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Sharma SK, McLean K, Hedley PE, Dale F, Daniels S, Bryan GJ. Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:180. [PMID: 38980417 PMCID: PMC11233353 DOI: 10.1007/s00122-024-04651-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/10/2024] [Indexed: 07/10/2024]
Abstract
KEY MESSAGE De novo genotyping in potato using methylation-sensitive GBS discovers SNPs largely confined to genic or gene-associated regions and displays enhanced effectiveness in estimating LD decay rates, population structure and detecting GWAS associations over 'fixed' SNP genotyping platform. Study also reports the genetic architectures including robust sequence-tagged marker-trait associations for sixteen important potato traits potentially carrying higher transferability across a wider range of germplasm. This study deploys recent advancements in polyploid analytical approaches to perform complex trait analyses in cultivated tetraploid potato. The study employs a 'fixed' SNP Infinium array platform and a 'flexible and open' genome complexity reduction-based sequencing method (GBS, genotyping-by-sequencing) to perform genome-wide association studies (GWAS) for several key potato traits including the assessment of population structure and linkage disequilibrium (LD) in the studied population. GBS SNPs discovered here were largely confined (~ 90%) to genic or gene-associated regions of the genome demonstrating the utility of using a methylation-sensitive restriction enzyme (PstI) for library construction. As compared to Infinium array SNPs, GBS SNPs displayed enhanced effectiveness in estimating LD decay rates and discriminating population subgroups. GWAS using a combined set of 30,363 SNPs identified 189 unique QTL marker-trait associations (QTL-MTAs) covering all studied traits. The majority of the QTL-MTAs were from GBS SNPs potentially illustrating the effectiveness of marker-dense de novo genotyping platforms in overcoming ascertainment bias and providing a more accurate correction for different levels of relatedness in GWAS models. GWAS also detected QTL 'hotspots' for several traits at previously known as well as newly identified genomic locations. Due to the current study exploiting genome-wide genotyping and de novo SNP discovery simultaneously on a large tetraploid panel representing a greater diversity of the cultivated potato gene pool, the reported sequence-tagged MTAs are likely to have higher transferability across a wider range of potato germplasm and increased utility for expediting genomics-assisted breeding for the several complex traits studied.
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Affiliation(s)
- Sanjeev Kumar Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Karen McLean
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Peter E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Finlay Dale
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
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Wang Y, Brown LH, Adams TM, Cheung YW, Li J, Young V, Todd DT, Armstrong MR, Neugebauer K, Kaur A, Harrower B, Oome S, Wang X, Bayer M, Hein I. SMRT-AgRenSeq-d in potato ( Solanum tuberosum) as a method to identify candidates for the nematode resistance Gpa5. HORTICULTURE RESEARCH 2023; 10:uhad211. [PMID: 38023472 PMCID: PMC10681002 DOI: 10.1093/hr/uhad211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023]
Abstract
Potato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes. To identify effective disease resistance genes in established varieties, we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR-AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score. Using a SMRT-RenSeq-based sequence representation of the NLRome from the cultivar Innovator, SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1, Rpi-R2-like, Rpi-R3a, and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1, which indicates absolute linkage in the panel. This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode (PCN) species Globodera pallida (pathotypes Pa2/3). Assuming that NLRs are involved in controlling many types of resistances, SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems.
