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Genetic Variation of a Lentil (Lens culinaris) Landrace during Three Generations of Breeding. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12010450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Genetic differentiation between 40 lentil genotypes was tested using molecular markers. The genotypes were produced from a Greek landrace of commercial interest via the honeycomb breeding methodology, i.e., single-plant selection in the absence of competition, across three successive pedigree generations. The selected genotypes from each generation were examined for genetic relationships using 15 SSR molecular markers with HRM analysis. As expected, low variation among consecutive generations at the level of 2.5–7.7% was detected. Analysis of molecular variance (AMOVA) revealed that partitioning of this variation was at higher percentage within each generation’s population than between them. Population structure analysis indicated that ongoing selection could effectively shift the allelic composition in each generation. The applied honeycomb breeding methodology that effectively improved progeny yield and seed quality increased the percentage of favorable alleles altering allelic composition but not eliminating genetic variation of the breeding population.
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Khoury CK, Brush S, Costich DE, Curry HA, de Haan S, Engels JMM, Guarino L, Hoban S, Mercer KL, Miller AJ, Nabhan GP, Perales HR, Richards C, Riggins C, Thormann I. Crop genetic erosion: understanding and responding to loss of crop diversity. THE NEW PHYTOLOGIST 2022; 233:84-118. [PMID: 34515358 DOI: 10.1111/nph.17733] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Crop diversity underpins the productivity, resilience and adaptive capacity of agriculture. Loss of this diversity, termed crop genetic erosion, is therefore concerning. While alarms regarding evident declines in crop diversity have been raised for over a century, the magnitude, trajectory, drivers and significance of these losses remain insufficiently understood. We outline the various definitions, measurements, scales and sources of information on crop genetic erosion. We then provide a synthesis of evidence regarding changes in the diversity of traditional crop landraces on farms, modern crop cultivars in agriculture, crop wild relatives in their natural habitats and crop genetic resources held in conservation repositories. This evidence indicates that marked losses, but also maintenance and increases in diversity, have occurred in all these contexts, the extent depending on species, taxonomic and geographic scale, and region, as well as analytical approach. We discuss steps needed to further advance knowledge around the agricultural and societal significance, as well as conservation implications, of crop genetic erosion. Finally, we propose actions to mitigate, stem and reverse further losses of crop diversity.
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Affiliation(s)
- Colin K Khoury
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537, Cali, Colombia
- Department of Biology, Saint Louis University, 1 N. Grand Blvd, St Louis, MO, 63103, USA
- San Diego Botanic Garden, 230 Quail Gardens Dr., Encinitas, CA, 92024, USA
| | - Stephen Brush
- University of California Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Denise E Costich
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, Km. 45, El Batán, 56237, Texcoco, México
| | - Helen Anne Curry
- Department of History and Philosophy of Science, University of Cambridge, Free School Lane, Cambridge, CB2 3RH, UK
| | - Stef de Haan
- International Potato Center (CIP), Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima, Peru
| | | | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Sean Hoban
- The Morton Arboretum, The Center for Tree Science, 4100 IL-53, Lisle, IL, 60532, USA
| | - Kristin L Mercer
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, 1 N. Grand Blvd, St Louis, MO, 63103, USA
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Gary P Nabhan
- Southwest Center and Institute of the Environment, University of Arizona, 1401 E. First St., PO Box 210185, Tucson, AZ, 85721-0185, USA
| | - Hugo R Perales
- Departamento de Agroecología, El Colegio de la Frontera Sur, San Cristóbal, Chiapas, 29290, México
| | - Chris Richards
- National Laboratory for Genetic Resources Preservation, United States Department of Agriculture, Agricultural Research Service, 1111 South Mason Street, Fort Collins, CO, 80521, USA
| | - Chance Riggins
- Department of Crop Sciences, University of Illinois, 331 Edward R. Madigan Lab, 1201 W. Gregory Dr., Urbana, IL, 61801, USA
| | - Imke Thormann
- Federal Office for Agriculture and Food (BLE), Information and Coordination Centre for Biological Diversity (IBV), Deichmanns Aue 29, 53179, Bonn, Germany
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Semagn K, Iqbal M, Alachiotis N, N'Diaye A, Pozniak C, Spaner D. Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array. Sci Rep 2021; 11:23773. [PMID: 34893626 PMCID: PMC8664822 DOI: 10.1038/s41598-021-02666-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022] Open
Abstract
Previous molecular characterization studies conducted in Canadian wheat cultivars shed some light on the impact of plant breeding on genetic diversity, but the number of varieties and markers used was small. Here, we used 28,798 markers of the wheat 90K single nucleotide polymorphisms to (a) assess the extent of genetic diversity, relationship, population structure, and divergence among 174 historical and modern Canadian spring wheat varieties registered from 1905 to 2018 and 22 unregistered lines (hereinafter referred to as cultivars), and (b) identify genomic regions that had undergone selection. About 91% of the pairs of cultivars differed by 20-40% of the scored alleles, but only 7% of the pairs had kinship coefficients of < 0.250, suggesting the presence of a high proportion of redundancy in allelic composition. Although the 196 cultivars represented eight wheat classes, our results from phylogenetic, principal component, and the model-based population structure analyses revealed three groups, with no clear structure among most wheat classes, breeding programs, and breeding periods. FST statistics computed among different categorical variables showed little genetic differentiation (< 0.05) among breeding periods and breeding programs, but a diverse level of genetic differentiation among wheat classes and predicted groups. Diversity indices were the highest and lowest among cultivars registered from 1970 to 1980 and from 2011 to 2018, respectively. Using two outlier detection methods, we identified from 524 to 2314 SNPs and 41 selective sweeps of which some are close to genes with known phenotype, including plant height, photoperiodism, vernalization, gluten strength, and disease resistance.
