BACKGROUND Narrow 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. RESULTS Sequence 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. CONCLUSIONS Despite 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.

中文翻译：

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基于ddRAD测序的芥菜种间SNPs鉴定和关联分析。

背景技术狭窄的遗传基础，复杂的异源四倍体基因组和重复元件的存在已导致芥菜（AABB; 2n = 4x = 36）的单核苷酸多态性（SNP）的发现步伐较慢。双摘要RAD（ddRAD）-一种降低基因组复杂性的技术，其后是NGS，用于从印度（Pusa Tarak，RSPR-01和Urvashi）和外来（Donskaja IV， Zem 1和EC287711）基因库。结果序列数据分析导致在两个基因库的基因型中以10倍的覆盖深度读取了六个基因型中的10,399个SNP。在基因组中还发现了总共44个高变区（核苷酸变异热点），其中93％被发现是编码基因/区域的一部分。鉴定出的SNP的功能是通过在MassARRAY®平台上对各种B.juncea基因型中的SNP子集进行基因分型来估计的。基于SNP基因分型的遗传多样性和种群研究将基因型分为两个不同的簇，主要基于产地。还对6个形态性状的基因型进行了特征分析，对其分析表明，印度和外来基因库的6个性状的平均值存在显着差异。对六个性状的关联分析在祖细胞基因组的A和B组的11个染色体上共鉴定出45个显着的标记性状关联。结论尽管多样性狭窄，但ddRAD测序仍能够鉴定两个基因库之间的大量核苷酸多态性。