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.
Highlights
Pigeonpea [Cajanus cajan (L.)] is a protein-rich food legume that serves the dietary needs of more than a billion people in the developing world (Valenzuela 2011)
With the advantage of Generation Sequencing (NGS) technologies and availability of the pigeonpea reference genome sequence (Varshney et al 2012), trait mapping approaches have mainly focused on mapping biotic stresses like sterility mosaic disease (SMD) and Fusarium wilt (FW) (Singh et al 2016a, 2016b; Singh et al 2017b; Saxena et al 2017a; 2017b), abiotic stress like drought (Sinha et al 2015), a marker for A4-derived cytoplasmic male sterile (CMS) (Sinha et al 2016), growth habit
MATERIALS AND METHODS Plant materials One F2 segregating population comprising 179 lines developed from a late duration (105 days to flowering (DF)) and obcordate leaf shape, ICP 5529 and an early duration (67 DF) lanceolate leaf genotype, ICP 11605 was used in the present study (Obala et al 2019)
Summary
Pigeonpea [Cajanus cajan (L.)] is a protein-rich food legume that serves the dietary needs of more than a billion people in the developing world (Valenzuela 2011). Genomics approaches are being deployed to identify genomic regions that confer resistance/tolerance for different stresses. Both biparental mapping and association mapping approaches have been utilized to dissect complex traits in pigeonpea (Bohra et al 2020). With the advantage of Generation Sequencing (NGS) technologies and availability of the pigeonpea reference genome sequence (Varshney et al 2012), trait mapping approaches have mainly focused on mapping biotic stresses like sterility mosaic disease (SMD) and Fusarium wilt (FW) (Singh et al 2016a, 2016b; Singh et al 2017b; Saxena et al 2017a; 2017b), abiotic stress like drought (Sinha et al 2015), a marker for A4-derived CMS (Sinha et al 2016), growth habit (Saxena et al.2017c), A4-CMS restoration (Saxena et al 2018), cleistogamous flower, shriveled seed and seed size (Yadav et al 2019), seed protein content (Obala et al 2019; Obala et al 2020)
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