Genomics of domestication related traits of Brassica juncea (L.) coss
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Date
2016
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Punjab Agricultural University, Ludhiana
Abstract
Present studies involved genetic and transcript analysis to explore directional selection and polyploidy in Brassica juncea, and its progenitor species, B. rapa and B. nigra. Patterns of population differentiation were investigated by genotyping a global collection of 235 germplasm lines with Sequence Tagged Site markers. Flowering loci (FLC and CO in B. rapa; FLC and LFY in B. juncea) appeared to be under directional selection. Transcript analysis using Tajima’s D test confirmed positive selection for FRI and FT in B. rapa and for FLC and LFY in B. juncea. Most flowering homoeologs did not contribute equally to the transcript pool of allotetraploid B. juncea. The expression bias seemed to be modulated by the background cytoplasm. MADS-box genes were investigated using sequence information curated from transcriptome sequencing data from three test species. These seemed to be evolving independently at the DNA sequence level. These genes also exhibited highly variable expression patterns in allotetraploid B. juncea in comparison to its progenitors. AGL18, AG, SHP1, SHP2, SEP1 and MAF5 appeared to be under positive selection in B. rapa. Same was true for AGL6, AGL16 and SHP2 genes in B. nigra. MADS-box genes carried highly conserved gene phylogeny. Impact of directional selection was investigated on size, metabolite composition and calorific value of the seeds. AP2 and ARF2 were identified as major targets of selection in both B. rapa and B. juncea. DA1 and CYP78A5 also showed evidences of positive selection. Directional selection was stronger for seed-size as compared to correlated oil content. Positive selection on seed-size is likely to have played a significant role in structuring regional variation in the germplasm.
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Keywords
Indian mustard, domestication, transcriptome sequencing, polyploidy gene expression, expression bias