are aiming to improve soybean grain yields both under well-watered (WW) and drought-stressed (DS) conditions, however, little is known about the genetic architecture of yield-related traits. Here, a panel of 188 soybean germplasm was used in a genome wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers linked to yield-related traits including pod number per plant (PN), biomass per plant (BM) and seed weight per plant (SW). The SLAF-seq genotyping was conducted on the population and three phenotype traits were examined in WW and DS conditions in four environments. Based on best linear unbiased prediction (BLUP) data and individual environmental analyses, 39 SNPs were significantly associated with three soybean traits under two conditions, which were tagged to 26 genomic regions by linkage disequilibrium (LD) analysis. Of these, six QTLs qPN-WW19.1, qPN-DS8.8, qBM-WW1, qBM-DS17.4, qSW-WW4 and qSW-DS8 were identified controlling PN, BM and SW of soybean. There were larger proportions of favorable haplotypes for locus qPN-WW19.1 and qSW-WW4 rather than qBM-WW1, qBM-DS17.4, qPN-DS8.8 and qSW-DS8 in both landraces and improved cultivars. In addition, several putative candidate genes such as Glyma.19G211300, Glyma.17G057100 and Glyma.04G124800, encoding E3 ubiquitin-protein ligase BAH1, WRKY transcription factor 11 and protein zinc induced facilitator-like 1, respectively, were predicted. We propose that the further exploration of these locus will facilitate accelerating breeding for high-yield soybean cultivars.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Wenbin Wang
- Institute of Crop Research, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Shuhong Song
- Institute of Crop Research, Liaoning Academy of Agricultural Sciences, Shenyang, China
| |
Collapse
|
3
|
Soto-Cerda BJ, Aravena G, Cloutier S. Genetic dissection of flowering time in flax (Linum usitatissimum L.) through single- and multi-locus genome-wide association studies. Mol Genet Genomics 2021; 296:877-891. [PMID: 33903955 DOI: 10.1007/s00438-021-01785-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/09/2021] [Indexed: 01/19/2023]
Abstract
In a rapidly changing climate, flowering time (FL) adaptation is important to maximize seed yield in flax (Linum usitatissimum L.). However, our understanding of the genetic mechanism underlying FL in this multipurpose crop remains limited. With the aim of dissecting the genetic architecture of FL in flax, a genome-wide association study (GWAS) was performed on 200 accessions of the flax core collection evaluated in four environments. Two single-locus and six multi-locus models were applied using 70,935 curated single nucleotide polymorphism (SNP) markers. A total of 40 quantitative trait nucleotides (QTNs) associated with 27 quantitative trait loci (QTL) were identified in at least two environments. The number of QTL with positive-effect alleles in accessions was significantly correlated with FL (r = 0.77 to 0.82), indicating principally additive gene actions. Nine QTL were significant in at least three of the four environments accounting for 3.06-14.71% of FL variation. These stable QTL spanned regions that harbored 27 Arabidopsis thaliana and Oryza sativa FL-related orthologous genes including FLOWERING LOCUS T (Lus10013532), FLOWERING LOCUS D (Lus10028817), transcriptional regulator SUPERMAN (Lus10021215), and gibberellin 2-beta-dioxygenase 2 (Lus10037816). In silico gene expression analysis of the 27 FL candidate gene orthologous suggested that they might play roles in the transition from vegetative to reproductive phase, flower development and fertilization. Our results provide new insights into the QTL architecture of flowering time in flax, identify potential candidate genes for further studies, and demonstrate the effectiveness of combining different GWAS models for the genetic dissection of complex traits.
Collapse
Affiliation(s)
- Braulio J Soto-Cerda
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, 4781158, Temuco, Chile.
| | - Gabriela Aravena
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, 4781158, Temuco, Chile
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| |
Collapse
|
4
|
Wu S, Alseekh S, Brotman Y, Fernie AR. Metabolomic Analysis of Natural Variation in Arabidopsis. Methods Mol Biol 2021; 2200:393-411. [PMID: 33175389 DOI: 10.1007/978-1-0716-0880-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Methodological advances in coupled-mass spectrometry (gas chromatography and liquid chromatography; GC-MS and LC-MS) have rendered the profiling of highly complex plant extracts relatively facile and allowed that their high-throughput use aids the investigation of a range of biological questions. Among these is the elucidation of the genetic factors underlying metabolite abundance. For this purpose genome-wide association studies (GWAS) are being widely adopted in Arabidopsis with the resultant quantitative trait loci being subjected to cross-validation by the use of recombinant inbred lines, introgression lines, and T-DNA insertional knockout lines.
Collapse
Affiliation(s)
- Si Wu
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Yariv Brotman
- Departments of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.
| |
Collapse
|
5
|
Abstract
Recent methodological advances in both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) have provided a deep understanding of metabolic regulation occurring in plant cells. The application of these techniques to agricultural systems is, however, subject to more complex interactions. Here we summarize a step-by-step modern metabolomics methodology that generates metabolome data toward the implementation of metabolomics in crop breeding. We describe a metabolic workflow, and provide guidelines for handling large sample numbers for the specific purpose of metabolic quantitative trait loci approaches.