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Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Muhammad Iqbal
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Nikolaos Alachiotis
- Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, 3230, Enschede, OV, The Netherlands
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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Ayalew H, Sorrells ME, Carver BF, Baenziger PS, Ma XF. Selection signatures across seven decades of hard winter wheat breeding in the Great Plains of the United States. THE PLANT GENOME 2020; 13:e20032. [PMID: 33217215 DOI: 10.1002/tpg2.20032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/15/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Classical plant breeding has been instrumental in changing the genetic makeup of crop plants for better ecological adaptation and improved quality. This paper provides insights of the genomic changes effected in hard winter wheat (Triticum aestivum L.) through decades of breeding and selection in the Great Plains of the United States. Population structure and differentiation analyses were conducted on 185 wheat cultivars released from 1943 to 2013. Cultivars were grouped into four distinct clusters using discriminant analysis of principal components (DAPC). One of the clusters was unique in that 15 out of the 18 individuals were recent releases (2000-2010), while 12 of the 18 shared the cultivar 'Jagger' in their genetic background. Jagger carries a 2NS/2AS translocation segment from Aegilops ventricosa, an important segment for resistance to several foliar diseases. Using the outlier approach, Wright's population fixation index (Fst) identified 450 loci that were directionally selected. The largest signature of selection was found on chromosome 2A. Genetic diversity was high while the inbreeding coefficient was low, indicating extensive hybridization and germplasm exchange among breeding programs within the region. Foliar disease pressure and selection for resistance helped shape the microevolution of wheat in the southern Great Plains. The results showed that high genetic diversity remains in hard winter wheat cultivars adapted to the Great Plains of the USA, and modern plant breeding did not cause any sizable reduction in genetic diversity of the crop in this region.
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Affiliation(s)
| | - Mark E Sorrells
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Brett F Carver
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - P Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Xue-Feng Ma
- Noble Research Institute, Ardmore, OK, 73401, USA
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AFLP-Based Analysis of Variation and Population Structure in Mutagenesis Induced Faba Bean. DIVERSITY 2020. [DOI: 10.3390/d12080303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Genetic diversity enrichment is urgently necessary to develop climate-resilient faba bean cultivars. The present study aimed to measure the enrichment of genetic diversity and changes in the population structure of faba bean, following induced mutagenesis. 120 samples, including 116 M2 mutant plants, generated by exposing the ILB4347 accession to four mutagen treatments (25 and 50 Gray gamma radiation and 0.01%, and 0.05% diethyl sulfate) and four reference genotypes were characterized using 11 amplified fragment length polymorphism (AFLP) primer combinations. The AFLP markers generated 1687 polymorphic alleles, including 756 alleles (45%) that were detected infrequently (f ≤ 0.1). The total allele count of the mutant plants ranged from 117 to 545. We observed a wide range of banding patterns and counts among the mutant plants, showing the high genetic diversity induced by mutation. Mutations also changed the population structure, by altering 31.78% of the total membership coefficient (Q). Although mutations changed the population structure, Nei’s genetic distance showed that the mutant population remained closely related to its control parent. This is the first report examining genetic diversity and population changes in faba bean mutant populations and, thus, could facilitate the application of induced mutagenesis during faba bean breeding.
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N’Diaye A, Haile JK, Nilsen KT, Walkowiak S, Ruan Y, Singh AK, Clarke FR, Clarke JM, Pozniak CJ. Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height. FRONTIERS IN PLANT SCIENCE 2018; 9:1589. [PMID: 30455711 PMCID: PMC6230583 DOI: 10.3389/fpls.2018.01589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/15/2018] [Indexed: 05/21/2023]
Abstract
Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.
