Abstract
Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information. The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches include TILLING and EcoTILLING, which make possible to screen mutant and germplasm collections for allelic variants in target genes. Re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms, like SSRs and SNPs, or the construction of high density genetic maps. All these tools and resources facilitate studying the genetic diversity, which is important for germplasm management, enhancement and use. Also, they allow the identification of markers linked to genes and QTLs, using a diversity of techniques like bulked segregant analysis (BSA), fine genetic mapping, or association mapping. These new markers are used for marker assisted selection, including marker assisted backcross selection, ‘breeding by design’, or new strategies, like genomic selection. In conclusion, advances in genomics are providing breeders with new tools and methodologies that allow a great leap forward in plant breeding, including the ‘superdomestication’ of crops and the genetic dissection and breeding for complex traits.
Highlights
Ever since the beginnings of the domestication of plants, some 10,000 years ago, plant breeding has been extremely successful in developing crops and varieties that have contributed to the development of modern societies, and have successively beatenMalthusian predictions [1]
Application of conventional pre-genomics scientific breeding methodologies has led to the development of modern cultivars, which have contributed to the dramatic improvement of yield of most major crops since the middle of the 20th century
For some major crops the pace experimented for genetic gains in yield and other complex traits in the 20th century will be difficult to be maintained if only existing pregenomics technologies are used [153]
Summary
Ever since the beginnings of the domestication of plants, some 10,000 years ago, plant breeding has been extremely successful in developing crops and varieties that have contributed to the development of modern societies, and have successively beaten (neo-)Malthusian predictions [1]. A fully sequenced and well annotated genome provides useful tools for the breeders, as it allows the discovery of genes, determining their position and function, as well as the development of large marker collections and high resolution maps. The aligment difficulties often associtated to the use of short Illumina GA reads (Table 1) are less problematic in species for which available reference genomes facilitates SNPs calling and genome positioning of genetic variation [81] For most of these species, limited collections of SSRs and SNPs were available from early resequencing efforts, previous to the advent of NGS, but new genome-wide re-sequencing is enlarging the SNP pools and making them more representative of the range of natural variation.
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