Elsevier

Plant Science

Volume 242, January 2016, Pages 3-13
Plant Science

Next generation breeding

https://doi.org/10.1016/j.plantsci.2015.07.010Get rights and content

Highlights

Abstract

The genomic revolution of the past decade has greatly improved our understanding of the genetic make-up of living organisms. The sequencing of crop genomes has completely changed our vision and interpretation of genome organization and evolution. Re-sequencing allows the identification of an unlimited number of markers as well as the analysis of germplasm allelic diversity based on allele mining approaches. High throughput marker technologies coupled with advanced phenotyping platforms provide new opportunities for discovering marker-trait associations which can sustain genomic-assisted breeding. The availability of genome sequencing information is enabling genome editing (site-specific mutagenesis), to obtain gene sequences desired by breeders. This review illustrates how next generation sequencing-derived information can be used to tailor genomic tools for different breeders’ needs to revolutionize crop improvement.

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

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