Genomics-assisted breeding – A revolutionary strategy for crop improvement

Leng, Pengfei; Lübberstedt, Thomas; Xu, Min

doi:10.1016/s2095-3119(17)61813-6

Cited by 59 publications

(35 citation statements)

References 112 publications

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“…As we have previously described, genotyping was conducted on homozygous lines and thus we did not expect any heterozygous genotypes. When the genotypic values for a marker was only 0 and 2, we considered the heterozygous calling [2] to be an error caused by the presence of the SNP marker flanking sequence in homoeologous genomes. In this case, the genotypes scored as 2 were recoded as 1.…”

Section: Discussionmentioning

confidence: 99%

“…Advances in molecular biology and high-throughput genotyping technologies have significantly impacted the field of molecular plant breeding, leading to shift from a phenotype-based to a genotype-based selection [2]. The integrated use of genomic and molecular tools in conventional phenotype selection programs has allowed the development of new breeding strategies such as marker assisted selection (MAS) and genomic selection.…”

Section: Introductionmentioning

confidence: 99%

“…The aim of the present study was to characterize two collections of durum and bread wheat landraces from CRF-INIA by using the DArTseq-GBS approach. The specific objectives of the present investigation were: (1) to assess the genomic diversity of a set of durum wheat accessions comprising 191 Spanish landraces and 23 reference varieties, (2) to assess the genomic diversity of a set of bread wheat accessions comprising 189 Spanish landraces and 29 reference varieties, and (3) to compare the genetic diversity of landraces and modern cultivars in both wheat species.…”

Section: Introductionmentioning

confidence: 99%

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Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

Pascual

Ruíz²,

López-Fernández

et al. 2020

BMC Genomics

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Background: One of the main goals of the plant breeding in the twenty-first century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results: The DArTseq GBS approach generated 10 K SNPs and 40 K high-quality DArT markers, which were located against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsp. durum, turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin. Conclusions: The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties, and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

Pascual

Ruíz²,

López-Fernández

et al. 2020

BMC Genomics

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“…The advances in molecular genetics have greater impact on plant breeding research. Application of molecular techniques in selection superior cultivars has shorter time consumption, less labor intensity, and increase efficiency in selection (Leng et al 2017). Marker-assisted selection strategies have been widely used in molecular plant breeding.…”

Section: Dna Analysismentioning

confidence: 99%

Phenotypic and genetic stability of new Indonesian melon cultivar (Cucumis melo L. ‘Melonia’) based on ISSR markers

et al. 2019

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Abstract. Daryono BS, Subiastuti AS, Fatmadanni A, Sartika D. 2019. Phenotypic and genetic stability of new Indonesian melon cultivar (Cucumis melo L. ‘Melonia’) based on ISSR markers. Biodiversitas 20: 1069-1075. Cucumis melo L. ‘Melonia’ was new Indonesian melon cultivars produced by segregation of Meloni cultivar. The Meloni cultivar has a yellowish-skinned color, orange flesh fruit, and sweet taste. The stability of phenotype and genotype characters of this new cultivars were assessed using 27 morphological traits and 4 ISSR primers, respectively. Phenotype characters in F2 and F3 populations have been stable on 25 of 27 morphological traits used, except in weight of seed cavity and color of skin fruit. The 4 ISSR markers were produced 41 fragments, contained 28 monomorphic DNA bands and 13 polymorphic DNA bands. All of DNA bands were scored and used for genetic similarity analysis using MVSP 3.1A Program. The highest genetic variation was produced by UBC-808 primer with a polymorphic percentage of 38.46%. All of ‘Melonia’ populations were clustered together with 100% similarity percentage. Compared to other cultivars, ‘Melonia’ had high similarity with ‘Meloni’ in 87.8%, meanwhile, ‘Melonia’ and Meloni cultivars had relationship with Melona at a similarity value of 70.7%.

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“…The application of biotechnological advances for exploring crop diversity like genotyping by sequencing, genotyping arrays, and pangenomics approaches [18] is another important strategy for assessing genetic diversity. Crop genome sequencing can provide insight into genetic variation through the re-sequencing [19]. Jiao et al (2012) re-sequenced 278 elite maize lines (USA and Chinese maize lines) and identified >27 million single-nucleotide polymorphisms (SNPs).…”

Section: Exploring the Unexplored: First Stepmentioning

confidence: 99%

Domesticating the Undomesticated for Global Food and Nutritional Security: Four Steps

et al. 2019

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Ensuring the food and nutritional demand of the ever-growing human population is a major sustainability challenge for humanity in this Anthropocene. The cultivation of climate resilient, adaptive and underutilized wild crops along with modern crop varieties is proposed as an innovative strategy for managing future agricultural production under the changing environmental conditions. Such underutilized and neglected wild crops have been recently projected by the Food and Agricultural Organization of the United Nations as ‘future smart crops’ as they are not only hardy, and resilient to changing climatic conditions, but also rich in nutrients. They need only minimal care and input, and therefore, they can be easily grown in degraded and nutrient-poor soil also. Moreover, they can be used for improving the adaptive traits of modern crops. The contribution of such neglected, and underutilized crops and their wild relatives to global food production is estimated to be around 115–120 billion US$ per annum. Therefore, the exploitation of such lesser utilized and yet to be used wild crops is highly significant for climate resilient agriculture and thereby providing a good quality of life to one and all. Here we provide four steps, namely: (i) exploring the unexplored, (ii) refining the unrefined traits, (iii) cultivating the uncultivated, and (iv) popularizing the unpopular for the sustainable utilization of such wild crops as a resilient strategy for ensuring food and nutritional security and also urge the timely adoption of suitable frameworks for the large-scale exploitation of such wild species for achieving the UN Sustainable Development Goals.

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Genomics-assisted breeding – A revolutionary strategy for crop improvement

Cited by 59 publications

References 112 publications

Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

Phenotypic and genetic stability of new Indonesian melon cultivar (Cucumis melo L. ‘Melonia’) based on ISSR markers

Domesticating the Undomesticated for Global Food and Nutritional Security: Four Steps

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