Parida-etal-Table S2.pdf

Identification of functionally relevant
potential genomic loci using an economical, simpler and user-friendly
genomics-assisted breeding strategy is vital for rapid genetic dissection of
complex flowering time quantitative trait in chickpea. A high-throughput multiple
QTL-seq strategy was employed in two inter (C. arietinum desi
accession ICC 4958 × C. reticulatum wild accession ICC 17160)- and intra
(ICC 4958 × C. arietinum kabuli accession ICC 8261)-specific RIL
mapping population to identify the major QTL genomic regions governing flowering
time in chickpea. The whole genome resequencing discovered 446475 and 150434
SNPs exhibiting differentiation between early- and late-flowering mapping
parents and bulks, constituted by pooling the homozygous individuals of extreme
flowering time phenotypic trait from each of two aforesaid RIL populations. The
multiple QTL-seq analysis using
these mined SNPs in two RIL mapping populations narrowed-down two longer
(907.1 kb and 1.99 Mb) major flowering time QTL genomic regions into the
high-resolution shorter (757.7 kb and 1.39 Mb) QTL intervals on chickpea
chromosome 4.
This essentially identified regulatory as well as coding
(non-synonymous/synonymous) novel SNP allelic variants from two efl1 (early
flowering 1) and GI (GIGANTEA)
genes regulating flowering time in chickpea. Interestingly, strong natural allelic
diversity reduction (88-91%) of two known flowering genes especially mapped at
major QTL intervals as compared to that of background genomic regions (where no
flowering time QTLs were mapped) (61.8%) in cultivated vis-à-vis wild Cicer
gene pools was evident inferring the significant impact of evolutionary
bottlenecks on these loci during chickpea domestication. Higher association
potential of coding non-synonymous and regulatory SNP alleles mined from efl1
(36-49%) and GI (33-42%) known flowering genes for early and late flowering
time differentiation among chickpea accessions was evident. The robustness and
validity of two functional allelic variants-containing genes localized at major
flowering time QTLs was apparent by their identification from multiple
intra-/inter-specific mapping populations of chickpea. The functionally
relevant molecular tags delineated can be of immense use for deciphering the
natural allelic diversity-based domestication pattern of flowering time and expediting
genomics-aided crop improvement to develop early flowering cultivars of
chickpea.