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Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirby T. Nilsen
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Fran R. Clarke
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - John M. Clarke
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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7
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Bokore FE, Cuthbert RD, Knox RE, Randhawa HS, Hiebert CW, DePauw RM, Singh AK, Singh A, Sharpe AG, N'Diaye A, Pozniak CJ, McCartney C, Ruan Y, Berraies S, Meyer B, Munro C, Hay A, Ammar K, Huerta-Espino J, Bhavani S. Quantitative trait loci for resistance to stripe rust of wheat revealed using global field nurseries and opportunities for stacking resistance genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2617-2635. [PMID: 28913655 DOI: 10.1007/s00122-017-2980-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/30/2017] [Indexed: 05/19/2023]
Abstract
Quantitative trait loci controlling stripe rust resistance were identified in adapted Canadian spring wheat cultivars providing opportunity for breeders to stack loci using marker-assisted breeding. Stripe rust or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is a devastating disease of common wheat (Triticum aestivum L.) in many regions of the world. The objectives of this research were to identify and map quantitative trait loci (QTL) associated with stripe rust resistance in adapted Canadian spring wheat cultivars that are effective globally, and investigate opportunities for stacking resistance. Doubled haploid (DH) populations from the crosses Vesper/Lillian, Vesper/Stettler, Carberry/Vesper, Stettler/Red Fife and Carberry/AC Cadillac were phenotyped for stripe rust severity and infection response in field nurseries in Canada (Lethbridge and Swift Current), New Zealand (Lincoln), Mexico (Toluca) and Kenya (Njoro), and genotyped with SNP markers. Six QTL for stripe rust resistance in the population of Vesper/Lillian, five in Vesper/Stettler, seven in Stettler/Red Fife, four in Carberry/Vesper and nine in Carberry/AC Cadillac were identified. Lillian contributed stripe rust resistance QTL on chromosomes 4B, 5A, 6B and 7D, AC Cadillac on 2A, 2B, 3B and 5B, Carberry on 1A, 1B, 4A, 4B, 7A and 7D, Stettler on 1A, 2A, 3D, 4A, 5B and 6A, Red Fife on 2D, 3B and 4B, and Vesper on 1B, 2B and 7A. QTL on 1A, 1B, 2A, 2B, 3B, 4A, 4B, 5B, 7A and 7D were observed in multiple parents. The populations are compelling sources of recombination of many stripe rust resistance QTL for stacking disease resistance. Gene pyramiding should be possible with little chance of linkage drag of detrimental genes as the source parents were mostly adapted cultivars widely grown in Canada.
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Affiliation(s)
- Firdissa E Bokore
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada.
| | - Richard D Cuthbert
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada.
| | - Ron E Knox
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Harpinder S Randhawa
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Colin W Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Ron M DePauw
- Advancing Wheat Technologies, 870 Field Drive, Swift Current, SK, S9H 4N5, Canada
| | - Asheesh K Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Andrew G Sharpe
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Amidou N'Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Curt McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Samia Berraies
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Brad Meyer
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Catherine Munro
- Plant and Food Research Canterbury Agriculture and Science Centre, Gerald St, Lincoln, 7608, New Zealand
| | - Andy Hay
- Plant and Food Research Canterbury Agriculture and Science Centre, Gerald St, Lincoln, 7608, New Zealand
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Apdo., Postal 6-6-41, 06600, Mexico, DF, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México INIFAP, Apdo., Postal 10, 56230, Chapingo, Edo. de México, Mexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
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Genome-wide indel/SSR scanning reveals significant loci associated with excellent agronomic traits of a cabbage (Brassica oleracea) elite parental line '01-20'. Sci Rep 2017; 7:41696. [PMID: 28164997 PMCID: PMC5292705 DOI: 10.1038/srep41696] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/23/2016] [Indexed: 01/05/2023] Open
Abstract
Elite parental lines are of great significance to crop breeding. To discover unique genomic loci associated with excellent economic traits in the elite cabbage inbred-line ‘01–20’, we performed comparisons of phenotypes as well as whole-genome insertion-deletion/simple sequence repeat loci between ‘01–20’ and each of its five sister lines. ‘01–20’ has a range of excellent agronomic traits, including early-maturing, and improvements in plant type and leaf colour. Eight unique loci were discovered for ‘01–20’ and ‘01-07-258’, another elite line similar to ‘01–20’ at the whole-genome level. In addition, two excellent double-haploid lines derived from a cross of ‘01–20’ also inherited these loci. Based on the quantitative trait locus association results, five of these loci were found to be associated with important agronomic traits, which could explain why the elite parent ‘01–20’ possesses greener outer leaves, a more compact and upright plant-type, rounder head, shorter core length, and better taste. Additionally, some of these loci have clustering effects for quantitative trait loci associated with different traits; therefore, important genes in these regions were analysed. The obtained results should enable marker-assisted multi-trait selection at the whole-genome level in cabbage breeding and provide insights into significant genome loci and their breeding effects.
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Cui D, Li J, Tang C, A X, Yu T, Ma X, Zhang E, Cao G, Xu F, Qiao Y, Dai L, Han L. Diachronic analysis of genetic diversity in rice landraces under on-farm conservation in Yunnan, China. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:155-68. [PMID: 26498440 DOI: 10.1007/s00122-015-2617-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 10/06/2015] [Indexed: 05/12/2023]
Abstract
Diachronic analysis showed no significant changes in the level of genetic diversity occurred over the past 27 years' domestication, which indicated genetic diversity was successfully maintained under on-farm conservation. Rice (Oryza sativa L.) is one of the earliest domesticated crop species. Its genetic diversity has been declining as a result of natural and artificial selection. In this study, we performed the first analysis of the levels and patterns of nucleotide variation in rice genomes under on-farm conservation in Yunnan during a 27-year period of domestication. We performed large-scale sequencing of 600 rice accessions with high diversity, which were collected in 1980 and 2007, using ten unlinked nuclear loci. Diachronic analysis showed no significant changes in the level of genetic diversity occurring over the past 27 years' domestication, which indicated genetic diversity was successfully maintained under on-farm conservation. Population structure revealed that the rice landraces could be grouped into two subpopulations, namely the indica and japonica groups. Interestingly, the alternate distribution of indica and japonica rice landraces could be found in each ecological zone. The results of AMOVA showed that on-farm conservation provides opportunities for continued differentiation and variation of landraces. Therefore, dynamic conservation measures such as on-farm conservation (which is a backup, complementary strategy to ex situ conservation) should be encouraged and enhanced, especially in crop genetic diversity centers. The results of this study offered accurate insights into short-term evolutionary processes and provided a scientific basis for on-farm management practices.
