51
|
Genome-based establishment of a high-yielding heterotic pattern for hybrid wheat breeding. Proc Natl Acad Sci U S A 2015; 112:15624-9. [PMID: 26663911 DOI: 10.1073/pnas.1514547112] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hybrid breeding promises to boost yield and stability. The single most important element in implementing hybrid breeding is the recognition of a high-yielding heterotic pattern. We have developed a three-step strategy for identifying heterotic patterns for hybrid breeding comprising the following elements. First, the full hybrid performance matrix is compiled using genomic prediction. Second, a high-yielding heterotic pattern is searched based on a developed simulated annealing algorithm. Third, the long-term success of the identified heterotic pattern is assessed by estimating the usefulness, selection limit, and representativeness of the heterotic pattern with respect to a defined base population. This three-step approach was successfully implemented and evaluated using a phenotypic and genomic wheat dataset comprising 1,604 hybrids and their 135 parents. Integration of metabolomic-based prediction was not as powerful as genomic prediction. We show that hybrid wheat breeding based on the identified heterotic pattern can boost grain yield through the exploitation of heterosis and enhance recurrent selection gain. Our strategy represents a key step forward in hybrid breeding and is relevant for self-pollinating crops, which are currently shifting from pure-line to high-yielding and resilient hybrid varieties.
Collapse
|
52
|
Schiavo G, Galimberti G, Calò DG, Samorè AB, Bertolini F, Russo V, Gallo M, Buttazzoni L, Fontanesi L. Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed. Anim Genet 2015; 47:181-91. [PMID: 26644200 DOI: 10.1111/age.12392] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2015] [Indexed: 01/20/2023]
Abstract
In this study, we investigated at the genome-wide level if 20 years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population.
Collapse
Affiliation(s)
- G Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - G Galimberti
- Department of Statistical Sciences 'Paolo Fortunati', University of Bologna, Via delle Belle Arti, 40126, Bologna, Italy
| | - D G Calò
- Department of Statistical Sciences 'Paolo Fortunati', University of Bologna, Via delle Belle Arti, 40126, Bologna, Italy
| | - A B Samorè
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - F Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - V Russo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - M Gallo
- Associazione Nazionale Allevatori Suini, Via L. Spallanzani 4, 00161, Roma, Italy
| | - L Buttazzoni
- Centro di Ricerca per la Produzione delle Carni e il Miglioramento Genetico, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Monterotondo, Roma, Italy
| | - L Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| |
Collapse
|
53
|
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.
Collapse
Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, AAFC Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, S7N0X2, Canada.
| |
Collapse
|
54
|
Tempelman RJ. Statistical and Computational Challenges in Whole Genome Prediction and Genome-Wide Association Analyses for Plant and Animal Breeding. JOURNAL OF AGRICULTURAL, BIOLOGICAL, AND ENVIRONMENTAL STATISTICS 2015. [DOI: 10.1007/s13253-015-0225-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
55
|
Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biol 2015; 16:57. [PMID: 25854118 PMCID: PMC4373242 DOI: 10.1186/s13059-015-0622-4] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.
Collapse
|
56
|
Steele EJ, Lloyd SS. Soma-to-germline feedback is implied by the extreme polymorphism at IGHV relative to MHC: The manifest polymorphism of the MHC appears greatly exceeded at Immunoglobulin loci, suggesting antigen-selected somatic V mutants penetrate Weismann's Barrier. Bioessays 2015; 37:557-69. [PMID: 25810320 DOI: 10.1002/bies.201400213] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/15/2015] [Accepted: 02/24/2015] [Indexed: 01/22/2023]
Abstract
Soma-to-germline feedback is forbidden under the neo-Darwinian paradigm. Nevertheless, there is a growing realization it occurs frequently in immunoglobulin (Ig) variable (V) region genes. This is a surprising development. It arises from a most unlikely source in light of the exposure of co-author EJS to the haplotype data of RL Dawkins and others on the polymorphism of the Major Histocompatibility Complex, which is generally assumed to be the most polymorphic region in the genome (spanning ∼4 Mb). The comparison between the magnitude of MHC polymorphism with estimates for the human heavy chain immunoglobulin V locus (spanning ∼1 Mb), suggests IGHV could be many orders of magnitude more polymorphic than the MHC. This conclusion needs airing in the literature as it implies generational churn and soma-to-germline gene feedback. Pedigree-based experimental strategies to resolve the IGHV issue are outlined.
