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Angmo D, Sharma SP, Kalia A. Breeding strategies for late blight resistance in potato crop: recent developments. Mol Biol Rep 2023; 50:7879-7891. [PMID: 37526862 DOI: 10.1007/s11033-023-08577-0] [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: 03/05/2023] [Accepted: 06/01/2023] [Indexed: 08/02/2023]
Abstract
Late blight (LB) is a serious disease that affects potato crop and is caused by Phytophthora infestans. Fungicides are commonly used to manage this disease, but this practice has led to the development of resistant strains and it also poses serious environmental and health risks. Therefore, breeding for resistance development can be the most effective strategies to control late blight. Various Solanum species have been utilized as a source of resistance genes to combat late blight disease. Several potential resistance genes and quantitative resistance loci (QRLs) have been identified and mapped through the application of molecular techniques. Furthermore, molecular markers closely linked to resistance genes or QRLs have been utilized to hasten the breeding process. However, the use of single-gene resistance can lead to the breakdown of resistance within a short period. To address this, breeding programs are now being focused on development of durable and broad-spectrum resistant cultivars by combining multiple resistant genes and QRLs using advanced molecular breeding tools such as marker-assisted selection (MAS) and cis-genic approaches. In addition to the strategies mentioned earlier, somatic hybridization has been utilized for the development and characterization of interspecific somatic hybrids. To further broaden the scope of late blight resistance breeding, approaches such as genomic selection, RNAi silencing, and various genome editing techniques can be employed. This study provides an overview of recent advances in various breeding strategies and their applications in improving the late blight resistance breeding program.
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Affiliation(s)
- Dechen Angmo
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.
| | - Sat Pal Sharma
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Anu Kalia
- Electron Microscopy and Nanoscience Laboratory, Department of Soil Science, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
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Banerjee N, Khan MS, Swapna M, Yadav S, Tiwari GJ, Jena SN, Patel JD, Manimekalai R, Kumar S, Dattamajuder SK, Kapur R, Koebernick JC, Singh RK. QTL mapping and identification of candidate genes linked to red rot resistance in sugarcane. 3 Biotech 2023; 13:82. [PMID: 36778768 PMCID: PMC9911584 DOI: 10.1007/s13205-023-03481-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/13/2023] [Indexed: 02/12/2023] Open
Abstract
Sugarcane (Saccharum species hybrid) is one of the most important commercial crops cultivated worldwide for products like white sugar, bagasse, ethanol, etc. Red rot is a major sugarcane disease caused by a hemi-biotrophic fungus, Colletotrichum falcatum Went., which can potentially cause a reduction in yield up to 100%. Breeding for red rot-resistant sugarcane varieties has become cumbersome due to its complex genome and frequent generation of new pathotypes of red rot fungus. In the present study, a genetic linkage map was developed using a selfed population of a popular sugarcane variety CoS 96268. A QTL linked to red rot resistance (qREDROT) was identified, which explained 26% of the total phenotypic variation for the trait. A genotype-phenotype network analysis performed to account for epistatic interactions, identified the key markers involved in red rot resistance. The differential expression of the genes located in the genomic region between the two flanking markers of the qREDROT as well as in the vicinity of the markers identified through the genotype-phenotype network analysis in a set of contrasting genotypes for red rot infection further confirmed the mapping results. Further, the expression analysis revealed that the plant defense-related gene coding 26S protease regulatory subunit is strongly associated with the red rot resistance. The findings can help in the screening of disease resistant genotypes for developing red rot-resistant varieties of sugarcane. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03481-7.