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Fu YB. Understanding crop genetic diversity under modern plant breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2131-42. [PMID: 26246331 PMCID: PMC4624815 DOI: 10.1007/s00122-015-2585-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/16/2015] [Indexed: 05/18/2023]
Abstract
Maximizing crop yield while at the same time minimizing crop failure for sustainable agriculture requires a better understanding of the impacts of plant breeding on crop genetic diversity. This review identifies knowledge gaps and shows the need for more research into genetic diversity changes under plant breeding. Modern plant breeding has made a profound impact on food production and will continue to play a vital role in world food security. For sustainable agriculture, a compromise should be sought between maximizing crop yield under changing climate and minimizing crop failure under unfavorable conditions. Such a compromise requires better understanding of the impacts of plant breeding on crop genetic diversity. Efforts have been made over the last three decades to assess crop genetic diversity using molecular marker technologies. However, these assessments have revealed some temporal diversity patterns that are largely inconsistent with our perception that modern plant breeding reduces crop genetic diversity. An attempt was made in this review to explain such discrepancies by examining empirical assessments of crop genetic diversity and theoretical investigations of genetic diversity changes over time under artificial selection. It was found that many crop genetic diversity assessments were not designed to assess diversity impacts from specific plant breeding programs, while others were experimentally inadequate and contained technical biases from the sampling of cultivars and genomes. Little attention has been paid to theoretical investigations on crop genetic diversity changes from plant breeding. A computer simulation of five simplified breeding schemes showed the substantial effects of plant breeding on the retention of heterozygosity over generations. It is clear that more efforts are needed to investigate crop genetic diversity in space and time under plant breeding to achieve sustainable crop production.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, AAFC Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, S7N0X2, Canada.
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11
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Hucl P, Briggs C, Graf RJ, Chibbar RN. Genetic Gains in Agronomic and Selected End-Use Quality Traits over a Century of Plant Breeding of Canada Western Red Spring Wheat. Cereal Chem 2015. [DOI: 10.1094/cchem-02-15-0029-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Pierre Hucl
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Connie Briggs
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Robert J. Graf
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, T1J 4B1, Canada
- Former address: Saskatchewan Wheat Pool (currently d.b.a. Viterra), Agricultural Research and Development, Saskatoon, SK, S7N 4L8, Canada
| | - Ravindra N. Chibbar
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
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12
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Laidò G, Marone D, Russo MA, Colecchia SA, Mastrangelo AM, De Vita P, Papa R. Linkage disequilibrium and genome-wide association mapping in tetraploid wheat (Triticum turgidum L.). PLoS One 2014; 9:e95211. [PMID: 24759998 PMCID: PMC3997356 DOI: 10.1371/journal.pone.0095211] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/25/2014] [Indexed: 11/18/2022] Open
Abstract
Association mapping is a powerful tool for the identification of quantitative trait loci through the exploitation of the differential decay of linkage disequilibrium (LD) between marker loci and genes of interest in natural and domesticated populations. Using a sample of 230 tetraploid wheat lines (Triticum turgidum ssp), which included naked and hulled accessions, we analysed the pattern of LD considering 26 simple sequence repeats and 970 mostly mapped diversity array technology loci. In addition, to validate the potential for association mapping in durum wheat, we evaluated the same genotypes for plant height, heading date, protein content, and thousand-kernel weight. Molecular and phenotypic data were used to: (i) investigate the genetic and phenotypic diversity; (ii) study the dynamics of LD across the durum wheat genome, by investigating the patterns of LD decay; and (iii) test the potential of our panel to identify marker–trait associations through the analysis of four quantitative traits of major agronomic importance. Moreover, we compared and validated the association mapping results with outlier detection analysis based on population divergence. Overall, in tetraploid wheat, the pattern of LD is extremely population dependent and is related to the domestication and breeding history of durum wheat. Comparing our data with several other studies in wheat, we confirm the position of many major genes and quantitative trait loci for the traits considered. Finally, the analysis of the selection signature represents a very useful complement to validate marker–trait associations.
