Agricultural development in the tropics lags behind development in the temperate latitudes due to the lack of advanced technology, and various biotic and abiotic factors. To cope with the increasing demand for food and other plant-based products, improved crop varieties have to be developed. To breed improved varieties, a better understanding of crop genetics is necessary. With the advent of next-generation DNA sequencing technologies, many important crop genomes have been sequenced. Primary importance has been given to food crops, including cereals, tuber crops, vegetables, and fruits.
The DNA sequence information is extremely valuable for identifying key genes controlling important agronomic traits and for identifying genetic variability among the cultivars. However, massive DNA re-sequencing and gene expression studies have to be performed to substantially improve our understanding of crop genetics. Application of the knowledge obtained from the genomes, transcriptomes, expression studies, and epigenetic studies would enable the development of improved varieties and may lead to a second green revolution.
Following the genome sequencing of the model plant Arabidopsis, a number of crop species have been sequenced, many being important to tropical countries. Most of the genome assemblies are in the draft stage and extensive work is ongoing in the direction of closing the gaps and re-sequencing. In addition to the genome sequence, transcriptomes and expressions profiles are also available for many crops. The large genome size and polyploidy exhibited by many crop species impedes the sequencing and further analysis. A high percentage of repeat elements is also a major hurdle in genome assembly. However, a platform has been established for many important crops and further research could lead to more information for application in crop breeding.
Advancement in sequencing technologies has had a great impact on crop genetics, enabling the sequencing of genomes and transcriptomes of several crops. Although reference genomes have been obtained for many important crops, massive re-sequencing and gene expression studies are essential to identify the key genes responsible for a desired trait and to find its allele variability. Utilization of this knowledge in crop breeding would empower the development of better crop varieties and may lead to a second green revolution. This would reduce the hunger of billions and revolutionize the economies of developing tropical countries.

Rona Mahmud
Associate Scientist

Figure: Next generation sequencing sequence