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Affiliation(s)
- Yuhan Wang
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Lynn H Brown
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Thomas M Adams
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Yuk Woon Cheung
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Jie Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
| | - Vanessa Young
- James Hutton Limited, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Drummond T Todd
- James Hutton Limited, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Miles R Armstrong
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Konrad Neugebauer
- Biomathematics and Statistics Scotland, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Amanpreet Kaur
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- Crop Research Centre, Teagasc, Oak Park, Carlow R93 XE12, Ireland
| | - Brian Harrower
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Stan Oome
- HZPC Research B.V. HZPC, Edisonweg 5, 8501 XG Joure, Netherlands
| | - Xiaodan Wang
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
| | - Micha Bayer
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Ingo Hein
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
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3
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Gartner U, Hein I, Brown LH, Chen X, Mantelin S, Sharma SK, Dandurand LM, Kuhl JC, Jones JT, Bryan GJ, Blok VC. Resisting Potato Cyst Nematodes With Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:661194. [PMID: 33841485 PMCID: PMC8027921 DOI: 10.3389/fpls.2021.661194] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/03/2021] [Indexed: 05/17/2023]
Abstract
Potato cyst nematodes (PCN) are economically important pests with a worldwide distribution in all temperate regions where potatoes are grown. Because above ground symptoms are non-specific, and detection of cysts in the soil is determined by the intensity of sampling, infestations are frequently spread before they are recognised. PCN cysts are resilient and persistent; their cargo of eggs can remain viable for over two decades, and thus once introduced PCN are very difficult to eradicate. Various control methods have been proposed, with resistant varieties being a key environmentally friendly and effective component of an integrated management programme. Wild and landrace relatives of cultivated potato have provided a source of PCN resistance genes that have been used in breeding programmes with varying levels of success. Producing a PCN resistant variety requires concerted effort over many years before it reaches what can be the biggest hurdle-commercial acceptance. Recent advances in potato genomics have provided tools to rapidly map resistance genes and to develop molecular markers to aid selection during breeding. This review will focus on the translation of these opportunities into durably PCN resistant varieties.
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Affiliation(s)
- Ulrike Gartner
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Ingo Hein
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Lynn H. Brown
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Xinwei Chen
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sophie Mantelin
- INRAE UMR Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Sanjeev K. Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Louise-Marie Dandurand
- Entomology, Plant Pathology and Nematology Department, University of Idaho, Moscow, ID, United States
| | - Joseph C. Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States
| | - John T. Jones
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Glenn J. Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Vivian C. Blok
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Vivian C. Blok,
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Prodhomme C, Vos PG, Paulo MJ, Tammes JE, Visser RGF, Vossen JH, van Eck HJ. Distribution of P1(D1) wart disease resistance in potato germplasm and GWAS identification of haplotype-specific SNP markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1859-1871. [PMID: 32043234 PMCID: PMC7237394 DOI: 10.1007/s00122-020-03559-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/28/2020] [Indexed: 05/21/2023]
Abstract
KEY MESSAGE A Genome-Wide Association Study using 330 commercial potato varieties identified haplotype specific SNP markers associated with pathotype 1(D1) wart disease resistance. Synchytrium endobioticum is a soilborne obligate biotrophic fungus responsible for wart disease. Growing resistant varieties is the most effective way to manage the disease. This paper addresses the challenge to apply molecular markers in potato breeding. Although markers linked to Sen1 were published before, the identification of haplotype-specific single-nucleotide polymorphisms may result in marker assays with high diagnostic value. To identify hs-SNP markers, we performed a genome-wide association study (GWAS) in a panel of 330 potato varieties representative of the commercial potato gene pool. SNP markers significantly associated with pathotype 1 resistance were identified on chromosome 11, at the position of the previously identified Sen1 locus. Haplotype specificity of the SNP markers was examined through the analysis of false positives and false negatives and validated in two independent full-sib populations. This paper illustrates why it is not always feasible to design markers without false positives and false negatives for marker-assisted selection. In the case of Sen1, founders could not be traced because of a lack of identity by descent and because of the decay of linkage disequilibrium between Sen1 and flanking SNP markers. Sen1 appeared to be the main source of pathotype 1 resistance in potato varieties, but it does not explain all the resistance observed. Recombination and introgression breeding may have introduced new, albeit rare haplotypes involved in pathotype 1 resistance. The GWAS approach, in such case, is instrumental to identify SNPs with the best possible diagnostic value for marker-assisted breeding.
