QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea

Singh, V and Sinha, P and Obala, J and Khan, A W and Chitikineni, A and Saxena, R K and Varshney, R K (2022) QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea. Heredity, 128. pp. 411-419. ISSN 1365-2540

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Abstract

To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement.

Item Type:	Article
Divisions:	Center of Excellence in Genomics and Systems Biology
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Genetic association study, Plant hybridization
Subjects:	Mandate crops > Pigeonpea Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	06 Feb 2024 08:06
Last Modified:	06 Feb 2024 08:06
URI:	http://oar.icrisat.org/id/eprint/12437
Official URL:	https://www.nature.com/articles/s41437-021-00486-x...
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	The work was supported in parts by the United States Agency for International Development (USAID)- India Mission, Department of Agriculture and Cooperation, Ministry of Agriculture, Government of India and Bill & Melinda Gates Foundation (grant number OPP1005131). This work has been undertaken as part of the CGIAR Research Program on Grain Legumes and Dry Land Cereals. ICRISAT is a member of CGIAR Consortium.
Links:	Google Scholar

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