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Affiliation(s)
- Nandita Banerjee
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Mohammad Suhail Khan
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - M. Swapna
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Sonia Yadav
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Gopal Ji Tiwari
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Satya N. Jena
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Jinesh D. Patel
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - R. Manimekalai
- Biotechnology Lab, Sugarcane Breeding Institute, Coimbatore, 641007 India
| | - Sanjeev Kumar
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - S. K. Dattamajuder
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Raman Kapur
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Jenny C. Koebernick
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - Ram K. Singh
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
- Present Address: Crop Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001 India
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3
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de Los Angeles Bohórquez-Quintero M, Galvis-Tarazona DY, Arias-Moreno DM, Ojeda-Peréz ZZ, Ochatt S, Rodríguez-Molano LE. Morphological and anatomical characterization of yellow diploid potato flower for effective breeding program. Sci Rep 2022; 12:16402. [PMID: 36180534 PMCID: PMC9525687 DOI: 10.1038/s41598-022-20439-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
The diploid yellow potato (Solanum tuberosum L. Phureja Group) is an important plant genetic resource. In this study, we report for the first time the characterization of anther development and pollen formation in the cultivar Criolla Colombia. The description of morphological and histological characters of buds and flowers at different developmental stages permitted to identify ten main stages, from the differentiation of the male cells of the sporangium, meiosis, microspores formation and maturation, to the release of mature pollen. In addition, the results provide a graphic guide of the development of the anther, through the sequential and orderly formation of the epidermis, the endothecium, the middle layer and the nutritive layer or tapetum. This microanatomical information will be useful for work focused on androgenesis and identification of gene regulation in floral biology and gamete formation. Therefore, this study determined that to efficiently obtain haploids, flower buds between 5 and 8.9 mm long (stage 6 to 8) should be used, in which tetrads and microspores are in the early uninucleate and binucleate stage.
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Affiliation(s)
- María de Los Angeles Bohórquez-Quintero
- Grupo de Investigación BIOPLASMA-UPTC, Escuela de Ciencias Biológicas, Facultad de Ciencias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Daicy Yaneth Galvis-Tarazona
- Grupo de Investigación BIOPLASMA-UPTC, Escuela de Ciencias Biológicas, Facultad de Ciencias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Diana Marcela Arias-Moreno
- Grupo de Investigación BIOPLASMA-UPTC, Escuela de Ciencias Biológicas, Facultad de Ciencias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia.
| | - Zaida Zarely Ojeda-Peréz
- Grupo de Investigación BIOPLASMA-UPTC, Escuela de Ciencias Biológicas, Facultad de Ciencias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Sergio Ochatt
- Agroécologie, INRAE, Insitut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Luis Ernesto Rodríguez-Molano
- Facultad de Ciencias Agrarias, Departamento de Agronomía, Universidad Nacional de Colombia, Carrera 30 Núm. 45-03, Edificio 500, Bogotá D.C., Colombia
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Díaz P, Sarmiento F, Mathew B, Ballvora A, Mosquera Vásquez T. Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS. PLoS One 2021; 16:e0259690. [PMID: 34748612 PMCID: PMC8575265 DOI: 10.1371/journal.pone.0259690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/24/2021] [Indexed: 11/19/2022] Open
Abstract
Water deficit, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Dissection of the genetic architecture of water deficit responses is highly desirable for developing water-deficit tolerant potato cultivars and enhancing the resilience of existing cultivars. This study examined genetic variation in response to water deficit in a panel of diploid potato and identified the QTL governing this trait via a genome-wide association study (GWAS). A panel of 104 diploid potato accessions were evaluated under both well-watered and water deficit treatments at tuber initiation stage. Drought stress index (DTI) was calculated to assess tolerance of the diploid potato genotypes to water deficit. The GWAS was conducted using a matrix of 47K single nucleotide polymorphisms (SNP), recently available for this population. We are reporting 38 QTL, seven for well-watered conditions, twenty-two for water deficit conditions and nine for DTI which explain between 12.6% and 44.1% of the phenotypic variance. A set of 6 QTL were found to be associated with more than one variable. Marker WDP-9.21 was found associated with tuber fresh weigh under WD and gene annotation analysis revealed co-localization with the Glucan/water dikinase (GWD) gene. Of the nine QTL detected from DTI on chromosomes 2,3,5,8,10 and 12, three candidate genes with a feasible role in water deficit response were identified. The findings of this study can be used in marker-assisted selection (MAS) for water- deficit tolerance breeding in potato.