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Affiliation(s)
- Charlotte Prodhomme
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Peter G Vos
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- HZPC Research B.V., Roptawei 4, 9123 JB, Metslawier, The Netherlands
| | - Maria João Paulo
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jasper E Tammes
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Averis Seeds B.V., Valtherblokken Z40, 7876 TC, Valthermond, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jack H Vossen
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Herman J van Eck
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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Ngernmuen A, Suktrakul W, Kate-Ngam S, Jantasuriyarat C. Transcriptome Comparison of Defense Responses in the Rice Variety 'Jao Hom Nin' Regarding Two Blast Resistant Genes, Pish and Pik. PLANTS 2020; 9:plants9060694. [PMID: 32485961 PMCID: PMC7356797 DOI: 10.3390/plants9060694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 11/24/2022]
Abstract
Jao Hom Nin (JHN) is a Thai rice variety with broad-spectrum resistant against rice blast fungus. JHN contains two rice blast resistant genes, Pish and Pik, located on chromosome 1 and on chromosome 11, respectively. To understand the blast resistance in JHN, the study of the defense mechanism related to the Pish and Pik genes is crucial. This study aimed to dissect defense response genes between the Pish and Pik genes using the RNA-seq technique. Differentially expressed genes (DEGs) of Pish and Pik backcross inbred lines were identified between 0 and 24 h after inoculation with rice blast spore suspension. The results showed that 1248 and 858 DEGs were unique to the Pish and Pik lines, respectively. The wall-associated kinase gene was unique to the Pish line and the zinc-finger-containing protein gene was unique to the Pik line. Pathogenicity-related proteins PR-4 and PR-10 were commonly found in both Pish and Pik lines. Moreover, DEGs functionally categorized in brassinosteriod, jasmonic acid, and salicylic acid pathways were detected in both Pish and Pik lines. These unique and shared genes in the Pish and Pik rice blast defense responses will help to dissect the mechanisms of plant defense and facilitate rice blast breeding programs.
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Affiliation(s)
- Athipat Ngernmuen
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkhen Campus, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.N.); (W.S.)
| | - Worrawit Suktrakul
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkhen Campus, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.N.); (W.S.)
| | - Sureeporn Kate-Ngam
- Department of Agronomy, Faculty of Agriculture, Ubon Ratchathani University, Warinchamrap, Ubon Ratchathani 34190, Thailand;
| | - Chatchawan Jantasuriyarat
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkhen Campus, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.N.); (W.S.)
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Kasetsart University, Bangkok 10900, Thailand
- Correspondence: ; Tel.: +662-562-5444
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6
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Slater AT, Schultz L, Lombardi M, Rodoni BC, Bottcher C, Cogan NOI, Forster JW. Screening for Resistance to PVY in Australian Potato Germplasm. Genes (Basel) 2020; 11:genes11040429. [PMID: 32316258 PMCID: PMC7230960 DOI: 10.3390/genes11040429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/02/2020] [Accepted: 04/06/2020] [Indexed: 11/16/2022] Open
Abstract
Potatoes are an important human food crop, but have a number of yield limiting factors, including disease susceptibility. Potato virus Y (PVY) is found worldwide, and is one of the main virus problems for potato growers. PVY is transmitted by aphids and mechanically by machinery, tools and people, and symptoms are variable across cultivars and strains, including being symptomless in some cultivars. Therefore, breeding resistant cultivars is the best way to control this virus. This study phenotypically screened 74 of the main commercial cultivars and a few other select cultivars grown in Australia, in order to identify sources of resistance to PVY. The cultivars were screened against PVYO and PVYNTN, with 23 out of 71 resistant to PVYO and 13 out of 74 resistant to PVYNTN, and all these 13 were resistant to both strains. When the phenotypic screening was compared to the results listed on the European Cultivated Potato Database, the majority of results were found to be consistent. We then evaluated three molecular markers RYSC3, M45, and STM0003 for the extreme resistance genes Ryadg and Rysto, to validate the usefulness of the markers for marker-assisted selection (MAS) on Australian germplasm. The degree of correlation between the resistance phenotypes and the RYSC3, M45, and STM0003 markers for Ryadg and Rysto conferred PVY resistance was determined. Three cultivars amplified the RYSC3 marker, while the M45 marker amplified the same 3 and an additional 9. Of the 12 cultivars, 11 phenotyped as resistant, but 1 was susceptible. The STM0003 marker was amplified from only 2 cultivars that both had resistant phenotypes. The RYSC3, M45, and STM0003 markers were therefore able to identify all the 13 cultivars that were resistant to both strains of PVY. Therefore, these markers will enable the identification of genotypes with resistance to PVY, and enable PVY resistant parents to be used for the development of superior progeny; these genetic markers can be used for MAS in the Australian potato breeding program.
