Genomics reveals new landscapes for crop improvement

Abstract

The sequencing of large and complex genomes of crop species, facilitated by new sequencing technologies and bioinformatic approaches, has provided new opportunities for crop improvement. Current challenges include understanding how genetic variation translates into phenotypic performance in the field.

Figure 1

Diverse outcomes of polyploidy in crop species. Three examples of the consequences of allopolyploidy (in which hybrids have sets of chromosomes derived from different species) in important crop species are shown. (a) Oilseed rape (canola) is derived from a recent hybridization of Brassica rapa (Chinese cabbage, turnip) and Brassica oleraceae (broccoli, cauliflower, cabbage). The progenitor of these Brassica species was hexaploid (compared to Arabidopsis) after two rounds of whole-genome duplication. Extensive gene loss, possibly via deletion mechanisms [18], has occurred in these species. Upon hybridization to form allotetraploid Brassica napus, gene loss is accelerated, producing novel patterns of allelic diversity [19]. (b) Bread wheat is an allohexaploid derived from the relatively recent hybridization of allotetraploid durum (pasta) wheat and wild goat grass, Aeglilops tauschii. The Ph1 locus in the B genome [37] prevents pairing between the A, B and D genomes, leading to diploid meiosis and genome stability. This maintains the extensive genetic diversity from the three progenitor Triticeae genomes that underpins wheat crop productivity. (c) Sugarcane (Saccharum sp.) is a complex and unstable polyploid that is cultivated by cuttings. Hybrids between S. officinarum, which has high sugar content, and S. spontaneum, a vigorous wild relative, have variable chromosomal content from each parent. The genomes are closely related to the ancestral diploid Sorghum [42].

Figure 2

The impact of whole genome sequencing on breeding. (a) Initial genetic maps consisted of few and sparse markers, many of which were anonymous markers (simple sequence repeats (SSR)) or markers based on restriction fragment length polymorphisms (RFLP). For example, if a phenotype of interest was affected by genetic variation within the SSR1-SSR2 interval, the complete region would be selected with little information about its gene content or allelic variation. (b) Whole genome sequencing of a closely related species enabled projection of gene content onto the target genetic map. This allowed breeders to postulate the presence of specific genes on the basis of conserved gene order across species (synteny), although this varies between species and regions. (c) Complete genome sequence in the target species provides breeders with an unprecedented wealth of information that allows them to access and identify variation that is useful for crop improvement. In addition to providing immediate access to gene content, putative gene function and precise genomic positions, the whole genome sequence facilitates the identification of both natural and induced (by TILLING) variation in germplasm collections and copy number variation between varieties. Promoter sequences allow epigenetic states to be surveyed, and expression levels can be monitored in different tissues or environments and in specific genetic backgrounds using RNAseq or microarrays. Integration of these layers of information can create gene networks, from which epistasis and target pathways can be identified. Furthermore, re-sequencing of varieties identifies a high density of SNP markers across genomic intervals, which enable genome-wide association studies (GWAS), genomic selection (GS) and more defined marker-assisted selection (MAS) strategies.