B. rapa is a major vegetable or oil crop in Asia and Europe, and has recently become a widely used model for the study of polyploid genome structure and evolution because it has the smallest genome (529 Mb) of the Brassica genus and, like all members of the tribe Brassiceae, has evolved from a hexaploid ancestor.

All the 10 chromosomes were chopped into manageable range of 50000 bp using PERL script. These fragments were given to MIcroSAtellite identification tool (MISA) to identify and find the location of perfect and compound microsatellites for all the chromosomes of the genome. The STR numbers, motifs, repeat number, length of the repeat, size of the repeat, repeat type, GC content, start and end position of the repeat and STR sequence has been compiled.Chromosome wise description of the STRs have been tabulated as well as represented as graphs. The mono, di, tri, tetra, penta and hexa type of microsatellites have been plotted to show the abundance of the type in chromosomes.In addition, facility to locate the STRs on chromosomes based on the position number is incorporated which may be very useful to the animal biotechnologists. The tabulation of simple versus compound shows the proportion of the same.

 

Scientific name	Common name	Family	Chr. no.	Genome Size (MB)
Brassica rapa	Field Mustard	Brassicaceae	10	~529

Table 1. Description of B. rapa genome

 

Type	Number	Percentage
Simple	111006	90.70
Compound	11382	9.30
Total	122388	100.00

Table 2. Distribution of microsatellite types in B. rapa genome

 

Figure 1. Graphical view of microsatellite types in B. rapa genome

 

Motif Type	Number	Percentage (%)
Mono	78188	70.44
Di	24130	21.74
Tri	7883	7.10
Tetra	527	0.47
Penta	157	0.14
Hexa	121	0.11

Table 3. Motif wise distribution of microsatellites in B. rapa genome

Chromosome	Simple						Compound
	Mono	Di	Tri	Tetra	Penta	Hexa
1	7738	2462	795	53	10	14	1158
2	8615	2597	777	56	14	12	1141
3	10423	2975	1141	60	21	19	1530
4	5959	1842	597	40	13	7	856
5	7239	2239	785	45	10	12	1075
6	7380	2331	788	60	19	12	1152
7	7948	2505	732	52	14	10	1142
8	6284	1895	583	44	18	7	933
9	11634	3707	1105	82	31	21	1698
10	4968	1577	580	35	7	7	697

Table 4. Motif wise distribution of microsatellites in B. rapa chromosomes

 

Figure 2. Graphical view of motif wise distribution of microsatellites in B. rapa genome

Size of STRs	Number of STRs
<10	78738
11-13	31138
14-16	7547
17-25	3965
>25	811

Table 5. Frequencies of STRs based on their sizes

 

Figure 3. Graphical view of STR frequencies based on their sizes

Chromosome No.	<10	11--13	14-16	17-25	>25
1	7954	3071	717	400	72
2	8460	3356	845	439	88
3	10449	4072	1029	499	100
4	5985	2363	581	295	70
5	7402	2854	695	369	72
6	7478	3045	727	382	93
7	7939	3208	736	415	82
8	6183	2544	641	322	64
9	11800	4656	1096	582	112
10	5088	1969	480	262	58

Table 6. Proportion of STRs based on their sizes chromosome wise