1
|
Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement. Nat Genet 2022; 54:1544-1552. [DOI: 10.1038/s41588-022-01189-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/18/2022] [Indexed: 11/06/2022]
|
2
|
Kale SM, Schulthess AW, Padmarasu S, Boeven PHG, Schacht J, Himmelbach A, Steuernagel B, Wulff BBH, Reif JC, Stein N, Mascher M. A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1730-1742. [PMID: 35562859 PMCID: PMC9398310 DOI: 10.1111/pbi.13843] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/06/2022] [Accepted: 04/23/2022] [Indexed: 06/15/2023]
Abstract
A resistance gene atlas is an integral component of the breeder's arsenal in the fight against evolving pathogens. Thanks to high-throughput sequencing, catalogues of resistance genes can be assembled even in crop species with large and polyploid genomes. Here, we report on capture sequencing and assembly of resistance gene homologs in a diversity panel of 907 winter wheat genotypes comprising ex situ genebank accessions and current elite cultivars. In addition, we use accurate long-read sequencing and chromosome conformation capture sequencing to construct a chromosome-scale genome sequence assembly of cv. Attraktion, an elite variety representative of European winter wheat. We illustrate the value of our resource for breeders and geneticists by (i) comparing the resistance gene complements in plant genetic resources and elite varieties and (ii) conducting genome-wide associations scans (GWAS) for the fungal diseases yellow rust and leaf rust using reference-based and reference-free GWAS approaches. The gene content under GWAS peaks was scrutinized in the assembly of cv. Attraktion.
Collapse
Affiliation(s)
- Sandip M. Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | | | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | | | - Brande B. H. Wulff
- John Innes CentreNorwich Research ParkNorwichUK
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- Center for Integrated Breeding Research (CiBreed)Georg‐August‐University GöttingenGöttingenGermany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| |
Collapse
|
3
|
Ma Y, Li D, Xu Z, Gu R, Wang P, Fu J, Wang J, Du W, Zhang H. Dissection of the Genetic Basis of Yield Traits in Line per se and Testcross Populations and Identification of Candidate Genes for Hybrid Performance in Maize. Int J Mol Sci 2022; 23:5074. [PMID: 35563470 PMCID: PMC9102962 DOI: 10.3390/ijms23095074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 12/31/2022] Open
Abstract
Dissecting the genetic basis of yield traits in hybrid populations and identifying the candidate genes are important for molecular crop breeding. In this study, a BC1F3:4 population, the line per se (LPS) population, was constructed by using elite inbred lines Zheng58 and PH4CV as the parental lines. The population was genotyped with 55,000 SNPs and testcrossed to Chang7-2 and PH6WC (two testers) to construct two testcross (TC) populations. The three populations were evaluated for hundred kernel weight (HKW) and yield per plant (YPP) in multiple environments. Marker-trait association analysis (MTA) identified 24 to 151 significant SNPs in the three populations. Comparison of the significant SNPs identified common and specific quantitative trait locus/loci (QTL) in the LPS and TC populations. Genetic feature analysis of these significant SNPs proved that these SNPs were associated with the tested traits and could be used to predict trait performance of both LPS and TC populations. RNA-seq analysis was performed using maize hybrid varieties and their parental lines, and differentially expressed genes (DEGs) between hybrid varieties and parental lines were identified. Comparison of the chromosome positions of DEGs with those of significant SNPs detected in the TC population identified potential candidate genes that might be related to hybrid performance. Combining RNA-seq analysis and MTA results identified candidate genes for hybrid performance, providing information that could be useful for maize hybrid breeding.
