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Johansson E, Lan Y, Olalekan O, Kuktaite R, Chawade A, Rahmatov M. Alien introgression to wheat for food security: functional and nutritional quality for novel products under climate change. Front Nutr 2024; 11:1393357. [PMID: 38933881 PMCID: PMC11199737 DOI: 10.3389/fnut.2024.1393357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
Crop yield and quality has increased globally during recent decades due to plant breeding, resulting in improved food security. However, climate change and shifts in human dietary habits and preferences display novel pressure on crop production to deliver enough quantity and quality to secure food for future generations. This review paper describes the current state-of-the-art and presents innovative approaches related to alien introgressions into wheat, focusing on aspects related to quality, functional characteristics, nutritional attributes, and development of novel food products. The benefits and opportunities that the novel and traditional plant breeding methods contribute to using alien germplasm in plant breeding are also discussed. In principle, gene introgressions from rye have been the most widely utilized alien gene source for wheat. Furthermore, the incorporation of novel resistance genes toward diseases and pests have been the most transferred type of genes into the wheat genome. The incorporation of novel resistance genes toward diseases and pests into the wheat genome is important in breeding for increased food security. Alien introgressions to wheat from e.g. rye and Aegilops spp. have also contributed to improved nutritional and functional quality. Recent studies have shown that introgressions to wheat of genes from chromosome 3 in rye have an impact on both yield, nutritional and functional quality, and quality stability during drought treatment, another character of high importance for food security under climate change scenarios. Additionally, the introgression of alien genes into wheat has the potential to improve the nutritional profiles of future food products, by contributing higher minerals levels or lower levels of anti-nutritional compounds into e.g., plant-based products substituting animal-based food alternatives. To conclude, the present review paper highlights great opportunities and shows a few examples of how food security and functional-nutritional quality in traditional and novel wheat products can be improved by the use of genes from alien sources, such as rye and other relatives to wheat. Novel and upcoming plant breeding methods such as genome-wide association studies, gene editing, genomic selection and speed breeding, have the potential to complement traditional technologies to keep pace with climate change and consumer eating habits.
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Affiliation(s)
- Eva Johansson
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Lomma, Sweden
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Xing X, Hu T, Wang Y, Li Y, Wang W, Hu H, Wei Q, Yan Y, Gan D, Bao C, Wang J. Construction of SNP fingerprints and genetic diversity analysis of radish ( Raphanus sativus L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1329890. [PMID: 38371408 PMCID: PMC10869463 DOI: 10.3389/fpls.2024.1329890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/12/2024] [Indexed: 02/20/2024]
Abstract
Radish (Raphanus sativus L.) is a vegetable crop with economic value and ecological significance in the genus Radish, family Brassicaceae. In recent years, developed countries have attached great importance to the collection and conservation of radish germplasm resources and their research and utilization, but the lack of population genetic information and molecular markers has hindered the development of the genetic breeding of radish. In this study, we integrated the radish genomic data published in databases for the development of single-nucleotide polymorphism (SNP) markers, and obtained a dataset of 308 high-quality SNPs under strict selection criteria. With the support of Kompetitive Allele-Specific PCR (KASP) technology, we screened a set of 32 candidate core SNP marker sets to analyse the genetic diversity of the collected 356 radish varieties. The results showed that the mean values of polymorphism information content (PIC), minor allele frequency (MAF), gene diversity and heterozygosity of the 32 candidate core SNP markers were 0.32, 0.30, 0.40 and 0.25, respectively. Population structural analysis, principal component analysis and genetic evolutionary tree analysis indicated that the 356 radish materials were best classified into two taxa, and that the two taxa of the material were closely genetically exchanged. Finally, on the basis of 32 candidate core SNP markers we calculated 15 core markers using a computer algorithm to construct a fingerprint map of 356 radish varieties. Furthermore, we constructed a core germplasm population consisting of 71 radish materials using 32 candidate core markers. In this study, we developed SNP markers for radish cultivar identification and genetic diversity analysis, and constructed DNA fingerprints, providing a basis for the identification of radish germplasm resources and molecular marker-assisted breeding as well as genetic research.