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Affiliation(s)
- Paula Díaz
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia-Sede Bogotá, Bogotá, Colombia
| | - Felipe Sarmiento
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia-Sede Bogotá, Bogotá, Colombia
| | - Boby Mathew
- Bayer CropScience, Monheim am Rhein, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation Plant Breeding, University of Bonn, Bonn, Germany
| | - Teresa Mosquera Vásquez
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia-Sede Bogotá, Bogotá, Colombia
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5
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Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees. PLANTS 2021; 10:plants10071440. [PMID: 34371639 PMCID: PMC8309273 DOI: 10.3390/plants10071440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 02/01/2023]
Abstract
Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.
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Garreta L, Cerón‐Souza I, Palacio MR, Reyes‐Herrera PH. MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms. Ecol Evol 2021; 11:7411-7426. [PMID: 34188823 PMCID: PMC8216910 DOI: 10.1002/ece3.7572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
The genome-wide association studies (GWASs) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of the model and nonmodel organisms. For this research question, the GWAS replication testing different parameters and models to validate the results' reproducibility is common. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software packages, two designed for polyploid data (GWASpoly and SHEsis) and two designed for diploid data (GAPIT and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in a graphical interface; it manages different genotype formats, including VCF. Moreover, it allows control for population structure, relatedness, and several quality control checks on genotype data. Besides, MultiGWAS can test for additive and dominant gene action models, and, through a proprietary scoring function, select the best model to report its associations. Finally, it generates several reports that facilitate identifying false associations from both the significant and the best-ranked association Single Nucleotide Polymorphisms (SNPs) among the four software packages. We tested MultiGWAS with public tetraploid potato data for tuber shape and several simulated data under both additive and dominant models. These tests demonstrated that MultiGWAS is better at detecting reliable associations than using each of the four software packages individually. Moreover, the parallel analysis of polyploid and diploid software that only offers MultiGWAS demonstrates its utility in understanding the best genetic model behind the SNP association in tetraploid organisms. Therefore, MultiGWAS probed to be an excellent alternative for wrapping GWAS replication in diploid and tetraploid organisms in a single analysis environment.
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Affiliation(s)
- Luis Garreta
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
| | - Ivania Cerón‐Souza
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
| | | | - Paula H. Reyes‐Herrera
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
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Cuervo-Alarcon L, Arend M, Müller M, Sperisen C, Finkeldey R, Krutovsky KV. A candidate gene association analysis identifies SNPs potentially involved in drought tolerance in European beech (Fagus sylvatica L.). Sci Rep 2021; 11:2386. [PMID: 33504857 PMCID: PMC7840767 DOI: 10.1038/s41598-021-81594-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
Studies of genetic variation underlying traits related to drought tolerance in forest trees are of great importance for understanding their adaptive potential under a climate change scenario. In this study, using a candidate gene approach, associations between SNPs and drought related traits were assessed in saplings of European beech (Fagus sylvatica L.) representing trees growing along steep precipitation gradients. The saplings were subjected to experimentally controlled drought treatments. Response of the saplings was assessed by the evaluation of stem diameter growth (SDG) and the chlorophyll fluorescence parameters FV/FM, PIabs, and PItot. The evaluation showed that saplings from xeric sites were less affected by the drought treatment. Five SNPs (7.14%) in three candidate genes were significantly associated with the evaluated traits; saplings with particular genotypes at these SNPs showed better performance under the drought treatment. The SNPs were located in the cytosolic class I small heat-shock protein, CTR/DRE binding transcription factor, and isocitrate dehydrogenase genes and explained 5.8-13.4% of the phenotypic variance. These findings provide insight into the genetic basis of traits related to drought tolerance in European beech and could support the development of forest conservation management strategies under future climatic conditions.
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Affiliation(s)
- Laura Cuervo-Alarcon
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Matthias Arend
- Physiological Plant Ecology, University of Basel, Schönbeinstrasse 6, 4056, Basel, Switzerland
| | - Markus Müller
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Christoph Sperisen
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Reiner Finkeldey
- University of Kassel, Mönchebergstrasse 19, 34109, Kassel, Germany
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., Moscow, Russia, 119333.
- Laboratory of Foresty Genomics, Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk, Russia, 660036.
