Toward the sequence-based breeding in legumes in the post-genome sequencing era
Efficiency of breeding programs of legume crops such as chickpea, pigeonpea and groundnut has been considerably improved over the past decade through deployment of modern genomic tools and technologies. For instance, next-generation sequencing technologies have facilitated availability of genome seq...
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| Veröffentlicht in: | Theoretical and applied genetics 2019-03, Vol.132 (3), p.797-816 |
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| creator | Varshney, Rajeev K. Pandey, Manish K. Bohra, Abhishek Singh, Vikas K. Thudi, Mahendar Saxena, Rachit K. |
| description | Efficiency of breeding programs of legume crops such as chickpea, pigeonpea and groundnut has been considerably improved over the past decade through deployment of modern genomic tools and technologies. For instance, next-generation sequencing technologies have facilitated availability of genome sequence assemblies, re-sequencing of several hundred lines, development of HapMaps, high-density genetic maps, a range of marker genotyping platforms and identification of markers associated with a number of agronomic traits in these legume crops. Although marker-assisted backcrossing and marker-assisted selection approaches have been used to develop superior lines in several cases, it is the need of the hour for continuous population improvement after every breeding cycle to accelerate genetic gain in the breeding programs. In this context, we propose a sequence-based breeding approach which includes use of independent or combination of parental selection, enhancing genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies. Also, adoption of speed breeding technology by generating 4–6 generations per year will be contributing to accelerate genetic gain. While we see a huge potential of the sequence-based breeding to revolutionize crop improvement programs in these legumes, we anticipate several challenges especially associated with high-quality and precise phenotyping at affordable costs, data analysis and management related to improving breeding operation efficiency. Finally, integration of improved seed systems and better agronomic packages with the development of improved varieties by using sequence-based breeding will ensure higher genetic gains in farmers’ fields. |
| doi_str_mv | 10.1007/s00122-018-3252-x |
| format | Article |
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For instance, next-generation sequencing technologies have facilitated availability of genome sequence assemblies, re-sequencing of several hundred lines, development of HapMaps, high-density genetic maps, a range of marker genotyping platforms and identification of markers associated with a number of agronomic traits in these legume crops. Although marker-assisted backcrossing and marker-assisted selection approaches have been used to develop superior lines in several cases, it is the need of the hour for continuous population improvement after every breeding cycle to accelerate genetic gain in the breeding programs. In this context, we propose a sequence-based breeding approach which includes use of independent or combination of parental selection, enhancing genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies. Also, adoption of speed breeding technology by generating 4–6 generations per year will be contributing to accelerate genetic gain. While we see a huge potential of the sequence-based breeding to revolutionize crop improvement programs in these legumes, we anticipate several challenges especially associated with high-quality and precise phenotyping at affordable costs, data analysis and management related to improving breeding operation efficiency. Finally, integration of improved seed systems and better agronomic packages with the development of improved varieties by using sequence-based breeding will ensure higher genetic gains in farmers’ fields.</description><identifier>ISSN: 0040-5752</identifier><identifier>ISSN: 1432-2242</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s00122-018-3252-x</identifier><identifier>PMID: 30560464</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Agricultural economics ; Agriculture ; agronomic traits ; Analysis ; backcrossing ; Biochemistry ; Biodiversity ; Biomedical and Life Sciences ; Biotechnology ; breeding programs ; chickpeas ; Commodity markets ; Crop improvement ; Crops ; cultivars ; Data processing ; DNA sequencing ; Fabaceae - genetics ; Farmers ; Gene mapping ; Genetic diversity ; genetic improvement ; genetic variation ; Genome, Plant ; Genomes ; Genomics ; Genotyping ; Genotyping Techniques ; high-throughput nucleotide sequencing ; High-Throughput Nucleotide Sequencing - methods ; Information management ; Legumes ; Life Sciences ; Marker-assisted selection ; New technologies for plant breeding ; Next-generation sequencing ; Nucleotide sequence ; peanuts ; phenotype ; Phenotyping ; pigeon peas ; Plant Biochemistry ; Plant breeding ; Plant Breeding - methods ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Quantitative Trait, Heritable ; Review ; Review Article ; Seeds ; Technology ; Ya Shi</subject><ispartof>Theoretical and applied genetics, 2019-03, Vol.132 (3), p.797-816</ispartof><rights>The Author(s) 2018</rights><rights>COPYRIGHT 2019 Springer</rights><rights>Theoretical and Applied Genetics is a copyright of Springer, (2018). 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Also, adoption of speed breeding technology by generating 4–6 generations per year will be contributing to accelerate genetic gain. While we see a huge potential of the sequence-based breeding to revolutionize crop improvement programs in these legumes, we anticipate several challenges especially associated with high-quality and precise phenotyping at affordable costs, data analysis and management related to improving breeding operation efficiency. 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| subjects | Agricultural economics Agriculture agronomic traits Analysis backcrossing Biochemistry Biodiversity Biomedical and Life Sciences Biotechnology breeding programs chickpeas Commodity markets Crop improvement Crops cultivars Data processing DNA sequencing Fabaceae - genetics Farmers Gene mapping Genetic diversity genetic improvement genetic variation Genome, Plant Genomes Genomics Genotyping Genotyping Techniques high-throughput nucleotide sequencing High-Throughput Nucleotide Sequencing - methods Information management Legumes Life Sciences Marker-assisted selection New technologies for plant breeding Next-generation sequencing Nucleotide sequence peanuts phenotype Phenotyping pigeon peas Plant Biochemistry Plant breeding Plant Breeding - methods Plant Breeding/Biotechnology Plant Genetics and Genomics Quantitative Trait, Heritable Review Review Article Seeds Technology Ya Shi |
| title | Toward the sequence-based breeding in legumes in the post-genome sequencing era |
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