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Affiliation(s)
- Xiaolin Xing
- School of Horticulture, Anhui Agricultural University, Hefei, China
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tianhua Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yikui Wang
- Institute of Vegetables, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yan Li
- Institute of Vegetables, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wuhong Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haijiao Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qingzhen Wei
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaqin Yan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Defang Gan
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Chonglai Bao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jinglei Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Farkas A, Gaál E, Ivanizs L, Blavet N, Said M, Holušová K, Szőke-Pázsi K, Spitkó T, Mikó P, Türkösi E, Kruppa K, Kovács P, Darkó É, Szakács É, Bartoš J, Doležel J, Molnár I. Chromosome genomics facilitates the marker development and selection of wheat-Aegilops biuncialis addition, substitution and translocation lines. Sci Rep 2023; 13:20499. [PMID: 37993509 PMCID: PMC10665447 DOI: 10.1038/s41598-023-47845-8] [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: 07/24/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
The annual goatgrass, Aegilops biuncialis is a rich source of genes with considerable agronomic value. This genetic potential can be exploited for wheat improvement through interspecific hybridization to increase stress resistance, grain quality and adaptability. However, the low throughput of cytogenetic selection hampers the development of alien introgressions. Using the sequence of flow-sorted chromosomes of diploid progenitors, the present study enabled the development of chromosome-specific markers. In total, 482 PCR markers were validated on wheat (Mv9kr1) and Ae. biuncialis (MvGB642) crossing partners, and 126 on wheat-Aegilops additions. Thirty-two markers specific for U- or M-chromosomes were used in combination with GISH and FISH for the screening of 44 Mv9kr1 × Ae. biuncialis BC3F3 genotypes. The predominance of chromosomes 4M and 5M, as well as the presence of chromosomal aberrations, may indicate that these chromosomes have a gametocidal effect. A new wheat-Ae. biuncialis disomic 4U addition, 4M(4D) and 5M(5D) substitutions, as well as several introgression lines were selected. Spike morphology and fertility indicated that the Aegilops 4M or 5M compensated well for the loss of 4D and 5D, respectively. The new cytogenetic stocks represent valuable genetic resources for the introgression of key genes alleles into wheat.
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Affiliation(s)
- András Farkas
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Eszter Gaál
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary.
| | - László Ivanizs
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Nicolas Blavet
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Mahmoud Said
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, Cairo, 12619, Egypt
| | - Kateřina Holušová
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Kitti Szőke-Pázsi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Tamás Spitkó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Péter Mikó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Edina Türkösi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Klaudia Kruppa
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Péter Kovács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Éva Darkó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Éva Szakács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Jan Bartoš
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - István Molnár
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
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Bhoite R, Smith R, Bansal U, Dowla M, Bariana H, Sharma D. Exome-based new allele-specific PCR markers and transferability for sodicity tolerance in bread wheat ( Triticum aestivum L.). PLANT DIRECT 2023; 7:e520. [PMID: 37600239 PMCID: PMC10435944 DOI: 10.1002/pld3.520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 07/10/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023]
Abstract
Targeted exome-based genotype by sequencing (t-GBS), a sequencing technology that tags SNPs and haplotypes in gene-rich regions was used in previous genome-wide association studies (GWAS) for sodicity tolerance in bread wheat. Thirty-nine novel SNPs including 18 haplotypes for yield and yield-components were identified. The present study aimed at developing SNP-derived markers by precisely locating new SNPs on ~180 bp allelic sequence of t-GBS, marker validation, and SNP functional characterization based on its exonic location. We identified unknown locations of significant SNPs/haplotypes by aligning allelic sequences on to IWGSC RefSeqv1.0 on respective chromosomes. Eighteen out of the target 39 SNP locations fulfilled the criteria for producing PCR markers, among which only eight produced polymorphic signals. These eight markers associated with yield, plants m-2, heads m-2, and harvest index, including a pleiotropic marker for yield, harvest index, and grains/head were validated for its amplification efficiency and phenotypic effects in focused identification germplasm strategy (FIGS) wheat set and a doubled haploid (DH) population (Scepter/IG107116). The phenotypic variation explained by these markers are in the range of 4.1-37.6 in the FIGS population. High throughput PCR-based genotyping using new markers and association with phenotypes in FIGS wheat set and DH population validated the effect of functional SNP on closely associated genes-calcineurin B-like- and dirigent protein, basic helix-loop-helix (BHLH-), plant homeodomain (PHD-) and helix-turn-helix myeloblastosis (HTH myb) type -transcription factor. Further, genome-wide SNP annotation using SnpEff tool confirmed that these SNPs are in gene regulatory regions (upstream, 3'-UTR, and intron) modifying gene expression and protein-coding. This integrated approach of marker design for t-GBS alleles, SNP functional annotation, and high-throughput genotyping of functional SNP offers translation solutions across crops and complex traits in crop improvement programs.