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.
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Khanbo S, Tangphatsornruang S, Piriyapongsa J, Wirojsirasak W, Punpee P, Klomsa-Ard P, Ukoskit K. Candidate gene association of gene expression data in sugarcane contrasting for sucrose content. Genomics 2020; 113:229-237. [PMID: 33321201 DOI: 10.1016/j.ygeno.2020.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022]
Abstract
Association mapping of gene expression data, generated from transcriptome and proteome studies, provides a means of understanding the functional significance and trait association potential of candidate genes. In this study, we applied candidate gene association mapping to validate sugarcane genes, using data from the starch and sucrose metabolism pathway, transcriptome, and proteome. We performed multiplex PCR targeted amplicon sequencing of 109 candidate genes, using NGS technology. A range of statistical models, both single-locus and multi-locus, were compared for minimization of false positives in association mapping of four sugar-related traits with different heritability. The Fixed and random model Circulating Probability Unification model effectively suppressed false positives for both low- and high-heritability traits. We identified favorable alleles of the candidate genes involved in signalling and transcriptional regulation. The results will support genetic improvement of sugarcane and may help clarify the genetic architecture of sugar-related traits.
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Affiliation(s)
- Supaporn Khanbo
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand
| | - Sithichoke Tangphatsornruang
- National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jittima Piriyapongsa
- National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Warodom Wirojsirasak
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Prapat Punpee
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Peeraya Klomsa-Ard
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand.
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Saidi A, Hajibarat Z. Application of Next Generation Sequencing, GWAS, RNA seq, WGRS, for genetic improvement of potato (Solanum tuberosum L.) under drought stress. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Dubey H, Rawal HC, Rohilla M, Lama U, Kumar PM, Bandyopadhyay T, Gogoi M, Singh NK, Mondal TK. TeaMiD: a comprehensive database of simple sequence repeat markers of tea. Database (Oxford) 2020; 2020:baaa013. [PMID: 32159215 PMCID: PMC7065459 DOI: 10.1093/database/baaa013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/05/2020] [Accepted: 01/25/2020] [Indexed: 12/05/2022]
Abstract
Tea is a highly cross-pollinated, woody, perennial tree. High heterozygosity combined with a long gestational period makes conventional breeding a cumbersome process. Therefore, marker-assisted breeding is a better alternative approach when compared with conventional breeding. Considering the large genome size of tea (~3 Gb), information about simple sequence repeat (SSR) is scanty. Thus, we have taken advantage of the recently published tea genomes to identify large numbers of SSR markers in the tea. Besides the genomic sequences, we identified SSRs from the other publicly available sequences such as RNA-seq, GSS, ESTs and organelle genomes (chloroplasts and mitochondrial) and also searched published literature to catalog validated set of tea SSR markers. The complete exercise yielded a total of 935 547 SSRs. Out of the total, 82 SSRs were selected for validation among a diverse set of tea genotypes. Six primers (each with four to six alleles, an average of five alleles per locus) out of the total 27 polymorphic primers were used for a diversity analysis in 36 tea genotypes with mean polymorphic information content of 0.61-0.76. Finally, using all the information generated in this study, we have developed a user-friendly database (TeaMiD; http://indianteagenome.in:8080/teamid/) that hosts SSR from all the six resources including three nuclear genomes of tea and transcriptome sequences of 17 Camellia wild species. Database URL: http://indianteagenome.in:8080/teamid/.