Collapse
Affiliation(s)
- Yuting Ma
- Agronomy College, Shenyang Agricultural University, Shenyang 110866, China;
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.L.); (P.W.); (J.F.)
| | - Dongdong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.L.); (P.W.); (J.F.)
| | - Zhenxiang Xu
- Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Z.X.); (R.G.); (J.W.)
| | - Riliang Gu
- Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Z.X.); (R.G.); (J.W.)
| | - Pingxi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.L.); (P.W.); (J.F.)
| | - Junjie Fu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.L.); (P.W.); (J.F.)
| | - Jianhua Wang
- Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Z.X.); (R.G.); (J.W.)
| | - Wanli Du
- Agronomy College, Shenyang Agricultural University, Shenyang 110866, China;
| | - Hongwei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.L.); (P.W.); (J.F.)
| |
Collapse
|
4
|
Singh R, Kumar K, Bharadwaj C, Verma PK. Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes. PLANTA 2022; 255:46. [PMID: 35076815 DOI: 10.1007/s00425-022-03827-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.
Collapse
Affiliation(s)
- Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110020, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
5
|
Rembe M, Reif JC, Ebmeyer E, Thorwarth P, Korzun V, Schacht J, Boeven PHG, Varenne P, Kazman E, Philipp N, Kollers S, Pfeiffer N, Longin CFH, Hartwig N, Gils M, Zhao Y. Reciprocal Recurrent Genomic Selection Is Impacted by Genotype-by-Environment Interactions. FRONTIERS IN PLANT SCIENCE 2021; 12:703419. [PMID: 34630453 PMCID: PMC8498042 DOI: 10.3389/fpls.2021.703419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Reciprocal recurrent genomic selection is a breeding strategy aimed at improving the hybrid performance of two base populations. It promises to significantly advance hybrid breeding in wheat. Against this backdrop, the main objective of this study was to empirically investigate the potential and limitations of reciprocal recurrent genomic selection. Genome-wide predictive equations were developed using genomic and phenotypic data from a comprehensive population of 1,604 single crosses between 120 female and 15 male wheat lines. Twenty superior female lines were selected for initiation of the reciprocal recurrent genomic selection program. Focusing on the female pool, one cycle was performed with genomic selection steps at the F2 (60 out of 629 plants) and the F5 stage (49 out of 382 plants). Selection gain for grain yield was evaluated at six locations. Analyses of the phenotypic data showed pronounced genotype-by-environment interactions with two environments that formed an outgroup compared to the environments used for the genome-wide prediction equations. Removing these two environments for further analysis resulted in a selection gain of 1.0 dt ha-1 compared to the hybrids of the original 20 parental lines. This underscores the potential of reciprocal recurrent genomic selection to promote hybrid wheat breeding, but also highlights the need to develop robust genome-wide predictive equations.
Collapse
Affiliation(s)
- Maximilian Rembe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | | | | | | | - Viktor Korzun
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
- Federal State Budgetary Institution of Science Federal Research Center “Kazan Scientific Center of Russian Academy of Sciences”, Kazan, Russia
| | - Johannes Schacht
- Limagrain Europe, Ferme de l'Etang – BP3−77390, Verneuil-l'Ètang, France
| | | | - Pierrick Varenne
- Limagrain Europe, Ferme de l'Etang – BP3−77390, Verneuil-l'Ètang, France
| | | | | | | | | | | | | | - Mario Gils
- Nordsaat Saatzucht GmbH, Langenstein, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| |
Collapse
|
6
|
Zhao Y, Thorwarth P, Jiang Y, Philipp N, Schulthess AW, Gils M, Boeven PHG, Longin CFH, Schacht J, Ebmeyer E, Korzun V, Mirdita V, Dörnte J, Avenhaus U, Horbach R, Cöster H, Holzapfel J, Ramgraber L, Kühnle S, Varenne P, Starke A, Schürmann F, Beier S, Scholz U, Liu F, Schmidt RH, Reif JC. Unlocking big data doubled the accuracy in predicting the grain yield in hybrid wheat. SCIENCE ADVANCES 2021; 7:7/24/eabf9106. [PMID: 34117061 PMCID: PMC8195483 DOI: 10.1126/sciadv.abf9106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/28/2021] [Indexed: 05/07/2023]
Abstract
The potential of big data to support businesses has been demonstrated in financial services, manufacturing, and telecommunications. Here, we report on efforts to enter a new data era in plant breeding by collecting genomic and phenotypic information from 12,858 wheat genotypes representing 6575 single-cross hybrids and 6283 inbred lines that were evaluated in six experimental series for yield in field trials encompassing ~125,000 plots. Integrating data resulted in twofold higher prediction ability compared with cases in which hybrid performance was predicted across individual experimental series. Our results suggest that combining data across breeding programs is a particularly appropriate strategy to exploit the potential of big data for predictive plant breeding. This paradigm shift can contribute to increasing yield and resilience, which is needed to feed the growing world population.