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Affiliation(s)
- Giovanni Laidò
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
| | - Daniela Marone
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
| | - Maria A. Russo
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
| | - Salvatore A. Colecchia
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
| | - Anna M. Mastrangelo
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
| | - Pasquale De Vita
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
| | - Roberto Papa
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
- * E-mail:
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Laidò G, Mangini G, Taranto F, Gadaleta A, Blanco A, Cattivelli L, Marone D, Mastrangelo AM, Papa R, De Vita P. Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data. PLoS One 2013; 8:e67280. [PMID: 23826256 PMCID: PMC3694930 DOI: 10.1371/journal.pone.0067280] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 05/17/2013] [Indexed: 11/24/2022] Open
Abstract
Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K = 2), both of the sets of molecular markers distinguished the durum wheat cultivars from the other tetraploid subspecies, and two distinct subgroups were detected within the durum wheat subspecies, which is in agreement with their origin and year of release. The genetic diversity of morphological traits and seed storage proteins was always lower in the improved durum cultivars registered after 1990, than in the intermediate and older ones. This marked effect on diversity was not observed for molecular markers, where there was only a weak reduction. At K >2, the SSR markers showed a greater degree of resolution than for DArT, with their identification of a greater number of groups within each subspecies. Analysis of DArT marker differentiation between the wheat subspecies indicated outlier loci that are potentially linked to genes controlling some important agronomic traits. Among the 211 loci identified under selection, 109 markers were recently mapped, and some of these markers were clustered into specific regions on chromosome arms 2BL, 3BS and 4AL, where several genes/quantitative trait loci (QTLs) are involved in the domestication of tetraploid wheats, such as the tenacious glumes (Tg) and brittle rachis (Br) characteristics. On the basis of these results, it can be assumed that the population structure of the tetraploid wheat collection partially reflects the evolutionary history of Triticum turgidum L. subspecies and the genetic potential of landraces and wild accessions for the detection of unexplored alleles.
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Affiliation(s)
- Giovanni Laidò
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
| | - Giacomo Mangini
- Department of Soil, Plant, and Food Sciences, Section of Genetics and Plant Breeding, University of Bari, Via Amendola, Bari, Italy
| | - Francesca Taranto
- Department of Soil, Plant, and Food Sciences, Section of Genetics and Plant Breeding, University of Bari, Via Amendola, Bari, Italy
| | - Agata Gadaleta
- Department of Soil, Plant, and Food Sciences, Section of Genetics and Plant Breeding, University of Bari, Via Amendola, Bari, Italy
| | - Antonio Blanco
- Department of Soil, Plant, and Food Sciences, Section of Genetics and Plant Breeding, University of Bari, Via Amendola, Bari, Italy
| | - Luigi Cattivelli
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
| | - Daniela Marone
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
| | - Anna M. Mastrangelo
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
| | - Roberto Papa
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
| | - Pasquale De Vita
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy
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14
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Ren J, Sun D, Chen L, You FM, Wang J, Peng Y, Nevo E, Sun D, Luo MC, Peng J. Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat. Int J Mol Sci 2013; 14:7061-88. [PMID: 23538839 PMCID: PMC3645677 DOI: 10.3390/ijms14047061] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 02/23/2013] [Accepted: 03/01/2013] [Indexed: 11/25/2022] Open
Abstract
Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity.
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Affiliation(s)
- Jing Ren
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daokun Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
| | - Liang Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
| | - Frank M. You
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; E-Mails: (F.M.Y.); (J.W.)
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB R3T 2M9, Canada
| | - Jirui Wang
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; E-Mails: (F.M.Y.); (J.W.)
| | - Yunliang Peng
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, Sichuan, China; E-Mail:
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel; E-Mail:
| | - Dongfa Sun
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430071, Hubei, China; E-Mail:
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; E-Mails: (F.M.Y.); (J.W.)
| | - Junhua Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
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15
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Evolution of wild cereals during 28 years of global warming in Israel. Proc Natl Acad Sci U S A 2012; 109:3412-5. [PMID: 22334646 DOI: 10.1073/pnas.1121411109] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Climate change is a major environmental stress threatening biodiversity and human civilization. The best hope to secure staple food for humans and animal feed by future crop improvement depends on wild progenitors. We examined 10 wild emmer wheat (Triticum dicoccoides Koern.) populations and 10 wild barley (Hordeum spontaneum K. Koch) populations in Israel, sampling them in 1980 and again in 2008, and performed phenotypic and genotypic analyses on the collected samples. We witnessed the profound adaptive changes of these wild cereals in Israel over the last 28 y in flowering time and simple sequence repeat allelic turnover. The revealed evolutionary changes imply unrealized risks present in genetic resources for crop improvement and human food production.
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16
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Fu YB, Peterson GW, McCallum BD, Huang L. Population-based resequencing analysis of improved wheat germplasm at wheat leaf rust resistance locus Lr21. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:271-281. [PMID: 20217382 DOI: 10.1007/s00122-010-1308-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 02/22/2010] [Indexed: 05/28/2023]
Abstract
Little is known about the genetic impacts of modern plant breeding on specific breeding target loci. Resequencing cloned genes can identify all mutations in single genes for population-based analyses of genetic changes in improved gene pools. Ninety-five wheat cultivars released in Canada from 1845 to 2004 were sequenced at the wheat leaf rust resistance locus Lr21. Characterization of the DNA fragment of length 4,071 bp, covering the Lr21 gene from -92 to +4,261, revealed 13 SNPs, four indels, 10 haplotypes, and 4 major haplotype groups. A new SCAR marker was developed to identify the resistant haplotype and haplotype groups. Non-synonymous polymorphic sites and haplotype numbers were increased over the 100 years of wheat breeding. Nucleotide diversity of the wheat cultivars was gradually reduced from 1845 to 1993 and increased after the release of the first Lr21 wheat cultivar AC Cora in 1994. Positive selection measured with Tajima's D was observed in the cultivars released before 1935. At least two recombination events were inferred in those cultivars released before 1993. Linkage disequilibrium at the locus was decreased over time. These findings demonstrate not only the effectiveness of the wheat breeding in the improvement of leaf rust resistance, but also are useful to understand the genetic influences of a long-term artificial selection on individual loci.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada.