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Affiliation(s)
- Himanshu Dubey
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Hukam C Rawal
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Megha Rohilla
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Urvashi Lama
- Darjeeling Tea Research and Development Centre, Tea Board, Ministry of Commerce, B.T.M. Sarani (Brabourne Road), Kolkata, West Bengal 700001, India
| | - P Mohan Kumar
- Darjeeling Tea Research and Development Centre, Tea Board, Ministry of Commerce, B.T.M. Sarani (Brabourne Road), Kolkata, West Bengal 700001, India
| | - Tanoy Bandyopadhyay
- Department of Biotechnology, Tocklai Experimental Station, Tea Research Association, Jorhat, Assam, India
| | - Madhurjya Gogoi
- Department of Biotechnology, Tocklai Experimental Station, Tea Research Association, Jorhat, Assam, India
| | - Nagendra Kumar Singh
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Tapan Kumar Mondal
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
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Astorkia M, Hernandez M, Bocs S, Lopez de Armentia E, Herran A, Ponce K, León O, Morales S, Quezada N, Orellana F, Wendra F, Sembiring Z, Asmono D, Ritter E. Association Mapping Between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids. PLANTS 2019; 8:plants8100377. [PMID: 31561627 PMCID: PMC6843369 DOI: 10.3390/plants8100377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 01/07/2023]
Abstract
Oil palm production is gaining importance in Central and South America. However, the main species Elaeis guineensis (Eg) is suffering severely from bud rod disease, restricting the potential cultivation areas. Therefore, breeding companies have started to work with interspecific Elaeis oleifera × Eg (Eo × Eg) hybrids which are tolerant to this disease. We performed association studies between candidate gene (CG) single nucleotide polymorphisms (SNP) and six production and 19 oil quality traits in 198 accessions of interspecific oil palm hybrids from five different origins. For this purpose, barcoded amplicons of initially 167 CG were produced from each genotype and sequenced with Ion Torrent. After sequence cleaning 115 SNP remained targeting 62 CG. The influence of the origins on the different traits was analyzed and a genetic diversity study was performed. Two generalized linear models (GLM) with principle component analysis (PCA) or structure (Q) matrixes as covariates and two mixed linear models (MLM) which included in addition a Kinship (K) matrix were applied for association mapping using GAPIT. False discovery rate (FDR) multiple testing corrections were applied in order to avoid Type I errors. However, with FDR adjusted p values no significant associations between SNP and traits were detected. If using unadjusted p values below 0.05, seven of the studied CG showed potential associations with production traits, while 23 CG may influence different quality traits. Under these conditions the current approach and the detected candidate genes could be exploited for selecting genotypes with superior CG alleles in Marker Assisted Selection systems.
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Affiliation(s)
- Maider Astorkia
- NEIKER Tecnalia, Campus Agroalimentario de Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain; (M.H.); (E.L.d.A.); (A.H.); (E.R.)
- Correspondence:
| | - Mónica Hernandez
- NEIKER Tecnalia, Campus Agroalimentario de Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain; (M.H.); (E.L.d.A.); (A.H.); (E.R.)
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, F-34398 Montpellier, France;
- AGAP, CIRAD, Univ Montpellier, INRA, Montpellier SupAgro, F-34398 Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, F-34398 Montpellier, France
| | - Emma Lopez de Armentia
- NEIKER Tecnalia, Campus Agroalimentario de Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain; (M.H.); (E.L.d.A.); (A.H.); (E.R.)
| | - Ana Herran
- NEIKER Tecnalia, Campus Agroalimentario de Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain; (M.H.); (E.L.d.A.); (A.H.); (E.R.)
| | - Kevin Ponce
- La Fabril SA, km 5.5 via Manta–Montecristi, Avenida 113, 130902 Manta, Ecuador; (K.P.); (S.M.); (N.Q.)
| | - Olga León
- Energy & Palma SA, Av. Atahualpa E3-49 y Juan Gonzales, Ed. Fundación Pérez Pallarez, Officina 4ª, Quito 170507, Ecuador; (O.L.); (F.O.)
| | - Shone Morales
- La Fabril SA, km 5.5 via Manta–Montecristi, Avenida 113, 130902 Manta, Ecuador; (K.P.); (S.M.); (N.Q.)
| | - Nathalie Quezada
- La Fabril SA, km 5.5 via Manta–Montecristi, Avenida 113, 130902 Manta, Ecuador; (K.P.); (S.M.); (N.Q.)
| | - Francisco Orellana
- Energy & Palma SA, Av. Atahualpa E3-49 y Juan Gonzales, Ed. Fundación Pérez Pallarez, Officina 4ª, Quito 170507, Ecuador; (O.L.); (F.O.)
| | - Fahmi Wendra
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788 Palembang 30127, Indonesia; (F.W.); (Z.S.); (D.A.)
| | - Zulhermana Sembiring
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788 Palembang 30127, Indonesia; (F.W.); (Z.S.); (D.A.)
| | - Dwi Asmono
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788 Palembang 30127, Indonesia; (F.W.); (Z.S.); (D.A.)
| | - Enrique Ritter
- NEIKER Tecnalia, Campus Agroalimentario de Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain; (M.H.); (E.L.d.A.); (A.H.); (E.R.)