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Affiliation(s)
- Anthony T. Slater
- Agriculture Victoria, AgriBio, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
- Correspondence:
| | - Lee Schultz
- Agriculture Victoria, AgriBio, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Maria Lombardi
- Agriculture Victoria, AgriBio, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Brendan C. Rodoni
- Agriculture Victoria, AgriBio, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Chris Bottcher
- Agriculture Victoria, AgriBio, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Noel O. I. Cogan
- Agriculture Victoria, AgriBio, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
| | - John W. Forster
- Agriculture Victoria, AgriBio, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
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7
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Kondrák M, Kopp A, Uri C, Sós-Hegedűs A, Csákvári E, Schiller M, Barta E, Cernák I, Polgár Z, Taller J, Bánfalvi Z. Mapping and DNA sequence characterisation of the Rysto locus conferring extreme virus resistance to potato cultivar 'White Lady'. PLoS One 2020; 15:e0224534. [PMID: 32231371 PMCID: PMC7108733 DOI: 10.1371/journal.pone.0224534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/01/2020] [Indexed: 11/29/2022] Open
Abstract
Virus resistance genes carried by wild plant species are valuable resources for plant breeding. The Rysto gene, conferring a broad spectrum of durable resistance, originated from Solanum stoloniferum and was introgressed into several commercial potato cultivars, including ‘White Lady’, by classical breeding. Rysto was mapped to chromosome XII in potato, and markers used for marker-assisted selection in breeding programmes were identified. Nevertheless, there was no information on the identity of the Rysto gene. To begin to reveal the identification of Rysto, fine-scale genetic mapping was performed which, in combination with chromosome walking, narrowed down the locus of the gene to approximately 1 Mb. DNA sequence analysis of the locus identified six full-length NBS-LRR-type (short NLR-type) putative resistance genes. Two of them, designated TMV2 and TMV3, were similar to a TMV resistance gene isolated from tobacco and to Y-1, which co-segregates with Ryadg, the extreme virus resistance gene originated from Solanum andigena and localised to chromosome XI. Furthermore, TMV2 of ‘White Lady’ was found to be 95% identical at the genomic sequence level with the recently isolated Rysto gene of the potato cultivar ‘Alicja’. In addition to the markers identified earlier, this work generated five tightly linked new markers which can serve potato breeding efforts for extreme virus resistance.
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Affiliation(s)
- Mihály Kondrák
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Andrea Kopp
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Csilla Uri
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | | | - Edina Csákvári
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Mátyás Schiller
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Endre Barta
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - István Cernák
- Potato Research Centre, University of Pannonia, Keszthely, Hungary
| | - Zsolt Polgár
- Potato Research Centre, University of Pannonia, Keszthely, Hungary
| | - János Taller
- Department of Plant Sciences and Biotechnology, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
| | - Zsófia Bánfalvi
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
- * E-mail:
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8
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Grech-Baran M, Witek K, Szajko K, Witek AI, Morgiewicz K, Wasilewicz-Flis I, Jakuczun H, Marczewski W, Jones JDG, Hennig J. Extreme resistance to Potato virus Y in potato carrying the Ry sto gene is mediated by a TIR-NLR immune receptor. PLANT BIOTECHNOLOGY JOURNAL 2020. [PMID: 31397954 DOI: 10.1101/445031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Potato virus Y (PVY) is a major potato (Solanum tuberosum L.) pathogen that causes severe annual crop losses worth billions of dollars worldwide. PVY is transmitted by aphids, and successful control of virus transmission requires the extensive use of environmentally damaging insecticides to reduce vector populations. Rysto , from the wild relative S. stoloniferum, confers extreme resistance (ER) to PVY and related viruses and is a valuable trait that is widely employed in potato resistance breeding programmes. Rysto was previously mapped to a region of potato chromosome XII, but the specific gene has not been identified to date. In this study, we isolated Rysto using resistance gene enrichment sequencing (RenSeq) and PacBio SMRT (Pacific Biosciences single-molecule real-time sequencing). Rysto was found to encode a nucleotide-binding leucine-rich repeat (NLR) protein with an N-terminal TIR domain and was sufficient for PVY perception and ER in transgenic potato plants. Rysto -dependent extreme resistance was temperature-independent and requires EDS1 and NRG1 proteins. Rysto may prove valuable for creating PVY-resistant cultivars of potato and other Solanaceae crops.