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17
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van de Wouw M, van Hintum T, Kik C, van Treuren R, Visser B. Genetic diversity trends in twentieth century crop cultivars: a meta analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:1241-52. [PMID: 20054521 PMCID: PMC2839474 DOI: 10.1007/s00122-009-1252-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Accepted: 12/14/2009] [Indexed: 05/19/2023]
Abstract
In recent years, an increasing number of papers has been published on the genetic diversity trends in crop cultivars released in the last century using a variety of molecular techniques. No clear general trends in diversity have emerged from these studies. Meta analytical techniques, using a study weight adapted for use with diversity indices, were applied to analyze these studies. In the meta analysis, 44 published papers were used, addressing diversity trends in released crop varieties in the twentieth century for eight different field crops, wheat being the most represented. The meta analysis demonstrated that overall in the long run no substantial reduction in the regional diversity of crop varieties released by plant breeders has taken place. A significant reduction of 6% in diversity in the 1960s as compared with the diversity in the 1950s was observed. Indications are that after the 1960s and 1970s breeders have been able to again increase the diversity in released varieties. Thus, a gradual narrowing of the genetic base of the varieties released by breeders could not be observed. Separate analyses for wheat and the group of other field crops and separate analyses on the basis of regions all showed similar trends in diversity.
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Affiliation(s)
- Mark van de Wouw
- Centre for Genetic Resources, The Netherlands, Wageningen University and Research Centre, Wageningen, The Netherlands.
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18
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ZHAO YG, Ofori A, LU CM. Genetic Diversity of European and Chinese Oilseed Brassica rapa Cultivars from Different Breeding Periods. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1671-2927(08)60297-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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ZHANG J, ZHAO TJ, GAI JY. Inheritance of Elite Alleles of Yield and Quality Traits in the Pedigrees of Major Cultivar Families Released in Huanghuai Valleys and Southern China. ZUOWU XUEBAO 2009. [DOI: 10.3724/sp.j.1006.2009.00191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Ofori A, Becker HC, Kopisch-Obuch FJ. Effect of crop improvement on genetic diversity in oilseed Brassica rapa (turnip-rape) cultivars, detected by SSR markers. J Appl Genet 2008; 49:207-12. [PMID: 18670055 DOI: 10.1007/bf03195615] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
With the improvement of seed quality, Brassica rapa oilseed germplasm went through 2 major breeding bottlenecks during the introgression of genes for zero erucic acid content and low glucosinolate content, respectively. This study investigates the impact of these bottlenecks on the genetic diversity in European winter B. rapa by comparing 3 open-pollinated cultivars, each representing a different breeding period. Diversity was estimated on 32 plants per cultivar, with 16 simple sequence repeat (SSR) markers covering each of the B. rapa linkage groups. There was no significant loss of genetic diversity over the 3 cultivars as indicated by allele number (ranging from 59 to 55), mean allele number (from 3.68 to 3.50), Shannon information index (from 0.94 to 0.87) and expected heterozygosity (from 0.53 to 0.48). About 83% of the total variation was attributed to within-cultivar variation, and the remaining 17% to between-cultivar variation by analysis of molecular variance (AMOVA). Individual plants were separated into the 3 cultivars by principal coordinate analysis (PCoA). In conclusion, genetic diversity within cultivars was high and quality breeding in B. rapa did not significantly reduce the genetic diversity of B. rapa winter cultivars, so there is no risk of decline in performance due to quality improvement.
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Affiliation(s)
- Atta Ofori
- Department of Crop Sciences, Georg-August-University Göttingen, Von-Siebold-Str. 8, 37075, Göttingen, Germany.
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21
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White J, Law JR, MacKay I, Chalmers KJ, Smith JSC, Kilian A, Powell W. The genetic diversity of UK, US and Australian cultivars of Triticum aestivum measured by DArT markers and considered by genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:439-53. [PMID: 18060539 DOI: 10.1007/s00122-007-0681-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Accepted: 11/13/2007] [Indexed: 05/02/2023]
Abstract
The genetic diversity of UK, US and Australian wheat varieties over the period of modern plant breeding is estimated using diversity array technology markers. Diversity is assessed by both genetic distance between varieties, by AMOVA and as the volumes of multi-dimensional convex hulls estimated from principal co-ordinate analysis. At the whole genome level the three populations are genetically distinct; this is also true of the B genome. However, the US and Australian D genomes are found to occupy the same region of diversity space and the A genomes for these countries are partially overlapping. The use of high-density genotyping with a common marker set allows an unprecedented direct comparison between the diversities of the national populations, between individual genomes and the fluctuation of diversity over time. The highest genetic diversity amongst varieties is reported in the Australian population followed by the US, which in turn is more diverse than the UK. However the average diversity of loci is higher in the US set than in the Australian. Non-random fluctuations in genetic diversity over time are observed.
