| Summary: | Genetic diversity analysis is a fundamental work for effective management and utilization of plant germplasm. <i>Brassica juncea</i> is an economically important crop, including both oilseed and vegetable types. In the present study, a total of 99 accessions of Brassicaceae family, including 84 mustard (50 oilseed and 34 vegetable types) in China and 15 other Brassicaceae accessions were evaluated for their genetic diversity using nuclear and mitochondrial molecular markers. All accessions were evaluated using 18 simple sequence repeats, 20 sequence related amplified polymorphisms, and 7 intron-exon splice junction primers, and in total, 232 polymorphic fragments were obtained. The unweighted pair-group method with arithmetic mean cluster analysis indicated that all accessions could be divided into three major clusters, with cluster I including all 50 oilseed mustard, cluster II including 34 vegetable mustard, and cluster III containing 15 other Brassicaceae accessions. The results of principal component analysis and population structure analysis were in accordance with the cluster result. Molecular variance analysis revealed that the genetic variation was 34.07% among populations and 65.93% within <i>Brassica</i> species, which indicates existence of considerable genetic variation among oilseed and vegetable <i>B</i>. <i>juncea</i> species. Based on an InDel and a SNP locus reported in <i>B</i>. <i>juncea</i> mitochondrial genome, all the 84 <i>B</i>. <i>juncea</i> mitochondrial genomes were divided into three mitotypes (MTs1-3), 22 accessions of MT1, 20 accessions of MT2, and 42 accessions of MT3. In addition, the results of the modified multiplex PCR, Indel and SNP could identify <i>pol</i>-, <i>cam</i>-, <i>nap-</i> (or MT4), <i>Bol</i>-, <i>Bni</i>-, <i>Esa</i>-, and <i>In</i>-cytoplasmic types in 15 other Brassicaceae accessions. Together, oilseed and vegetable <i>B. juncea</i> can be used for broadening the genetic background for each other.
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