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Affiliation(s)
- Marta Grech-Baran
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Katarzyna Szajko
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów, Poland
| | | | - Karolina Morgiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Iwona Wasilewicz-Flis
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów, Poland
| | - Henryka Jakuczun
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów, Poland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów, Poland
| | | | - Jacek Hennig
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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9
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Torrance L, Cowan GH, McLean K, MacFarlane S, Al-Abedy AN, Armstrong M, Lim TY, Hein I, Bryan GJ. Natural resistance to Potato virus Y in Solanum tuberosum Group Phureja. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:967-980. [PMID: 31950199 PMCID: PMC7021755 DOI: 10.1007/s00122-019-03521-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/20/2019] [Indexed: 05/22/2023]
Abstract
Novel major gene resistance against Potato virus Y in diploid populations of Solanum tuberosum Groups Phureja and Tuberosum was biologically and genetically characterised. Named Ry(o)phu, it mapped to chromosome 9. A new source of genetic resistance derived from Solanum tuberosum Group Phureja against Potato virus Y (PVY) was identified and genetically characterised in three diploid biparental potato populations. Segregation data for two populations (05H1 and 08H1) suggested the presence of a single dominant gene for resistance to PVY which, following DaRT analysis of the 08H1 cross, was mapped to chromosome 9. More detailed genetic analysis of resistance utilised a well-characterised SNP-linkage map for the 06H1 population, together with newly generated marker data. In these plants, which have both S. tuberosum Group Phureja and S. tuberosum Group Tuberosum in their pedigree, the resistance was shown to map to chromosome 9 at a locus not previously associated with PVY resistance, although there is evidence for at least one other genetic factor controlling PVY infection. The resistance factor location on chromosome 9 (named as Ry(o)phu) suggests a potential role of NB-LRR genes in this resistance. Phenotypic analysis using a GUS-tagged virus revealed that a small amount of PVY replication occurred in occasional groups of epidermal cells in inoculated leaves of resistant plants, without inducing any visible hypersensitive response. However, the virus did not enter the vascular system and systemic spread was completely prevented.
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Affiliation(s)
- Lesley Torrance
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
- The School of Biology, The University of St Andrews, St Andrews, KY16 9ST, UK.
| | - Graham H Cowan
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Karen McLean
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Aqeel N Al-Abedy
- Plant Protection Department, College of Agriculture, University of Kerbala, Kerbala, Iraq
| | - Miles Armstrong
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Tze-Yin Lim
- Columbia University, New York, NY, 10027, USA
| | - Ingo Hein
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences at the James Hutton Institute, School of Life Sciences, University of Dundee, Dundee, DD2 5DA, UK
| | - Glenn J Bryan
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
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10
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Grech‐Baran M, Witek K, Szajko K, Witek AI, Morgiewicz K, Wasilewicz‐Flis I, Jakuczun H, Marczewski W, Jones JDG, Hennig J. Extreme resistance to Potato virus Y in potato carrying the Ry sto gene is mediated by a TIR-NLR immune receptor. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:655-667. [PMID: 31397954 PMCID: PMC7004898 DOI: 10.1111/pbi.13230] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 05/19/2023]
Abstract
Potato virus Y (PVY) is a major potato (Solanum tuberosum L.) pathogen that causes severe annual crop losses worth billions of dollars worldwide. PVY is transmitted by aphids, and successful control of virus transmission requires the extensive use of environmentally damaging insecticides to reduce vector populations. Rysto , from the wild relative S. stoloniferum, confers extreme resistance (ER) to PVY and related viruses and is a valuable trait that is widely employed in potato resistance breeding programmes. Rysto was previously mapped to a region of potato chromosome XII, but the specific gene has not been identified to date. In this study, we isolated Rysto using resistance gene enrichment sequencing (RenSeq) and PacBio SMRT (Pacific Biosciences single-molecule real-time sequencing). Rysto was found to encode a nucleotide-binding leucine-rich repeat (NLR) protein with an N-terminal TIR domain and was sufficient for PVY perception and ER in transgenic potato plants. Rysto -dependent extreme resistance was temperature-independent and requires EDS1 and NRG1 proteins. Rysto may prove valuable for creating PVY-resistant cultivars of potato and other Solanaceae crops.
