Next generation breeding
Introduction
The development of next generation sequencing (NGS) technologies has made DNA sequencing high throughput and very cost effective. Consequently, many opportunities are being opened to explore the relationships between genetic and phenotypic diversity with a resolution never reached before. Reference genome sequences have been published for many crop species [1] and many more genome sequencing projects are in progress (http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi; http://plants.ensembl.org/index.html; http://phytozome.jgi.doe.gov/pz/portal.html). The sequences of crop genomes provide a useful starting point to explore genome organization and evolution and provide insight into genetic variation through partial or complete re-sequencing of different accessions [2]. Re-sequencing, leading to arrays of high-density single-nucleotide polymorphisms (SNPs), is allowing whole-genome scans to identify haplotype blocks that are significantly correlated with quantitative trait variation. The distribution of low cost sequencing technologies offers new opportunities to shape genetic diversity according to the needs of modern agriculture and, in turn, has a number of practical consequences for plant breeding: i) the analysis of genetic diversity can be based on genome re-sequencing; ii) genome wide association studies (GWAS) become an attractive approach for quantitative trait loci (QTLs) mapping in plants since broad genetic resources can be scanned for marker-trait association without any limitation of marker availability; iii) the great number of markers support genomic selection; and iv) the genome sequences allow the targeted modification of specific genes through genome editing technologies or identification of suitable mutations within mutagenized populations, resulting in the introduction of new allelic variants in the genome of cultivated varieties. Conversely, these achievements highlight new bottlenecks for breeding progress, particularly the phenotyping capacity (in terms of both precision and throughput [3]), and recombination frequency [4].
Over the last decades, plant breeding has moved from being a completely phenotyping-based process to having an increased reliance on some level of genotype-based selection [5]. This trend is expected to increase in the coming years as the NGS-based knowledge will be translated into “Next Generation Breeding”. In this review, we consider current trends and future prospects for the application of genomic instruments in the improvement of plant breeding performance.
Section snippets
Genome sequencing and sequence-based markers
Molecular markers have been available for more than 25 years, nevertheless the advent of NGS represented a breakthrough in this field. Before NGS, a typical linkage map was based on few hundreds markers. In the age of NGS, thousands of markers can be easily included in any map, including in species with little a priori genome information available. With NGS technologies the DNA marker identification has shifted from fragment-based (RFLPs, AFLPs, microsatellites) to sequence-based polymorphisms
Mining plant diversity: from genotype to phenotype
Many valuable genes and alleles are stored in seed bank collections, hidden in cultivars, landraces, mutagenized populations and wild species. The identification of these genes requires both genome information and phenotyping capacities. With the advent of NGS technologies a different dimension to the exploration of plant diversity arose. Extensive insights into plant genome composition and organization have been gained from the genome sequencing and new findings on plant origin and evolution
Collecting genetic information through meta-analysis
The statistical combination of a huge amount of molecular and phenotypic data, obtained from publications and omics databases, provides opportunities to unravel complex traits in crops through genome-wide meta-analysis, and is becoming a promising approach for crop breeding. Meta-analysis, with the support of dedicated statistical procedures, enables the evaluation of key genetic, genomic and environmental variables and their impact on crop agronomic performance, by exploiting and then
Marker-trait associations in large germplasm collections
The genetic bases of many traits have been conventionally dissected by linkage analysis in segregating mapping populations (e.g. Double Haploids -DHs, Recombinant Inbreed lines -RILs) or using nearly isogenic lines (NILs) developed using several backcrosses [58]. Nevertheless, the estimated effects are specific to the same or genetically related populations and are often not transferable to other genetic backgrounds, thus limiting their practical application for breeding purposes [58]. In the
Genome-wide prediction of breeding value and genomic selection
There are two main strategies to assist breeding with molecular selection: to use molecular markers that map near or within specific loci with known phenotypic effects (marker-assisted selection, MAS) or to exploit all available markers as predictors of breeding value (genomic selection, GS). MAS is used to drive the selection of a relative small set of genes having major phenotypic effects [77], [78], and much information on these tools is available also through crop-dedicated websites (e.g.
Plant improvement through genome editing
Genome editing, i.e. the targeted modification of a gene, allows generation of new allelic variants in the genome of cultivated species; it represents an alternative to standard breeding processes based on recombination and, to some extent, to genetic transformation. Genome editing relies on the induction of double strand breaks in DNA in a targeted part of the genome using an engineered DNA-binding protein. Sequence-specific nucleases, including zinc finger nucleases (ZFN), and transcription
The control of genetic recombination
Even with all the new available technologies, plant breeding still depends on recombination. New genes/alleles are required to be recombined into advanced lines and despite the great number of markers available, recombination is still required to give new allele combinations for tightly linked loci. It is therefore essential to develop tools capable of increasing crossover incidence to break negative allele associations.
To ensure proper segregation at metaphase I, each pair of chromosomes have
Conclusions
Current breeding programs rely on integrating phenotypic selection in standard breeding schemes (e.g. pedigree, backcross, progeny test for combinatory efficiency) with molecular inputs (e.g. MAS and genetic transformation for GM plants). The availability of NGS, bio-informatics resources and phenotyping platforms is moving plant breeding a step forward and a next generation breeding strategies resulting from combining of genetic resources with advanced technologies can be foreseen for the near
Acknowledgement
This work was supported by FP7 project WHEALBI (Wheat and barley Legacy for Breeding Improvement).
