ArticleBMC plant biology2019
ddRAD sequencing-based identification of inter-genepool SNPs and association analysis in Brassica juncea.
Article in BMC plant biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 15 citations in OpenAlex.
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- Whole-genome sequencing reveals genetic diversity, population structure, and core collection construction in Korean peach (Frontiers in plant science · 2025Article
- Identification of Genomic Regions Associated with High Grain Zn Content in Polished Rice Using Genotyping-by-Sequencing (GBS).Plants (Basel, Switzerland) · 2022Article
- Genome-Wide Association Reveals Trait Loci for Seed Glucosinolate Accumulation in Indian Mustard (Plants (Basel, Switzerland) · 2022Article
- Identification of Promising RILs for High Grain Zinc Through Genotype × Environment Analysis and Stable Grain Zinc QTL Using SSRs and SNPs in Rice (Frontiers in plant science · 2021Article
- Stable SNP Allele Associations With High Grain Zinc Content in Polished Rice (Frontiers in genetics · 2020Article
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10 authors at 3 institutions in 1 country.
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Abstract
backgroundNarrow genetic base, complex allo-tetraploid genome and presence of repetitive elements have led the discovery of single nucleotide polymorphisms (SNPs) in Brassica juncea (AABB; 2n = 4x = 36) at a slower pace. Double digest RAD (ddRAD) - a genome complexity reduction technique followed by NGS was used to generate a total of 23 million paired-end reads from three genotypes each of Indian (Pusa Tarak, RSPR-01 and Urvashi) and Exotic (Donskaja IV, Zem 1 and EC287711) genepools.
resultsSequence data analysis led to the identification of 10,399 SNPs in six genotypes at a read depth of 10x coverage among the genotypes of two genepools. A total of 44 hyper-variable regions (nucleotide variation hotspots) were also found in the genome, of which 93% were found to be a part of coding genes/regions. The functionality of the identified SNPs was estimated by genotyping a subset of SNPs on MassARRAY® platform among a diverse set of B. juncea genotypes. SNP genotyping-based genetic diversity and population studies placed the genotypes into two distinct clusters based mostly on the place of origin. The genotypes were also characterized for six morphological traits, analysis of which revealed a significant difference in the mean values between Indian and Exotic genepools for six traits. The association analysis for six traits identified a total of 45 significant marker-trait associations on 11 chromosomes of A- and B- group of progenitor genomes.
conclusionsDespite narrow diversity, the ddRAD sequencing was able to identify large number of nucleotide polymorphisms between the two genepools. Association analysis led to the identification of common SNPs/genomic regions associated between flowering and maturity traits, thereby underscoring the possible role of common chromosomal regions-harboring genes controlling flowering and maturity in Brassica juncea.
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