Collapse
Affiliation(s)
- Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Patrick Thorwarth
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70593 Stuttgart, Germany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Norman Philipp
- Syngenta Seeds GmbH, Kroppenstedterstr. 4, 39398 Hadmersleben, Germany
| | - Albert W Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Mario Gils
- Nordsaat Saatzucht GmbH, , Böhnshauserstr. 1, 38895 Langenstein, Germany
| | | | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70593 Stuttgart, Germany
| | | | - Erhard Ebmeyer
- KWS LOCHOW GmbH, Ferdinand-von-Lochow-Str. 5, 29303 Bergen, Germany
| | - Viktor Korzun
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37574 Einbeck, Germany
- Federal State Budgetary Institution of Science Federal Research Center, "Kazan Scientific Center of Russian Academy of Sciences," ul. Lobachevskogo, 2/31, Kazan, 420111 Tatarstan, Russian Federation
| | - Vilson Mirdita
- BASF Agricultural Solutions Seed GmbH, OT Gatersleben, Am Schwabeplan 8, 06466 Seeland, Germany
| | - Jost Dörnte
- Deutsche Saatveredelung AG, Leutewitz 26, 01665 Käbschütztal, Germany
| | - Ulrike Avenhaus
- W. von Borries-Eckendorf GmbH & Co. KG, Hovedisserstr. 92, 33818 Leopoldshöhe, Germany
| | - Ralf Horbach
- Saatzucht Bauer GmbH & Co. KG, Hofmarkstr.1, 93083 Niederträubling, Germany
| | | | - Josef Holzapfel
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg, Germany
| | - Ludwig Ramgraber
- Saatzucht Josef Breun GmbH & Co. KG, Amselweg 1, 91074 Herzogenaurach, Germany
| | - Simon Kühnle
- Pflanzenzucht Oberlimpurg, Oberlimpurg 2, 74523 Schwäbisch Hall, Germany
| | - Pierrick Varenne
- Limagrain Europe, Ferme de l'Etang BP3, 77390 Verneuil l'Etang, France
| | - Anne Starke
- Limagrain GmbH, Salderstr. 4, 31226 Peine-Rosenthal, Germany
| | | | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Fang Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Renate H Schmidt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany.
| |
Collapse
|
7
|
Wu J, Yu R, Wang H, Zhou C, Huang S, Jiao H, Yu S, Nie X, Wang Q, Liu S, Weining S, Singh RP, Bhavani S, Kang Z, Han D, Zeng Q. A large-scale genomic association analysis identifies the candidate causal genes conferring stripe rust resistance under multiple field environments. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:177-191. [PMID: 32677132 PMCID: PMC7769225 DOI: 10.1111/pbi.13452] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 05/02/2023]
Abstract
The incorporation of resistance genes into wheat commercial varieties is the ideal strategy to combat stripe or yellow rust (YR). In a search for novel resistance genes, we performed a large-scale genomic association analysis with high-density 660K single nucleotide polymorphism (SNP) arrays to determine the genetic components of YR resistance in 411 spring wheat lines. Following quality control, 371 972 SNPs were screened, covering over 50% of the high-confidence annotated gene space. Nineteen stable genomic regions harbouring 292 significant SNPs were associated with adult-plant YR resistance across nine environments. Of these, 14 SNPs were localized in the proximity of known loci widely used in breeding. Obvious candidate SNP variants were identified in certain confidence intervals, such as the cloned gene Yr18 and the major locus on chromosome 2BL, despite a large extent of linkage disequilibrium. The number of causal SNP variants was refined using an independent validation panel and consideration of the estimated functional importance of each nucleotide polymorphism. Interestingly, four natural polymorphisms causing amino acid changes in the gene TraesCS2B01G513100 that encodes a serine/threonine protein kinase (STPK) were significantly involved in YR responses. Gene expression and mutation analysis confirmed that STPK played an important role in YR resistance. PCR markers were developed to identify the favourable TraesCS2B01G513100 haplotype for marker-assisted breeding. These results demonstrate that high-resolution SNP-based GWAS enables the rapid identification of putative resistance genes and can be used to improve the efficiency of marker-assisted selection in wheat disease resistance breeding.