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Affiliation(s)
- Roopali Bhoite
- Grains Genetic ImprovementDepartment of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Rosemary Smith
- Grains Genetic ImprovementDepartment of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Urmil Bansal
- Plant Breeding Institute, School of Life Sciences, Faculty of ScienceThe University of SydneyCobbittyNew South WalesAustralia
| | - Mirza Dowla
- Grains Genetic ImprovementDepartment of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Harbans Bariana
- School of ScienceWestern Sydney UniversityRichmondNew South WalesAustralia
| | - Darshan Sharma
- Grains Genetic ImprovementDepartment of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
- College of Science, Health, Engineering and EducationMurdoch UniversityPerthWestern AustraliaAustralia
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Coombes B, Fellers JP, Grewal S, Rusholme‐Pilcher R, Hubbart‐Edwards S, Yang C, Joynson R, King IP, King J, Hall A. Whole-genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:482-496. [PMID: 35598169 PMCID: PMC9946142 DOI: 10.1111/pbi.13859] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/28/2022] [Accepted: 05/15/2022] [Indexed: 05/29/2023]
Abstract
Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat's wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that novel introgressed genes are rarely expressed and those that directly replace a wheat orthologue have a tendency towards downregulation, with no discernible compensation in the expression of homoeologous copies. This study explores the genomic impact of introgression breeding and provides a schematic that can be followed to characterize introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilization of introgression pre-breeding material in wheat breeding programmes.
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Affiliation(s)
| | - John P. Fellers
- USDA–ARS Hard Winter Wheat Genetics Research UnitManhattanKansas66506USA
| | - Surbhi Grewal
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | | | - Stella Hubbart‐Edwards
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | - Cai‐yun Yang
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | | | - Ian P. King
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | - Julie King
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
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Türkösi E, Ivanizs L, Farkas A, Gaál E, Kruppa K, Kovács P, Szakács É, Szőke-Pázsi K, Said M, Cápal P, Griffiths S, Doležel J, Molnár I. Transfer of the ph1b Deletion Chromosome 5B From Chinese Spring Wheat Into a Winter Wheat Line and Induction of Chromosome Rearrangements in Wheat- Aegilops biuncialis Hybrids. FRONTIERS IN PLANT SCIENCE 2022; 13:875676. [PMID: 35769292 PMCID: PMC9234525 DOI: 10.3389/fpls.2022.875676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/09/2022] [Indexed: 06/10/2023]
Abstract
Effective utilization of genetic diversity in wild relatives to improve wheat requires recombination between wheat and alien chromosomes. However, this is suppressed by the Pairing homoeologous gene, Ph1, on the long arm of wheat chromosome 5B. A deletion mutant of the Ph1 locus (ph1b) has been used widely to induce homoeologous recombination in wheat × alien hybrids. However, the original ph1b mutation, developed in Chinese Spring (CS) background has poor agronomic performance. Hence, alien introgression lines are first backcrossed with adapted wheat genotypes and after this step, alien chromosome segments are introduced into breeding lines. In this work, the ph1b mutation was transferred from two CSph1b mutants into winter wheat line Mv9kr1. Homozygous genotypes Mv9kr1 ph1b/ph1b exhibited improved plant and spike morphology compared to Chinese Spring. Flow cytometric chromosome analysis confirmed reduced DNA content of the mutant 5B chromosome in both wheat genotype relative to the wild type chromosome. The ph1b mutation in the Mv9kr1 genotype allowed wheat-alien chromosome pairing in meiosis of Mv9kr1ph1b_K × Aegilops biuncialis F1 hybrids, predominantly with the Mb-genome chromosomes of Aegilops relative to those of the Ub genome. High frequency of wheat-Aegilops chromosome interactions resulted in rearranged chromosomes identified in the new Mv9kr1ph1b × Ae. Biuncialis amphiploids, making these lines valuable sources for alien introgressions. The new Mv9kr1ph1b mutant genotype is a unique resource to support alien introgression breeding of hexaploid wheat.