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Affiliation(s)
- J White
- National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 OLE, UK.
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22
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The genetic diversity of UK, US and Australian cultivars of Triticum aestivum measured by DArT markers and considered by genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007. [PMID: 18060539 DOI: 10.1007/s00122‐007‐0681‐3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
The genetic diversity of UK, US and Australian wheat varieties over the period of modern plant breeding is estimated using diversity array technology markers. Diversity is assessed by both genetic distance between varieties, by AMOVA and as the volumes of multi-dimensional convex hulls estimated from principal co-ordinate analysis. At the whole genome level the three populations are genetically distinct; this is also true of the B genome. However, the US and Australian D genomes are found to occupy the same region of diversity space and the A genomes for these countries are partially overlapping. The use of high-density genotyping with a common marker set allows an unprecedented direct comparison between the diversities of the national populations, between individual genomes and the fluctuation of diversity over time. The highest genetic diversity amongst varieties is reported in the Australian population followed by the US, which in turn is more diverse than the UK. However the average diversity of loci is higher in the US set than in the Australian. Non-random fluctuations in genetic diversity over time are observed.
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23
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Novoselskaya-Dragovich AY, Fisenko AV, Imasheva AG, Pukhalskiy VA. Comparative analysis of the genetic diversity dynamics at gliadin loci in the winter common wheat Triticum aestivum L. cultivars developed in Serbia and Italy over 40 years of scientific breeding. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407110051] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Wang HY, Wei YM, Yan ZH, Zheng YL. EST-SSR DNA polymorphism in durum wheat (Triticum durum L.) collections. J Appl Genet 2007; 48:35-42. [PMID: 17272859 DOI: 10.1007/bf03194655] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
SSRs derived from EST were molecular markers belonging to the transcribed region of the genome. Therefore, any polymorphism detected using EST-SSRs might reflect the better relationship among species or varieties. Using wheat EST-SSR markers, 60 durum wheat (Triticum durum L.) accessions from seven countries were investigated. Twenty-five primer pairs could amplify successfully in the 60 durum wheat accessions, of which tri-nucleotide repeats were the dominant type, and revealed 26 loci on all seven wheat homologous chromosome groups. A total of 87 eSSR alleles were detected, and the number of alleles detected by a single pair of primers ranged from 1 to 11, with an average of 3.3 alleles per locus. Higher numbers of alleles and PIC were identified on the B genome than those on the A genome.
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Affiliation(s)
- Han-Yan Wang
- Triticeae Research Institute, Sichuan Agricultural University, Ya'an, Sichuan China
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25
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Abstract
The major cereal crops grown in Canada are wheat (11 Mha), barley (4 Mha), and oat (1.5 Mha). Over 90% of the total cereal production area is in the western provinces of Manitoba, Saskatchewan,and Alberta. Historically, the disease of major concern in wheat was stem rust, caused by Puccinia graminis f. sp. tritici. The first significant stem rust resistant cultivar in Canada was Thatcher, grown extensively from 1939 until the early 1970s. The stem rust resistance in Thatcher was relatively effective, with the exception of susceptibility to race 15B epidemic in the 1950s. Thatcher, however, was very susceptible to leaf rust, caused by Puccinia triticina. Over time, improved resistance to both stem and leaf rust was achieved with the release of cultivars with additional genes for resistance, primarily Sr2, Sr6, Sr7a, Sr9b, Lr13, Lr14a, Lr16, and Lr34. Over the years genetic resistance has adequately controlled stem rust but leaf rust continues to cause significant losses, partially due to changes in the P. triticina population which reduced the effectiveness of resistance genes such as Lr13 and Lr16. Stripe rust on wheat, caused by Puccinia striiformis f. sp. tritici, was historically a problem under irrigation in southern Alberta, but since 2000 it has been found annually in the central Canadian prairies and southern Ontario. The genetic basis of resistance to stripe rust in most Canadian wheat cultivars has not been determined, although Yr18 provides partial resistance in many cultivars. In contrast to wheat, rust diseases have generally not caused concern for barley producers. Stem rust, caused by P. graminis f. sp. tritici, is the primary concern for barley growers, and has been controlled through use of gene Rpg1 since 1947. In 1988 race QCCJ with virulence on Rpg1 was detected in the prairie region but to date has not caused significant economic losses in barley. The resistance gene rpg4 is effective against QCCJ, but no commercial varieties have yet been produced with rpg4. In oat, both stem rust, caused by Puccinia graminis f. sp. avenae, and crown rust, caused by Puccinia coronata f. sp. avenae, have caused significant yield losses. Both rusts have been controlled mainly through host resistance and early planting. Stem rust resistance genes Pg2 and Pg13 have been the most effective and occur in many current oat cultivars. However, in 1998, 2 races, NA67 and NA76, with virulence on both Pg2 and Pg13 were detected in the prairie region. Currently, race NA67 is predominant in the prairie region and thus all Canadian cultivars are susceptible to stem rust. Since the 1980s, improved resistance to crown rust has been achieved through use of resistance derived from Avena sterilis. Pc39 was the first of the genes derived from this wild relative to be deployed in a new cultivar, followed by the release of cultivars possessing both Pc38 and Pc39. These 2 genes remained effective until the early 1990s. From 1994 onward, a series of cultivars with the highly effective Pc68 gene introgressed from A. sterilis were released. Virulence to Pc68 appeared in 2001, and in 2005 cultivars with this gene were severely rusted. The cultivar Leggett with Pc68 plus the highly effective Pc94 gene from the diploid A. strigosa was released in 2004. Rhamnus cathartica, the alternate host of P. coronata, is widespread in Canada and removal of these woody shrubs in the vicinity of oat fields is important to reduce the severity of crown rust. The increased use of fungicides on all cereals in the past 10 years has been fairly effective in rust control but represents an added input cost for producers.