Collapse
Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. .,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| |
Collapse
|
6
|
Ezenwaka L, Rabbi I, Onyeka J, Kulakow P, Egesi C. Identification of additional /novel QTL associated with resistance to cassava green mite in a biparental mapping population. PLoS One 2020; 15:e0231008. [PMID: 32240258 PMCID: PMC7117712 DOI: 10.1371/journal.pone.0231008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/13/2020] [Indexed: 11/19/2022] Open
Abstract
Cassava green mite [CGM, Mononychellus tanajoa (Bondar)] is the most destructive dry-season pest in most cassava production areas. The pest is responsible for cassava fresh root yield losses of over 80%. Deployment of CGM resistant cultivars is the most cost-effective and sustainable approach of alleviating such production losses. The purposes of this study were to validate the stability of CGM resistance genes found in previously published results, to identify new genes for CGM resistance in bi-parental mapping population and estimate the heritability of the trait. A total of 109 F1 progeny derived from a cross between CGM resistant parent, TMEB778 and a very susceptible parent, TMEB419 were evaluated under CGM hotspot areas in Nigeria for two cropping seasons. A total of 42,204 SNP markers with MAF ≥ 0.05 were used for single-marker analysis. The most significant QTL (S12_7962234) was identified on the left arm on chromosome 12 which explained high phenotypic variance and harboured significant single nucleotide polymorphism (SNP) markers conferring resistance to CGM and leaf pubescence (LP). Colocalization of the most significant SNP associated with resistance to CGM and LP on chromosome 12 is possibly an indication of a beneficial pleiotropic effect or are physically linked. These significant SNPs markers were intersected with the gene annotations and 33 unique genes were identified within SNPs at 4 - 8MB on chromosome 12. Among these genes, nine novel candidate genes namely; Manes.12077600, Manes.12G086200, Manes.12G061200, Manes.12G083100, Manes.12G082000, Manes.12G094100, Manes.12G075600, Manes.12G091400 and Manes.12G069300 highly expressed direct link to cassava green mite resistance. Pyramiding the new QTL/genes identified on chromosome 12 in this study with previously discovered loci, such on chromosome 8, will facilitate breeding varieties that are highly resistant CGM.
Collapse
Affiliation(s)
- Lydia Ezenwaka
- National Root Crops Research Institute, NRCRI, Umudike, Nigeria
| | - Ismail Rabbi
- International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Joseph Onyeka
- National Root Crops Research Institute, NRCRI, Umudike, Nigeria
| | - Peter Kulakow
- International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Chiedozie Egesi
- National Root Crops Research Institute, NRCRI, Umudike, Nigeria
- International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States of America
- * E-mail:
| |
Collapse
|
7
|
Marrano A, Martínez‐García PJ, Bianco L, Sideli GM, Di Pierro EA, Leslie CA, Stevens KA, Crepeau MW, Troggio M, Langley CH, Neale DB. A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density Axiom™ J. regia 700K SNP genotyping array. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1027-1036. [PMID: 30515952 PMCID: PMC6523593 DOI: 10.1111/pbi.13034] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/22/2018] [Accepted: 10/28/2018] [Indexed: 05/02/2023]
Abstract
Over the last 20 years, global production of Persian walnut (Juglans regia L.) has grown enormously, likely reflecting increased consumption due to its numerous benefits to human health. However, advances in genome-wide association (GWA) studies and genomic selection (GS) for agronomically important traits in walnut remain limited due to the lack of powerful genomic tools. Here, we present the development and validation of a high-density 700K single nucleotide polymorphism (SNP) array in Persian walnut. Over 609K high-quality SNPs have been thoroughly selected from a set of 9.6 m genome-wide variants, previously identified from the high-depth re-sequencing of 27 founders of the Walnut Improvement Program (WIP) of University of California, Davis. To validate the effectiveness of the array, we genotyped a collection of 1284 walnut trees, including 1167 progeny of 48 WIP families and 26 walnut cultivars. More than half of the SNPs (55.7%) fell in the highest quality class of 'Poly High Resolution' (PHR) polymorphisms, which were used to assess the WIP pedigree integrity. We identified 151 new parent-offspring relationships, all confirmed with the Mendelian inheritance test. In addition, we explored the genetic variability among cultivars of different origin, revealing how the varieties from Europe and California were differentiated from Asian accessions. Both the reconstruction of the WIP pedigree and population structure analysis confirmed the effectiveness of the Applied Biosystems™ Axiom™ J. regia 700K SNP array, which initiates a novel genomic and advanced phase in walnut genetics and breeding.
Collapse
Affiliation(s)
| | | | - Luca Bianco
- Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeTNItaly
| | - Gina M. Sideli
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Erica A. Di Pierro
- Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeTNItaly
| | | | | | - Marc W. Crepeau
- Department of Evolution and EcologyUniversity of CaliforniaDavisCAUSA
| | - Michela Troggio
- Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeTNItaly
| | | | - David B. Neale
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| |
Collapse
|
8
|
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] [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
| |
Collapse
|