Collapse
Affiliation(s)
- Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Rui Yu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Haiying Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
| | - Cai'e Zhou
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Hanxuan Jiao
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Song Weining
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Ravi Prakash Singh
- International Maize and Wheat Improvement Center (CIMMYT)TexcocoEstado de MexicoMexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT)TexcocoEstado de MexicoMexico
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| |
Collapse
|
8
|
Liu F, Jiang Y, Zhao Y, Schulthess AW, Reif JC. Haplotype-based genome-wide association increases the predictability of leaf rust (Puccinia triticina) resistance in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6958-6968. [PMID: 32827041 DOI: 10.1093/jxb/eraa387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/17/2020] [Indexed: 05/12/2023]
Abstract
Resistance breeding is crucial for sustainable control of wheat leaf rust and single nucleotide polymorphism (SNP)-based genome-wide association studies (GWAS) are widely used to dissect leaf rust resistance. Unfortunately, GWAS based on SNPs often explained only a small proportion of the genetic variation. We compared SNP-based GWAS with a method based on functional haplotypes (FH) considering epistasis in a comprehensive hybrid wheat mapping population composed of 133 parents plus their 1574 hybrids and characterized with 626 245 high-quality SNPs. In total, 2408 and 1 139 828 significant associations were detected in the mapping population by using SNP-based and FH-based GWAS, respectively. These associations mapped to 25 and 69 candidate regions, correspondingly. SNP-based GWAS highlighted two already-known resistance genes, Lr22a and Lr34-B, while FH-based GWAS detected associations not only on these genes but also on two additional genes, Lr10 and Lr1. As revealed by a second hybrid wheat population for independent validation, the use of detected associations from SNP-based and FH-based GWAS reached predictabilities of 11.72% and 22.86%, respectively. Therefore, FH-based GWAS is not only more powerful for detecting associations, but also improves the accuracy of marker-assisted selection compared with the SNP-based approach.
Collapse
Affiliation(s)
- Fang Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Albert W Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| |
Collapse
|
9
|
Beukert U, Thorwarth P, Zhao Y, Longin CFH, Serfling A, Ordon F, Reif JC. Comparing the Potential of Marker-Assisted Selection and Genomic Prediction for Improving Rust Resistance in Hybrid Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:594113. [PMID: 33193553 PMCID: PMC7655876 DOI: 10.3389/fpls.2020.594113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/05/2020] [Indexed: 05/20/2023]
Abstract
Improving leaf rust and stripe rust resistance is a central goal in wheat breeding. The objectives of this study were to (1) elucidate the genetic basis of leaf rust and stripe rust resistance in a hybrid wheat population, (2) compare the findings using a previously published hybrid wheat data set, and (3) contrast the prediction accuracy with those of genome-wide prediction. The hybrid wheat population included 1,744 single crosses from 236 parental lines. The genotypes were fingerprinted using a 15k SNP array and evaluated for leaf rust and stripe rust resistance in multi-location field trials. We observed a high congruency of putative quantitative trait loci (QTL) for leaf rust resistance between both populations. This was not the case for stripe rust resistance. Accordingly, prediction accuracy of the detected QTL was moderate for leaf rust but low for stripe rust resistance. Genome-wide selection increased the prediction accuracy slightly for stripe rust albeit at a low level but not for leaf rust. Thus, our findings suggest that marker-assisted selection seems to be a robust and efficient tool to improve leaf rust resistance in European wheat hybrids.
Collapse
Affiliation(s)
- Ulrike Beukert
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Patrick Thorwarth
- State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Jochen C. Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- *Correspondence: Jochen C. Reif,
| |
Collapse
|