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26
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Hai L, Wagner C, Friedt W. Quantitative structure analysis of genetic diversity among spring bread wheats (Triticum aestivum L.) from different geographical regions. Genetica 2006; 130:213-25. [PMID: 17048074 DOI: 10.1007/s10709-006-9008-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Accepted: 07/13/2006] [Indexed: 11/25/2022]
Abstract
Genetic diversity in spring bread wheat (T. aestivum L.) was studied in a total of 69 accessions. For this purpose, 52 microsatellite (SSR) markers were used and a total of 406 alleles were detected, of which 182 (44.8%) occurred at a frequency of <5% (rare alleles). The number of alleles per locus ranged from 2 to 14 with an average of 7.81. The largest number of alleles per locus occurred in the B genome (8.65) as compared to the A (8.43) and D (5.93) genomes, respectively. The polymorphism index content (PIC) value varied from 0.24 to 0.89 with an average of 0.68. The highest PIC for all accessions was found in the B genome (0.71) as compared to the A (0.68) and D genomes (0.63). Genetic distance-based method (standard UPGMA clustering) and a model-based method (structure analysis) were used for cluster analysis. The two methods led to analogical results. Analysis of molecular variance (AMOVA) showed that 80.6% of the total variation could be explained by the variance within the geographical groups. In comparison to the diversity detected for all accessions (H ( e ) = 0.68), genetic diversity among European spring bread wheats was H ( e ) = 0.65. A comparatively higher diversity was observed between wheat varieties from Southern European countries (Austria/Switzerland, Portugal/Spain) corresponding to those from other regions.
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Affiliation(s)
- Lin Hai
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus-Liebig University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany
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27
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Dragovich AY, Zima VG, Fisenko AV, Bespalova LA, Bukreeva GI, Mel’nikova EE, Shchipkova NI, Pukhalskiy VA. A comparison of two existing catalogs of the alleles of gliadin-coding loci in winter common wheat. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406080102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Maras M, Sušnik S, Šuštar-Vozlič J, Meglič V. Temporal changes in genetic diversity of common bean (Phaseolus vulgaris L.) accessions cultivated between 1800 and 2000. RUSS J GENET+ 2006. [DOI: 10.1134/s102279540607012x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Fu YB, Peterson GW, Yu JK, Gao L, Jia J, Richards KW. Impact of plant breeding on genetic diversity of the Canadian hard red spring wheat germplasm as revealed by EST-derived SSR markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:1239-47. [PMID: 16465549 DOI: 10.1007/s00122-006-0225-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 01/15/2006] [Indexed: 05/06/2023]
Abstract
Genetic diversity changes in wheat germplasm have been studied using different molecular markers, but little is known about the impact of plant breeding on the transcribed segments of the wheat genome. The objective of this study was to assess diversity changes in 75 Canadian hard red wheat cultivars released from 1845 to 2004 using 37 EST-derived microsatellite (eSSR) markers. These markers were derived from at least 19 transcribed sequences with putative functions assigned and sampled 17 wheat chromosomes. A total of 138 eSSR alleles was detected, and their allelic frequencies ranged from 0.01 to 0.99 with an average of 0.41. Allelic counts were significantly reduced at three loci for cultivars released after 1990. Sixteen alleles at 14 loci in pre-1910 cultivars were lost in cultivars released after 1990. The lost alleles had frequencies ranging from 0.03 to 0.17 and averaging 0.07. Partitioning the eSSR variation showed the four ancestral families accounted for 14.7% of the variation, followed by the six breeding periods with 12.8% and the eight breeding programs with 5.8%. A genetic shift was observed in the cultivars released over the six breeding periods, reflecting the various breeding efforts. These results illustrate the impact of the Canadian wheat breeding on the transcriptional segments of the wheat genome. These findings, along with those from genomic SSR markers, suggest the Canadian wheat breeding programs have reduced genetic diversity in the hard red spring wheat.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada S7N 0X2.
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