Construction of a high-density genetic map and QTL analysis for yield, yield components and agronomic traits in chickpea (Cicer arietinum L.)

Rutwik Barmukh; Khela Ram Soren; Praveen Madugula; Priyanka Gangwar; P S Shanmugavadivel; Chellapilla Bharadwaj; Aravind K Konda; Sushil K Chaturvedi; Aditi Bhandari; Kritika Rajain; Narendra Pratap Singh; Manish Roorkiwal; Rajeev K Varshney

doi:10.1371/journal.pone.0251669

Construction of a high-density genetic map and QTL analysis for yield, yield components and agronomic traits in chickpea (Cicer arietinum L.)

PLoS One. 2021 May 14;16(5):e0251669. doi: 10.1371/journal.pone.0251669. eCollection 2021.

Authors

Affiliations

¹ Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
² Department of Genetics, Osmania University, Hyderabad, India.
³ ICAR-Indian Institute of Pulses Research, Kanpur, UP, India.
⁴ Division of Genetics, Indian Agricultural Research Institute, Delhi, India.
⁵ Rani Lakshmi Bai Central Agricultural University, Jhansi, India.

Abstract

Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92-3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom®CicerSNP array, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minor-effect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosome Mapping*
Cicer / genetics*
Crops, Agricultural / genetics*
Genome, Plant*
Polymorphism, Single Nucleotide*
Quantitative Trait, Heritable*

Grants and funding

The authors thank Department of Agriculture and Cooperation & Farmers Welfare, Ministry of Agriculture and Farmers Welfare, Government of India; Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India through Indo-Australian Biotechnology Fund (IABF); and the Tropical Legumes Project funded by Bill & Melinda Gates Foundation (OPP1114827) for financial assistance in parts. MR and RKV thank the Department of Science and Technology, Government of India for providing funding support through the INSPIRE Faculty Scheme and Early Career Research Award – SERB, and the JC Bose National Fellowship, respectively. RB acknowledges funding support from the Council of Scientific and Industrial Research (CSIR), India, for the award of the research fellowship. The work reported in this article was undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals. ICRISAT is a member of the CGIAR Consortium.