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

Authors: VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; MOHAN, MURALI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; GAUR, POORAN - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; GANGARAO, NVPR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; BOHRA, ABHISHEK - Indian Institute Of Pulses Research (IIPR); SAWARGAONKAR, SHRIKANT - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; KIMURTO, PAUL - Egerton University; JANILA, PASUPULETI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; SAXENA, K - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; FIKRE, ASNAKE - Ethiopian Agricultural Research; SHARMA, MAMTA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; PRATAP, ADITYA - Indian Institute Of Pulses Research (IIPR); TRIPATHI, SHAILESH - Indian Agricultural Research Institute; DATTA, SUBHOJIT - Indian Institute Of Pulses Research (IIPR); CHATURVEDI, S - Indian Institute Of Pulses Research (IIPR); MALLIKARJUNA, NALINI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; ANURADHA, G - Acharya Ng Ranga Agricultural University (ANGRAU); BABBAR, ANITA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; CHOUDHARY, ARBIND - Indian Institute Of Pulses Research (IIPR) Off-Season Research Station; MHASE, M - Mahatma Phule Krishi Vidyapeeth (MPKV); BHARADWAJ, CH - Indian Agricultural Research Institute; MANNUR, D - University Of Agricultural Sciences And Veterinary Medicine - Romania; HARER, P - Mahatma Phule Krishi Vidyapeeth (MPKV); Guo, Baozhu; LIANG, XUANXQIANG - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; NADARAJAN, N - Indian Institute Of Pulses Research (IIPR); GOWDA, C - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: Biotechnology Advances
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/3/2013
Publication Date: 3/4/2013
Citation: Varshney, R.K., Mohan, M., Gaur, P.M., Gangarao, N., Pandey, M.K., Bohra, A., Sawargaonkar, S.L., Kimurto, P.K., Janila, P., Saxena, K.B., Fikre, A., Sharma, M., Pratap, A., Tripathi, S., Datta, S., Chaturvedi, S.K., Mallikarjuna, N., Anuradha, G., Babbar, A., Choudhary, A.K., Mhase, M.B., Bharadwaj, C., Mannur, D.M., Harer, P.N., Guo, B., Liang, X., Nadarajan, N., Gowda, C. 2013. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnology Advances. 31:1120-1134.

Interpretive Summary: Food legumes, including chickpea, pigeonpea, and peanut or groundnut, form an important constituent of agricultural food crops consumed globally and complement cereal crops as source of dietary protein (ranging from 20-40%). In addition to providing important micronutrients to humans they also fix atmospheric nitrogen in the soil increasing fertility and. Legumes are grown increasingly on a large-scale in semi-arid tropics (SAT). Advances in sequencing and genotyping technologies have enabled generation of DNA markers in chickpea, pigeonpea and peanut. Based on these resources, genetic maps as well as physical maps for these legume species have also been developed. Nevertheless, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops for breeding and genetic improvement such as molecular marker-assisted breeding has been initiated in these crops. While generating sequence or genotyping data will be trivial, the legume scientists need to work on precise and cost-effective phenotyping and developing the decision support tools and breeders-friendly “tool box” or databases to ensure undertaking integrated breeding approaches for crop improvement. Use of integrated genomics and breeding approach in these legume crops is expected to enhance crop productivity in marginal environments ensuring food security in developing countries.

Technical Abstract: Advances in sequencing and genotyping technologies have enabled generation of several thousand markers including SSRs, SNPs, DArTs, hundreds of thousands transcript reads and BAC-end sequences 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. Genomics-assisted breeding approaches 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 resistance and Ascochyta blight resistance in chickpea; late leaf spot, leaf rust and nematode resistance in groundnut have also been initiated. However, it is essential to consider other modern breeding approaches like marker-assisted recurrent selection (MARS), advanced-backcross (AB-backcross) breeding and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for crop improvement. In addition, development of specialized populations such as multiparents advanced generation intercross (MAGIC) will broaden the genetic base of cultivated gene pool. Use of integrated genomics and breeding approach in these legume crops is expected to enhance crop productivity in marginal environments ensuring food security in developing countries.