A genome-wide analysis of simple sequence repeats in maize and the development of polymorphism markers from next-generation sequence data

Table 1 The distribution of SSRs in different areas of genome

Genome regions	Overall SSRs^a				Unique SSRs^b					Unique SSRs with polymorphisms^c					Rateⁱ(%)
	Count	Interval^d (Kbp)	Length^e (bp)	GC^f (%)	Count	Interval^d (Kbp)	Length (bp)	GC (%)	Rate^g(%)	Count	Interval^d(Kbp)	Length (bp)	GC (%)	Rate^h (%)
Promotor	14202	5.51	20.98	31.26	11158	7.01	18.98	36.63	78.57	5297	14.78	13.94	24.94	46.42	37.30
5'UTR	3350	4.13	20.93	53.76	3002	4.61	19.64	62.57	89.61	1175	11.79	15.94	45.45	38.59	35.07
3'UTR	3776	5.38	18.18	30.93	3347	6.07	16.61	38.42	88.64	1930	10.52	12.79	21.02	57.13	51.11
CDS	5737	18.79	22.03	70.77	4933	21.85	20.39	80.12	85.99	890	121.12	17.23	64.89	17.86	15.51
INTRON	19232	7.64	19.11	37.89	15367	9.56	17.89	45.34	79.90	7779	18.90	14.18	31.66	49.52	40.45
INTERGENIC	138796	13.67	20.42	43.19	49635	38.23	19.45	41.91	35.76	19955	95.08	13.85	37.33	37.81	14.38
Total^j	179681	11.46	20.34	42.39	82694	24.90	19.09	43.90	46.02	35046	58.74	13.96	34.38	40.52	19.50

^aThe overall SSRs were identified on the whole 10 chromosomes;
^bThe unique SSRs were SSRs with unique flanking sequences on the genome;
^cUnique SSRs with polymorphisms were SSRs with length information results in ten or more than ten genomes, and PIC Value ≥ 0.5;
^dInterval was calculated by number/Kb;
^eSSR average length was expressed in base pairs (bp);
^fGC content was evaluated by percentages (%);
^gThis rate was the percentage of unique SSRs against overall SSRs;
^hThis rate was the percentage of unique SSRs with polymorphisms against unique SSRs;
ⁱThis rate was the percentage of unique SSRs with polymorphisms against overall SSRs;
^jThere were 179681 SSRs in total, due to the alternative splicing occurring in maize genome, and the same SSRs might be divided into different regions and double counting.

ISSN: 1756-0500