QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea
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Date
2022
Journal Title
Journal ISSN
Volume Title
Publisher
Heredity
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 lateflowering
plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTLseq
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.
Description
Keywords
QTL-seq, Candidate genes, Flowering, Leaf shape, Pigeonpea
Citation
Singh, V., Sinha, P., Obala, J., Khan, A. W., Chitikineni, A., Saxena, R. K., & Varshney, R. K. (2022). QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea. Heredity, 128(6), 411-419. https://doi.org/10.1038/s41437-021-00486-x