M-FISH and SNP genotyping of B-genome introgression lines of Brassica napus L.
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Date
2021
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Punjab Agricultural University, Ludhiana
Abstract
Genomic patterns of introgression were investigated from B genome of Brassica carinata/ B.
juncea into 54 introgression lines (ILs) of Brassica napus using various bioinformatic and
cytogenetic tools. Published genome sequences of both B. napus and B. nigra were used
together as a reference for SNP calling and genotyping of introgression lines which were
resequenced at 10X. By comparison with the parental and three diploid species (B. rapa, B.
nigra and B. oleracea) as controls, the specific SNPs/alleles amplified in the different
genomes were distinguished. Missing/divergent regions of chromosomes belonging to A and
C genomes were interpreted as substituted regions of B. napus and amplified/ similar
segments for B genome chromosomes were identified as substituting regions from B.
carinata/ B. juncea. Small but obvious signals of introgression from the eight chromosomes
of the B genome were detected across all chromosomes of B. napus excluding two
chromosomes (A06 and A08). The size of substituting B genome segment ranged from 5, 089
bps to 35, 967 bps. In total, 58 fragments from eight chromosomes covering only 0.1% of B
genome were identified to substitute the A/C genomes of B. napus. In contrast, the proportion
of substituted genome of B. napus was quite large (29% of total genome). IL-1 and IL-33
revealed maximum and minimum proportion of substituted genome (32.17 Mbps and 0.17
Mbps). In situ analysis largely confirmed the bioinformatic results by depicting relatively
more exchanges between B and C than between A and B genomes mainly at terminal or
subterminal positions. Rich phenotypic variation was documented in the introgression lines
for pod shatter resistance and various yield related traits such as days to 50% and 100%
flowering, total plant and raceme height, number of primary and secondary branches, number
of pods on main axis, pod length, seed yield/plot, seeds/pod, 1000 seed weight. Pod rupture
energy in introgression lines ranged from 3 to 9. 7mJ for the first year and from 4.2 to 12mJ
for the second year of evaluation. ILs showing high pod strength carried some of shared B
genome fragments that were unique from other susceptible lines. These genomic regions may
be associated with pod shattering resistance and validated in future by association studies and
gene annotation process. Marker assisted selection for validated genes will further help to
develop fine-tuned secondary introgression lines carrying small and targeted introgressed
segments in backcross programs.
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Citation
Tigadi, Santosh B (2021). M-FISH and SNP genotyping of B-genome introgression lines of Brassica napus L. (Unpublished M.Sc. thesis). Punjab Agricultural University, Ludhiana, Punjab, India.