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Affiliation(s)
- Edina Türkösi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - László Ivanizs
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - András Farkas
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Eszter Gaál
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Klaudia Kruppa
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Péter Kovács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
- Institute of Genetics and Biotechnology, Szent István Campus, MATE, Gödöllő, Hungary
| | - Éva Szakács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Kitti Szőke-Pázsi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Mahmoud Said
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Field Crops Research Institute, Agricultural Research Centre, Giza, Egypt
| | - Petr Cápal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | | | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - István Molnár
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
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Medina-Lozano I, Díaz A. Applications of Genomic Tools in Plant Breeding: Crop Biofortification. Int J Mol Sci 2022; 23:3086. [PMID: 35328507 PMCID: PMC8950180 DOI: 10.3390/ijms23063086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 12/02/2022] Open
Abstract
Crop breeding has mainly been focused on increasing productivity, either directly or by decreasing the losses caused by biotic and abiotic stresses (that is, incorporating resistance to diseases and enhancing tolerance to adverse conditions, respectively). Quite the opposite, little attention has been paid to improve the nutritional value of crops. It has not been until recently that crop biofortification has become an objective within breeding programs, through either conventional methods or genetic engineering. There are many steps along this long path, from the initial evaluation of germplasm for the content of nutrients and health-promoting compounds to the development of biofortified varieties, with the available and future genomic tools assisting scientists and breeders in reaching their objectives as well as speeding up the process. This review offers a compendium of the genomic technologies used to explore and create biodiversity, to associate the traits of interest to the genome, and to transfer the genomic regions responsible for the desirable characteristics into potential new varieties. Finally, a glimpse of future perspectives and challenges in this emerging area is offered by taking the present scenario and the slow progress of the regulatory framework as the starting point.
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Affiliation(s)
- Inés Medina-Lozano
- Departamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, Avda. Montañana 930, 50059 Zaragoza, Spain;
- Instituto Agroalimentario de Aragón—IA2, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Aurora Díaz
- Departamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, Avda. Montañana 930, 50059 Zaragoza, Spain;
- Instituto Agroalimentario de Aragón—IA2, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, 50013 Zaragoza, Spain
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Grewal S, Coombes B, Joynson R, Hall A, Fellers J, Yang CY, Scholefield D, Ashling S, Isaac P, King IP, King J. Chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines. THE PLANT GENOME 2022; 15:e20193. [PMID: 35102721 DOI: 10.1002/tpg2.20193] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/20/2021] [Indexed: 05/23/2023]
Abstract
Many wild-relative species are being used in prebreeding programs to increase the genetic diversity of wheat (Triticum aestivum L.). Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterize wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based Kompetitive allele-specific polymerase chain reaction (KASP) markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and polymerase chain reaction (PCR)-amplicon-based sequencing of the wild species. But chromosome-specific KASP assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum (Boiss.) Eig and development of a de novo SNP discovery pipeline that generated ∼38,000 SNPs in unique wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as diagnostic for Am. muticum in a wheat background. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome-specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | | | - Ryan Joynson
- Earlham Institute, Norwich Research Park, Norwich, UK
- Current address: Limagrain Europe, Clermont-Ferrand, France
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - John Fellers
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Cai-Yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Peter Isaac
- iDna Genetics Ltd., Norwich Research Park, Norwich, UK
| | - Ian P King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
