Orphan legume crops enter the genomics era!

Many of the world's most important food legumes are grown in arid and semi-arid regions of Africa and Asia, where crop productivity is hampered by biotic and abiotic stresses. Until recently, these crops have also suffered from a dearth of genomic and molecular-genetic resources and thus were 'orphans' of the genome revolution. However, the community of legume researchers has begun a concerted effort to change this situation. The driving force is a series of international collaborations that benefit from recent advances in genome sequencing and genotyping technologies. The focus of these activities is the development of genome-scale data sets that can be used in high-throughput approaches to facilitate genomics-assisted breeding in these legumes.

Varshney RK ，Close TJ ，Singh NK ，Hoisington DA ，Cook DR ... -  《-》

Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics.

Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.

Varshney RK ，Mohan SM ，Gaur PM ，Gangarao NV ，Pandey MK ，Bohra A ，Sawargaonkar SL ，Chitikineni A ，Kimurto PK ，Janila P ，Saxena KB ，Fikre A ，Sharma M ，Rathore A ，Pratap A ，Tripathi S ，Datta S ，Chaturvedi SK ，Mallikarjuna N ，Anuradha G ，Babbar A ，Choudhary AK ，Mhase MB ，Bharadwaj Ch ，Mannur DM ，Harer PN ，Guo B ，Liang X ，Nadarajan N ，Gowda CL ... -  《-》

Structural analyses of the genomes in legumes.

The genome sequencing of two model legumes and soybean (Glycine max) is near completion. In addition, genomic information, such as ESTs, genomic sequences, and DNA markers has been intensively collected from a variety of crop legumes using new genomic technologies. The accumulating information provides an opportunity to perform comparative analyses to decipher the evolutionary process of genomic structures and functions in leguminous plants. Furthermore, it can serve as a basis to exchange knowledge among the model and crop legumes, which, when combined with the new experimental techniques developed in the model legumes, will not only facilitate an understanding of the basic genetic systems in crop legumes, but also accelerate the breeding process.

Sato S ，Isobe S ，Tabata S 《-》

Translating Medicago truncatula genomics to crop legumes.

Genomic resources developed in the model legume, Medicago truncatula, have the potential to accelerate practical advances in crop legumes. M. truncatula is closely related to many economically important legumes, frequently displaying genome-scale synteny. Translating genome data from M. truncatula should be highly effective in marker development, gene discovery, and positional cloning in crop legumes. The M. truncatula genome sequence also provides valuable insights about gene families of practical importance, especially those that are legume-specific. The M. truncatula genome sequence should also simplify the assembly of next-generation sequence data in closely related taxa, especially alfalfa. Genomic resources, such as whole-genome arrays, make it possible to pursue detailed questions about gene expression in both M. truncatula and related crop species, while tagged mutant populations simplify the process of determining gene function.

Young ND ，Udvardi M 《-》

Summaries of legume genomics projects from around the globe. Community resources for crops and models.

VandenBosch KA ，Stacey G 《-》