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Affiliation(s)
- Marta Grech‐Baran
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Kamil Witek
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Katarzyna Szajko
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | | | - Karolina Morgiewicz
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Iwona Wasilewicz‐Flis
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | - Henryka Jakuczun
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | | | - Jacek Hennig
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
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11
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MacKenzie TDB, Nie X, Bisht V, Singh M. Proliferation of Recombinant PVY Strains in Two Potato-Producing Regions of Canada, and Symptom Expression in 30 Important Potato Varieties with Different PVY Strains. PLANT DISEASE 2019; 103:2221-2230. [PMID: 31287755 DOI: 10.1094/pdis-09-18-1564-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Potato virus Y (PVY) exists as several strains with distinct symptomology and tuber yield effects in different potato varieties. Recently, new recombinant strains have proliferated and dominated local populations around the world. In this study, PVYO, PVYN:O, PVYN-Wi, and PVYNTN strains were tracked across Canada from 2014 to 2017, showing rapid evolution of populations away from the traditionally dominant PVYO to recombinants PVYN-Wi (western Canada) and PVYNTN (eastern Canada). Simultaneously, 30 potato varieties were inoculated with PVYO, PVYN:O, and PVYNTN in controlled greenhouse experiments. Foliar symptoms of primary (mechanical inoculation mimicking aphid infection) and secondary (tuber seedborne) infection were cataloged, and tuber yield measured. On average, and generally similar in primary and secondary infection, symptom expression and yield reduction were most severe with PVYO, followed by PVYN:O and PVYNTN. Strong mosaic symptoms were most commonly expressed with PVYO infection, and only seen with PVYN:O or PVYNTN in 15 and 3 varieties, respectively. Across variety-strain combinations, yield reduction was correlated with symptom severity, most strongly in PVYO-infected plants (e.g., AC Chaleur, Beljade, Envol, Norland, and Pacific Russet), and four varieties exhibited tuber necrotic ringspot disease with PVYNTN (AC Chaleur, Envol, Pacific Russet, and Yukon Gold).
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Affiliation(s)
- Tyler D B MacKenzie
- Agricultural Certification Services Inc., Fredericton, New Brunswick, E3B 8B7, Canada
| | - Xianzhou Nie
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Vikram Bisht
- Manitoba Agriculture, Carman, Manitoba R0G 0J0, Canada
| | - Mathuresh Singh
- Agricultural Certification Services Inc., Fredericton, New Brunswick, E3B 8B7, Canada
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12
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Khalid M, Afzal F, Gul A, Amir R, Subhani A, Ahmed Z, Mahmood Z, Xia X, Rasheed A, He Z. Molecular Characterization of 87 Functional Genes in Wheat Diversity Panel and Their Association With Phenotypes Under Well-Watered and Water-Limited Conditions. FRONTIERS IN PLANT SCIENCE 2019; 10:717. [PMID: 31214230 PMCID: PMC6558208 DOI: 10.3389/fpls.2019.00717] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/15/2019] [Indexed: 05/18/2023]
Abstract
Modern breeding imposed selection for improved productivity that largely influenced the frequency of superior alleles underpinning traits of breeding interest. Therefore, molecular diagnosis for the allelic variations of such genes is important to manipulate beneficial alleles in wheat molecular breeding. We analyzed a diversity panel largely consisted of advanced lines derived from synthetic hexaploid wheats for allelic variation at 87 functional genes or loci of breeding importance using 124 high-throughput KASP markers. We also developed two KASP markers for water-soluble carbohydrate genes (TaSST-D1 and TaSST-A1) associated with plant height and thousand grain weight (TGW) in the diversity panel. KASP genotyping results indicated that beneficial alleles for genes underpinning flowering time (Ppd-D1 and Vrn-D3), thousand grain weight (TaCKX-D1, TaTGW6-A1, TaSus1-7B, and TaCwi-D1), water-soluble carbohydrates (TaSST-A1), yellow-pigment content (Psy-B1 and Zds-D1), and root lesion nematodes (Rlnn1) were fixed in diversity panel with frequency ranged from 96.4 to 100%. The association analysis of functional genes with agronomic and biochemical traits under well-watered (WW) and water-limited (WL) conditions revealed that 21 marker-trait associations (MTAs) were consistently detected in both moisture conditions. The major developmental genes such as Vrn-A1, Rht-D1, and Ppd-B1 had the confounding effect on several agronomic traits including plant height, grain size and weight, and grain yield in both WW and WL conditions. The accumulation of favorable alleles for grain size and weight genes additively enhanced grain weight in the diversity panel. Graphical genotyping approach was used to identify accessions with maximum number of favorable alleles, thus likely to have high breeding value. These results improved our knowledge on the selection of favorable and unfavorable alleles through unconscious selection breeding and identified the opportunities to deploy alleles with effects in wheat breeding.