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King J, Grewal S, Othmeni M, Coombes B, Yang CY, Walter N, Ashling S, Scholefield D, Walker J, Hubbart-Edwards S, Hall A, King IP. Introgression of the Triticum timopheevii Genome Into Wheat Detected by Chromosome-Specific Kompetitive Allele Specific PCR Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:919519. [PMID: 35720607 PMCID: PMC9198554 DOI: 10.3389/fpls.2022.919519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/12/2022] [Indexed: 05/08/2023]
Abstract
Triticum timopheevii (2n = 28, A t A t GG) is a tetraploid wild relative species with great potential to increase the genetic diversity of hexaploid wheat Triticum aestivum (2n = 42, AABBDD) for various important agronomic traits. A breeding scheme that propagated advanced backcrossed populations of wheat-T. timopheevii introgression lines through further backcrossing and self-fertilisation resulted in the generation of 99 introgression lines (ILs) that carried 309 homozygous segments from the A t and G subgenomes of T. timopheevii. These introgressions contained 89 and 74 unique segments from the A t and G subgenomes, respectively. These overlapping segments covered 98.9% of the T. timopheevii genome that has now been introgressed into bread wheat cv. Paragon including the entirety of all T. timopheevii chromosomes via varying sized segments except for chromosomes 3A t , 4G, and 6G. Homozygous ILs contained between one and eight of these introgressions with an average of three per introgression line. These homozygous introgressions were detected through the development of a set of 480 chromosome-specific Kompetitive allele specific PCR (KASP) markers that are well-distributed across the wheat genome. Of these, 149 were developed in this study based on single nucleotide polymorphisms (SNPs) discovered through whole genome sequencing of T. timopheevii. A majority of these KASP markers were also found to be T. timopheevii subgenome specific with 182 detecting A t subgenome and 275 detecting G subgenome segments. These markers showed that 98% of the A t segments had recombined with the A genome of wheat and 74% of the G genome segments had recombined with the B genome of wheat with the rest recombining with the D genome of wheat. These results were validated through multi-colour in situ hybridisation analysis. Together these homozygous wheat-T. timopheevii ILs and chromosome-specific KASP markers provide an invaluable resource to wheat breeders for trait discovery to combat biotic and abiotic stress factors affecting wheat production due to climate change.
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Affiliation(s)
- Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- *Correspondence: Julie King,
| | - Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- Surbhi Grewal,
| | - Manel Othmeni
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | | | - Cai-yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Nicola Walter
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Jack Walker
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | | | - Ian Phillip King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
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10
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Othmeni M, Grewal S, Walker J, Yang CY, King IP, King J. Assessing the Potential of Using the Langdon 5D(5B) Substitution Line for the Introgression of Aegilops tauschii Into Durum Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:927728. [PMID: 35873983 PMCID: PMC9302120 DOI: 10.3389/fpls.2022.927728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/07/2022] [Indexed: 05/17/2023]
Abstract
Aegilops tauschii, the D-genome donor of hexaploid wheat, provides a source of genetic variation that could be used for tetraploid (durum) wheat improvement. In addition to the genes for wheat quality on the D-genome, which differentiate between bread and durum wheats in terms of end-use properties, genes coding for resistances to biotic and abiotic stresses are also present on the D-genome which would be useful in durum wheat. The introgression of Ae. tauschii into durum wheat, however, requires cytogenetic manipulation to induce homoeologous chromosome pairing to promote recombination. For this purpose, the introgression of Ae. tauschii into durum wheat was performed through a bridge cross of the wild species to the Langdon 5D(5B) disomic substitution line that lacks the Ph1 locus present on chromosome 5B, followed by a cross of the F1 to the durum wheat cultivar Om Rabi 5. Subsequent generations were self-fertilized, and these were screened for D-genome introgressions using (i) D-genome-specific Kompetitive Allele-Specific PCR (KASP) markers and (ii) KASP markers polymorphic between the 5D chromosomes of wheat, present in the Langdon 5D(5B) substitution line, and of Ae. tauschii. Homozygous introgression lines were confirmed using genomic and fluorescence in situ hybridization. The results showed that the use of the Langdon 5D(5B) disomic substitution line did not promote D-genome introgression across all linkage groups with only a limited success in the introgression of Ae. tauschii 5D segments into durum wheat.
