TY - JOUR
T1 - Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea
AU - Khan, Aamir W.
AU - Garg, Vanika
AU - Sun, Shuai
AU - Gupta, Saurabh
AU - Dudchenko, Olga
AU - Roorkiwal, Manish
AU - Chitikineni, Annapurna
AU - Bayer, Philipp E.
AU - Shi, Chengcheng
AU - Upadhyaya, Hari D.
AU - Bohra, Abhishek
AU - Bharadwaj, Chellapilla
AU - Mir, Reyazul Rouf
AU - Baruch, Kobi
AU - Yang, Bicheng
AU - Coyne, Clarice J.
AU - Bansal, Kailash C.
AU - Nguyen, Henry T.
AU - Ronen, Gil
AU - Aiden, Erez Lieberman
AU - Veneklaas, Erik
AU - Siddique, Kadambot H.M.
AU - Liu, Xin
AU - Edwards, David
AU - Varshney, Rajeev K.
PY - 2024/6
Y1 - 2024/6
N2 - Chickpea (Cicer arietinum L.)—an important legume crop cultivated in arid and semiarid regions—has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.
AB - Chickpea (Cicer arietinum L.)—an important legume crop cultivated in arid and semiarid regions—has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.
UR - http://www.scopus.com/inward/record.url?scp=85194047045&partnerID=8YFLogxK
U2 - 10.1038/s41588-024-01760-4
DO - 10.1038/s41588-024-01760-4
M3 - Article
C2 - 38783120
AN - SCOPUS:85194047045
SN - 1061-4036
VL - 56
SP - 1225
EP - 1234
JO - Nature Genetics
JF - Nature Genetics
IS - 6
ER -