Glossary
- CRISPR
- Clustered Regularly Interspaced Short Palindromic Repeats/Cas9(CRISPR-associated) is a tool based on the reprogramming of CRISPR/Cas9 endonuclease activity normally acting in prokaryote cells to target a specific sequencing, using short non-coding RNAs designed on the basis of the targeted sequence. Cas9 nuclease is used for genome engineering applications, and a single guide RNA (sgRNA) homologous to a target sequence is used to drive the CRISPR/Cas complex and to induce desired
References (146)
- et al.
A high-density SNP genotyping array for rice biology and molecular breeding
Mol. Plant
(2014) - et al.
An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley
BMC Genomics
(2014) In silico archeogenomics unveils modern plant genome organization, regulation and evolution
Curr. Opin. Plant Biol.
(2012)- et al.
Plant genome sequencing – applications for crop improvement
Curr. Opin. Biotechnol.
(2014) - et al.
Allele-mining of rice blast resistance genes at AC134922 locus
Biochem. Biophys. Res. Commun.
(2014) - et al.
Transposable elements and the plant pan-genomes
Curr. Opin. Plant Biol.
(2007) - et al.
Current challenges and future perspectives of plant and agricultural biotechnology
Trends Biotechnol.
(2015) - et al.
Physiological responses to Megafol® treatments in tomato plants under drought stress: a phenomic and molecular approach
Sci. Hortic.
(2014) - et al.
Field high-throughput phenotyping: the new crop breeding frontier
Trends Plant Sci.
(2014) - et al.
Assessment of the quality of meta-analysis in agronomy
Agric. Ecosyst. Environ.
(2012)
Applications of single nucleotide polymorphisms in crop genetics
Curr. Opin. Plant Biol.
From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development
Curr. Opin. Plant Biol.
Population genetics of genomics-based crop improvement methods
Trends Genet.
Genomic selection: genome-wide prediction in plant improvement
Trends Plant Sci.
The CRISPR/Cas9 system for plant genome editing and beyond
Biotechnol. Adv.
Plant genome editing by novel tools: TALEN and other sequence specific nucleases
Curr. Opin. Biotechnol.
The first 5 plant genomes
The Plant Genome
Emerging Knowledge from genome sequencing of crop species
Mol. Biotechnol.
Future scenarios for plant phenotyping
Ann. Rev. Plant Biol.
The impact of recombination on short-term selection gain in plant breeding experiments
Theor. Appl. Genet.
Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding
PLoS Biol.
Rapid genomic characterization of the genus vitis
PLoS One
A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome
PLoS One
Development of a large SNP genotyping array and generation of high-density genetic maps in tomato
PLoS One
Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm
PLoS One
Development and evaluation of SoySNP50K, a high-density genotyping array for soybean
PLoS One
Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley
Nat. Genet.
Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array
Plant Biotechnol. J.
Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh)
PloS One
Advances in plant genome sequencing
Plant J.
Rapid and cost effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
Genome Res.
A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
PLoS One
QTL mapping in eggplant reveals clusters of yield-related loci and orthology with the tomato genome
PLoS One
High-density genetic map construction and QTLs analysis of grain yield-related traits in Sesame (Sesamum indicum L.) based on RAD-Seq techonology
BMC Plant Biol.
Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines
PLoS Genet.
Genomic prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs
Heredity
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond
Plant J.
A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
Genome Biol.
A map of rice genome variation reveals the origin of cultivated rice
Nature
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
Nat. Biotechnol.
Progress toward understanding heterosis in crop plants
Annu. Rev. Plant Biol.
The 3000 rice genomes project: new opportunities and challenges for future rice research
GigaScience
Allele mining in Solanum: conserved homologues of Rpi-blb1 are identified in Solanum stoloniferum
Theor. Appl. Genet.
Wheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene Pm3: a large scale allele mining project
BMC Plant Biol.
Development and validation of functional marker targeting an InDel in the major rice blast disease resistance gene Pi54 (Pik h)
Mol. Breed.
Haplotype variability and identification of new functional alleles at the Rdg2a leaf stripe resistance gene locus
Theor. Appl. Genet.
Discovery of rare mutations in populations: TILLING by sequencing
Plant Physiol.
Identification of novel rice low phytic acid mutations via TILLING by sequencing
Mol. Breed.
Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing
Plant Cell
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
Nat. Biotechnol.
Cited by (129)
Drones in agriculture: A review and bibliometric analysis
2022, Computers and Electronics in AgricultureCitation Excerpt :Overall, we observe that the publications in cluster 2 focus on the main advantages of UAVs in remote phenotyping, yield estimation, crop surface modeling, and plant counting. Future studies can dig deeper by developing new methods for remote phenotyping that can automate and optimize the processing of remotely sensed data (Barabaschi et al., 2016; Liebisch et al., 2015; Mochida et al., 2015; S. Zhou et al., 2021). In addition, the performance of IoT sensors mounted on UAVs and the trade-off between their costs, labor, and precision of yield estimation need to be researched in the future (Ju & Son, 2018a, 2018b; Xie & Yang, 2020; Yue et al., 2018).
Drones in agriculture: analysis of different countries
2023, BIO Web of Conferences