Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.)

Table 1 BAC-end sequence (BES) characteristics

Annotation	Retro-element (RE)	Genes (G)	G + RE	Transposable elements (TE)	G + TE	Non-annotated (NA)	Totals
Total ends	17928	17255	2,566	327	148	44,157	82,381
Total unique clusters ^a	7,401	11,233	913	201	44	32,147	51,939
Average cluster depth	2.42	1.54	2.81	1.63	3.36	1.37	1.69
Total unique sequence ^b	58,25,082	81,60,879	7,59,831	1,54,620	44,218	2,02,54,481	3,51,99,111
Total clusters with SSRs	302	1,083	13	11	0	3,188	4,597
Total SSRs	593	1,483	21	15	0	4100	6,212
SSRs/100 Kbp	10.2	18.2	2.8	9.7	0	20	17.7
Selected SSR-BESs ^d	124	646	4	2	0	1943	2,719
Polymorphic SSRs ^c	32	241	0	0	0	568	839
Average number of alleles	5.0 ± 1.7	5.4 ± 1.7	na	na	na	5.8 ± 2.1	5.7 ± 2.0
Average PIC value	0.53 ± 0.20	0.58 ± 0.18	na	na	na	0.57 ± .19	0.57 ± 0.18

^aTotal unique clusters represent the total number of sequence clusters plus the number of singleton (non-clustered) sequences.
^bTotal unique sequence represents the sum of the nucleotide length of all unique sequence clusters.
^cThree polymorphic markers are from BAC ends annotated as "chloroplast" and are not listed in this table.
^d2,964 SSR markers were derived from 2,719 BESs, with some BESs containing multiple SSRs

ISSN: 1471-2229