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Affiliation(s)
- Maria Khalid
- Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Fakiha Afzal
- Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Alvina Gul
- Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Rabia Amir
- Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Abid Subhani
- Barani Agriculture Research Institute (BARI), Chakwal, Pakistan
| | - Zubair Ahmed
- Crop Science Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Zahid Mahmood
- Crop Science Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- International Maize and Wheat Improvement Centre (CIMMYT), CAAS, Beijing, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- International Maize and Wheat Improvement Centre (CIMMYT), CAAS, Beijing, China
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13
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Sharma SK, MacKenzie K, McLean K, Dale F, Daniels S, Bryan GJ. Linkage Disequilibrium and Evaluation of Genome-Wide Association Mapping Models in Tetraploid Potato. G3 (BETHESDA, MD.) 2018; 8:3185-3202. [PMID: 30082329 PMCID: PMC6169395 DOI: 10.1534/g3.118.200377] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/30/2018] [Indexed: 11/18/2022]
Abstract
Genome-wide association studies (GWAS) have become a powerful tool for analyzing complex traits in crop plants. The current study evaluates the efficacy of various GWAS models and methods for elucidating population structure in potato. The presence of significant population structure can lead to detection of spurious marker-trait associations, as well as mask true ones. While appropriate statistical models are needed to detect true marker-trait associations, in most published potato GWAS, a 'one model fits all traits' approach has been adopted. We have examined various GWAS models on a large association panel comprising diverse tetraploid potato cultivars and breeding lines, genotyped with single nucleotide polymorphism (SNP) markers. Phenotypic data were generated for 20 quantitative traits assessed in different environments. Best Linear Unbiased Estimates (BLUEs) for these traits were obtained for use in assessing GWAS models. Goodness of fit of GWAS models, derived using different combinations of kinship and population structure for all traits, was evaluated using Quantile-Quantile (Q-Q) plots and genomic control inflation factors (λGC). Kinship was found to play a major role in correcting population confounding effects and results advocate a 'trait-specific' fit of different GWAS models. A survey of genome-wide linkage disequilibrium (LD), one of the critical factors affecting GWAS, is also presented and our findings are compared to other recent studies in potato. The genetic material used here, and the outputs of this study represent a novel resource for genetic analysis in potato.
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Affiliation(s)
| | - Katrin MacKenzie
- Biomathematics and Statistics Scotland (BioSS), Dundee DD2 5DA, UK
| | | | - Finlay Dale
- The James Hutton Institute, Dundee DD2 5DA, UK
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14
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Herrera MDR, Vidalon LJ, Montenegro JD, Riccio C, Guzman F, Bartolini I, Ghislain M. Molecular and genetic characterization of the Ry adg locus on chromosome XI from Andigena potatoes conferring extreme resistance to potato virus Y. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1925-1938. [PMID: 29855674 PMCID: PMC6096621 DOI: 10.1007/s00122-018-3123-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/24/2018] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE We have elucidated the Andigena origin of the potato Ryadg gene on chromosome XI of CIP breeding lines and developed two marker assays to facilitate its introgression in potato by marker-assisted selection. Potato virus Y (PVY) is causing yield and quality losses forcing farmers to renew periodically their seeds from clean stocks. Two loci for extreme resistance to PVY, one on chromosome XI and the other on XII, have been identified and used in breeding. The latter corresponds to a well-known source of resistance (Solanum stoloniferum), whereas the one on chromosome XI was reported from S. stoloniferum and S. tuberosum group Andigena as well. To elucidate its taxonomic origin in our breeding lines, we analyzed the nucleotide sequences of tightly linked markers (M45, M6) and screened 251 landraces of S. tuberosum group Andigena for the presence of this gene. Our results indicate that the PVY resistance allele on chromosome XI in our breeding lines originated from S. tuberosum group Andigena. We have developed two marker assays to accelerate the introgression of Ryadg gene into breeding lines by marker-assisted selection (MAS). First, we have multiplexed RYSC3, M6 and M45 DNA markers flanking the Ryadg gene and validated it on potato varieties with known presence/absence of the Ryadg gene and a progeny of 6,521 individuals. Secondly, we developed an allele-dosage assay particularly useful to identify multiplex Ryadg progenitors. The assay based on high-resolution melting analysis at the M6 marker confirmed Ryadg plex level as nulliplex, simplex and duplex progenitors and few triplex progenies. These marker assays have been validated and can be used to facilitate MAS in potato breeding.
