A joint research initiative between the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and three ICAR institutions, the Indian Institute of Pulses Research (IIPR, Uttar Pradesh), Dr Rajendra Prasad Central Agricultural University (RPCAU, Bihar), and the Indian Agricultural Research Institute (IARI, Assam), has led to the identification of a gene, Ccsmd04, that is associated with resistance to Sterility Mosaic Disease (SMD) in pigeonpea.
SMD is a serious disease in pigeonpea crops, with the potential to cause yield losses of up to 90 percent. The newly published study, InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein control sterility mosaic disease resistance in pigeonpea, establishes a genetic basis for resistance to the disease.
Gene Discovery and Research Methodology
The research team identified Ccsmd04 in the widely cultivated ICRISAT bred variety ‘Asha’ (ICPL 87119), which has known resistance to SMD. The identification process involved advanced genomics, phenomics, and high powered computational analysis. The gene encodes a dormancy/auxin-associated protein, and its function was compared across resistant and susceptible varieties.
Reference genomes from ‘Asha’ and the susceptible variety ‘Maruti’ were analysed, along with samples from a genetic population showing extreme resistance or susceptibility traits. The analysis revealed that susceptible lines had four frameshift mutations in Ccsmd04 that affected the proper functioning of the dormancy/auxin associated protein, resulting in the absence of resistance.
Marker Development for Breeding Programs
Alongside the gene discovery, the study validated four functional InDel markers linked to SMD resistance. These markers can be applied in pigeonpea breeding programs for early generation selection, allowing breeders to identify resistant plants with greater precision and at an earlier stage of development. The Ccsmd04 gene also presents potential for genetic improvement through targeted gene editing approaches.
“This is a landmark discovery by ICRISAT and ICAR researchers, considering the severity of SMD in the region. The identified genetic variants, genes and markers hold immense potential for breeding more resistant pigeonpea varieties.”
Longstanding Research Background
ICRISAT has been engaged in research on host plant resistance to SMD since 1975. Over the decades, multiple resistant pigeonpea varieties have been developed; however, field performance has often been inconsistent due to variability in the virus causing SMD and in its mite vector. This genomic insight offers a clear pathway for more effective breeding strategies by addressing the molecular basis of resistance.
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“We deeply value our longstanding partnership with ICAR and the support from CGIAR and the Gates Foundation for this work. ICRISAT’s genomics and pre breeding program focuses on integrating genomic insights into the breeding pipeline, and disease resistance remains a top priority given its direct impact on farmer livelihoods and the environment.”
“We’ve identified a resistance gene and validated four functional InDel markers associated with SMD resistance; these markers can now be used to screen pigeonpea breeding progenies for early generation selection of SMD resistance. This gene information can also be valuable for genetic improvement through gene editing.”
Future Research Directions
The next phase of research will focus on identifying additional resistance genes, including those from wild relatives of pigeonpea, to ensure more stable and long lasting resistance in varied field conditions. The project aims to strengthen collaborative research and accelerate the breeding of SMD resistant pigeonpea varieties. This work aligns with India’s broader goal of achieving self sufficiency in pulse production and reducing crop losses due to disease.