Collapse
Affiliation(s)
- Edward J Steele
- C.Y. O'Connor ERADE Village Foundation, Piara Waters, WA, Australia
| | | |
Collapse
|
57
|
The transmuted log-logistic regression model: a new model for time up to first calving of cows. Stat Pap (Berl) 2015. [DOI: 10.1007/s00362-015-0671-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
58
|
Jonas E, de Koning DJ. Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs. Front Genet 2015; 6:49. [PMID: 25750652 PMCID: PMC4335173 DOI: 10.3389/fgene.2015.00049] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/02/2015] [Indexed: 12/22/2022] Open
Abstract
Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios.
Collapse
Affiliation(s)
- Elisabeth Jonas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences , Uppsala, Sweden
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences , Uppsala, Sweden
| |
Collapse
|
59
|
Farrell LL, Schoenebeck JJ, Wiener P, Clements DN, Summers KM. The challenges of pedigree dog health: approaches to combating inherited disease. Canine Genet Epidemiol 2015; 2:3. [PMID: 26401331 PMCID: PMC4579364 DOI: 10.1186/s40575-015-0014-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/13/2015] [Indexed: 01/29/2023] Open
Abstract
The issue of inherited disorders and poor health in pedigree dogs has been widely discussed in recent years. With the advent of genome-wide sequencing technologies and the increasing development of new diagnostic DNA disease tests, the full extent and prevalence of inherited disorders in pedigree dogs is now being realized. In this review we discuss the challenges facing pedigree dog breeds: the common pitfalls and problems associated with combating single gene mediated disorders, phenotypic selection on complex disorders, and ways of managing genetic diversity. Breeding strategies incorporating screening schemes have been shown to be successful in significantly reducing the prevalence of an inherited disorder and improving the overall health in certain breeds. However, with 215 breeds officially recognized by the Kennel Club in the United Kingdom and 396 inherited disorders currently identified, many breeds have reached the point at which successfully breeding away from susceptible individuals at a population-wide scale will require new genomic selection strategies in combination with currently available breeding schemes. Whilst DNA-based tests identifying disease causing mutation(s) remain the most informative and effective approach for single gene disorder disease management, they must be used along with current screening schemes, genomic selection, and pedigree information in breeding programs in the effort to maintain genetic diversity while also significantly reducing the number of inherited disorders in pedigree dogs.
Collapse
Affiliation(s)
- Lindsay L Farrell
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Jeffrey J Schoenebeck
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Pamela Wiener
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Dylan N Clements
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Kim M Summers
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| |
Collapse
|
60
|
Abstract
Statistical methodology has played a key role in scientific animal breeding. Approximately one hundred years of statistical developments in animal breeding are reviewed. Some of the scientific foundations of the field are discussed, and many milestones are examined from historical and critical perspectives. The review concludes with a discussion of some future challenges and opportunities arising from the massive amount of data generated by livestock, plant, and human genome projects.
Collapse
|
61
|
Hu Z, Yang RC. Marker-based estimation of genetic parameters in genomics. PLoS One 2014; 9:e102715. [PMID: 25025305 PMCID: PMC4099369 DOI: 10.1371/journal.pone.0102715] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 06/23/2014] [Indexed: 12/02/2022] Open
Abstract
Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing ‘big’ genomic data sets.
Collapse
Affiliation(s)
- Zhiqiu Hu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Rong-Cai Yang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- Alberta Agriculture and Rural Development, Edmonton, Alberta, Canada
- * E-mail:
| |
Collapse
|