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Affiliation(s)
| | - Laura Jara Vidalon
- Applied Biotechnology Laboratory, International Potato Center, P.O. Box 1558, Lima 12, Peru
| | - Juan D. Montenegro
- Applied Biotechnology Laboratory, International Potato Center, P.O. Box 1558, Lima 12, Peru
- Present Address: Australian Genome Research Facility, University of Queensland, Brisbane, QLD 4072 Australia
| | - Cinzia Riccio
- Applied Biotechnology Laboratory, International Potato Center, P.O. Box 1558, Lima 12, Peru
| | - Frank Guzman
- Applied Biotechnology Laboratory, International Potato Center, P.O. Box 1558, Lima 12, Peru
- Present Address: Postgraduate Program in Cellular and Molecular Biology (PPGBCM) - Biotechnology Center (CBiot), UFRGS, Bento Gonçalves Ave. 9500/Building, 43431 Porto Alegre, RS Brazil
| | - Ida Bartolini
- Applied Biotechnology Laboratory, International Potato Center, P.O. Box 1558, Lima 12, Peru
- Present Address: Laboratorio de Biología Molecular del Servicio Nacional de Sanidad Agraria (SENASA), Av La Universidad 1915, La Molina, Lima 12, Peru
| | - Marc Ghislain
- Applied Biotechnology Laboratory, International Potato Center, P.O. Box 1558, Lima 12, Peru
- International Potato Center, P.O. Box 25171, Nairobi, 00603 Kenya
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15
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Soriano JM, Villegas D, Sorrells ME, Royo C. Durum Wheat Landraces from East and West Regions of the Mediterranean Basin Are Genetically Distinct for Yield Components and Phenology. FRONTIERS IN PLANT SCIENCE 2018; 9:80. [PMID: 29472936 PMCID: PMC5809869 DOI: 10.3389/fpls.2018.00080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/15/2018] [Indexed: 05/03/2023]
Abstract
Genetic diversity of durum wheat landraces is a powerful tool for the introgression of new alleles of commercial interest in breeding programs. In a previous study, our team structured a collection of 172 durum wheat landraces from 21 Mediterranean countries in four genetic populations related to their geographical origin: east Mediterranean (17), east Balkan and Turkey (23), west Balkan and Egypt (25), and West Mediterranean (73), leaving 34 genotypes as admixed, and association mapping was carried out for important agronomic traits. Using a subset of this collection, the current study identified 23 marker alleles with a differential frequency in landraces from east and west regions of the Mediterranean Basin, which affected important agronomic traits. Eastern landraces had higher frequencies than the western ones of alleles increasing the number of spikes (wPt-5385 on chromosome 1B), grains per m2 (wPt-0841 on chromosome 7B), and grain filling duration (7 significant marker trait associations). Eastern landraces had higher frequencies of marker alleles located on chromosomes 4A, 5B, and 6B associated with reduced cycle length, and lighter grains than the western ones. Also for lower kernel weight, four marker alleles were located on chromosome 1A. Breeders may use the molecular markers identified in the current study for improving yield under specific Mediterranean environments.
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Affiliation(s)
- Jose M. Soriano
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology, Lleida, Spain
| | - Dolors Villegas
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology, Lleida, Spain
| | - Mark E. Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Conxita Royo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology, Lleida, Spain
- *Correspondence: Conxita Royo
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