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11
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Yang G, Zheng Q, Hu P, Li H, Luo Q, Li B, Li Z. Cytogenetic identification and molecular marker development for the novel stripe rust-resistant wheat- Thinopyrum intermedium translocation line WTT11. ABIOTECH 2021; 2:343-356. [PMID: 36304423 PMCID: PMC9590478 DOI: 10.1007/s42994-021-00060-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/23/2021] [Indexed: 02/02/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat (Triticum aestivum L.) worldwide. Xiaoyan 78829, a partial amphidiploid developed by crossing common wheat with Thinopyrum intermedium, is immune to wheat stripe rust. To transfer the resistance gene of this excellent germplasm resource to wheat, the translocation line WTT11 was produced by pollen irradiation and assessed for immunity to stripe rust races CYR32, CYR33 and CYR34. A novel stripe rust-resistance locus derived from Th. intermedium was confirmed by linkage and diagnostic marker analyses. Molecular cytogenetic analyses revealed that WTT11 carries a TTh·2DL translocation. The breakpoint of 1B was located at 95.5 MB, and the alien segments were found to be homoeologous to wheat-group chromosomes 6 and 7 according to a wheat660K single-nucleotide polymorphism (SNP) array analysis. Ten previously developed PCR-based markers were confirmed to rapidly trace the alien segments of WTT11, and 20 kompetitive allele-specific PCR (KASP) markers were developed to enable genotyping of Th. intermedium and common wheat. Evaluation of agronomic traits in two consecutive crop seasons uncovered some favorable agronomic traits in WTT11, such as lower plant height and longer main panicles, that may be applicable to wheat improvement. As a novel genetic resource, the new resistance locus may be useful for wheat disease-resistance breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-021-00060-3.
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Affiliation(s)
- Guotang Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Pan Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongwei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Bin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
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12
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Grewal S, Guwela V, Newell C, Yang CY, Ashling S, Scholefield D, Hubbart-Edwards S, Burridge A, Stride A, King IP, King J. Generation of Doubled Haploid Wheat- Triticum urartu Introgression Lines and Their Characterisation Using Chromosome-Specific KASP Markers. FRONTIERS IN PLANT SCIENCE 2021; 12:643636. [PMID: 34054892 PMCID: PMC8155260 DOI: 10.3389/fpls.2021.643636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/19/2021] [Indexed: 05/07/2023]
Abstract
Wheat is one of the most important food and protein sources in the world and although, in recent years wheat breeders have achieved yield gains, they are not sufficient to meet the demands of an ever-growing population. Development of high yielding wheat varieties, resilient to abiotic and biotic stress resulting from climate change, has been limited by wheat's narrow genetic base. In contrast to wheat, the wild relatives of wheat provide a vast reservoir of genetic variation for most, if not all, agronomic traits. Previous studies by the authors have shown the transfer of genetic variation from T. urartu into bread wheat. However, before the introgression lines can be exploited for trait analysis, they are required to have stable transmission of the introgressions to the next generation. In this work, we describe the generation of 86 doubled haploid (DH) wheat-T. urartu introgression lines that carry homozygous introgressions which are stably inherited. The DH lines were characterised using the Axiom® Wheat Relative Genotyping Array and 151 KASP markers to identify 65 unique T. urartu introgressions in a bread wheat background. DH production has helped accelerate the breeding process and facilitated the early release of homozygous wheat-T. urartu introgression lines. Together with the KASP markers, this valuable resource could greatly advance identification of beneficial alleles that can be used in wheat improvement.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Veronica Guwela
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Claire Newell
- Limagrain UK Limited, Bury St Edmunds, United Kingdom
| | - Cai-yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Amanda Burridge
- School of Biological Sciences, University of Bristol, United Kingdom
| | - Alex Stride
- Limagrain UK Limited, Bury St Edmunds, United Kingdom
| | - Ian P. King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- *Correspondence: Julie King,
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