Analysing Brassica rapa genome by comparing natural accessions and the derivatives extracted from B. juncea allotetraploid
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Date
2020
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Punjab Agricultural University, Ludhiana
Abstract
Present studies were conceived to undertake a comprehensive characterization of the
phenotypic and molecular genetic diversities available in a large germplasm set comprising 195
fixed genotypes of Brassica rapa (AA; 2n=20). These included derived B. rapa lines extracted
from B. juncea (AABB; 2n=36). DArTseq platform was used to sequence genomic DNA
samples to aid SNP discovery. Field experiments were conducted during 2017-18 and 2018-19
over two sowing dates each at the forms of Punjab Agricultural University, Ludhiana.
Morphological characterizations involved 18 traits representing flowering, crop architecture,
yield components and seed quality. Molecular diversity analysis revealed that derived B. rapa
clustered separately from the natural B. rapa. Natural B. rapa, itself formed two major groups
with several subgroups representing variations among various subspecies of oleifera forms.
Analysis of variance for phenotypic traits indicated significance of genotypic and genotype x
environment interactions. Coefficient of variations was high for flowering, plant height,
secondary branches and yield per plant. CV was lowest for pod length. Genome wide
association studies were conducted using GAPIT 3 software. MLMM and Blink were preferred
algorithms. We identified a large number of MTA’s involving target traits. Many of these were
exclusive for DR. Annotation helped to predict candidate genes in the genomic region
associated with the significant SNPs. Fifteen candidate genes were predicted for flowering
traits. These genes are involved in the photoperiodic, gibberellic acid signaling pathways that
control the expression of flowering genes. Several genes regulating flower development,
maintenance of floral organ identity, regulation of timing of transition from vegetative to
reproductive phase were also identified. For yield related traits we predicted genes involved in
the growth and development, maintenance of shoot apical meristem, development of lateral
organs, branching, auxin growth factors and leaf morphogenesis on A09. Two very important
genes, IKU2 and LACS8 were identified for seed size. Candidate genes predicted for seed
quality traits included genes involved in regulation of seed storage and reserves such as oil,
protein and GSL. In conclusions, our studies have helped to catalogue molecular-genetic and
phenotypic diversities present in B. rapa. These also established derived B. rapa as a genetic
resource distinct from natural B. rapa. Many candidates were predicted for regulating key
economic traits in the crop. Identified loci can be used in future marker-assisted selection
(MAS) after due validation.
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Citation
Snehdeep Kaur (2020). Analysing Brassica rapa genome by comparing natural accessions and the derivatives extracted from B. juncea allotetraploid (Unpublished Ph.D. Dissertation). Punjab Agricultural University, Ludhiana, Punjab, India.