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Juyo Rojas DK, Soto Sedano JC, Ballvora A, Léon J, Mosquera Vásquez T. Novel organ-specific genetic factors for quantitative resistance to late blight in potato. PLoS One 2019; 14:e0213818. [PMID: 31310605 PMCID: PMC6634379 DOI: 10.1371/journal.pone.0213818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/23/2019] [Indexed: 01/25/2023] Open
Abstract
Potato, Solanum tuberosum, is one of the major consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site–associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain between 13.7% and 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including a leucine-rich repeat kinase.
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Affiliation(s)
| | | | - Agim Ballvora
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Jens Léon
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Teresa Mosquera Vásquez
- Universidad Nacional de Colombia, sede Bogotá, Facultad de Ciencias Agrarias, Bogotá, Colombia
- * E-mail:
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Juyo Rojas DK, Soto Sedano JC, Ballvora A, Léon J, Mosquera Vásquez T. Novel organ-specific genetic factors for quantitative resistance to late blight in potato. PLoS One 2019. [PMID: 31310605 DOI: 10.1101/567289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Potato, Solanum tuberosum, is one of the major consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site-associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain between 13.7% and 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including a leucine-rich repeat kinase.
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Affiliation(s)
| | | | - Agim Ballvora
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Jens Léon
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Teresa Mosquera Vásquez
- Universidad Nacional de Colombia, sede Bogotá, Facultad de Ciencias Agrarias, Bogotá, Colombia
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Enciso-Rodriguez F, Douches D, Lopez-Cruz M, Coombs J, de Los Campos G. Genomic Selection for Late Blight and Common Scab Resistance in Tetraploid Potato ( Solanum tuberosum). G3 (BETHESDA, MD.) 2018; 8:2471-2481. [PMID: 29794167 PMCID: PMC6027896 DOI: 10.1534/g3.118.200273] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Potato (Solanum tuberosum) is a staple food crop and is considered one of the main sources of carbohydrates worldwide. Late blight (Phytophthora infestans) and common scab (Streptomyces scabies) are two of the primary production constraints faced by potato farming. Previous studies have identified a few resistance genes for both late blight and common scab; however, these genes explain only a limited fraction of the heritability of these diseases. Genomic selection has been demonstrated to be an effective methodology for breeding value prediction in many major crops (e.g., maize and wheat). However, the technology has received little attention in potato breeding. We present the first genomic selection study involving late blight and common scab in tetraploid potato. Our data involves 4,110 (Single Nucleotide Polymorphisms, SNPs) and phenotypic field evaluations for late blight (n=1,763) and common scab (n=3,885) collected in seven and nine years, respectively. We report moderately high genomic heritability estimates (0.46 ± 0.04 and 0.45 ± 0.017, for late blight and common scab, respectively). The extent of genotype-by-year interaction was high for late blight and low for common scab. Our assessment of prediction accuracy demonstrates the applicability of genomic prediction for tetraploid potato breeding. For both traits, we found that more than 90% of the genetic variance could be captured with an additive model. For common scab, the highest prediction accuracy was achieved using an additive model. For late blight, small but statistically significant gains in prediction accuracy were achieved using a model that accounted for both additive and dominance effects. Using whole-genome regression models we identified SNPs located in previously reported hotspots regions for late blight, on genes associated with systemic disease resistance responses, and a new locus located in a WRKY transcription factor for common scab.
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Affiliation(s)
| | | | | | | | - Gustavo de Los Campos
- Department of Epidemiology & Biostatistics
- Department of Statistics & Probability
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, 48824
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