Transcriptome sequencing for SNP discovery across Cucumis melo

BMC Genomics

Table 2 SNPs identified in the eight pools of C. melo genotypes resequenced with SOLiD

Pool	Sequence length¹	Total N° SNPs²	SNPs/kb	N° SNPs with MAF < 0.7 (%)³
C. melo subespecies agrestis
1) African agrestis	13,230,637 bp	117,204	8.9	9,133 (7.8)
2) Asian agrestis-acidulus	14,275,353 bp	96,460	6.8	10,197 (10.6)
3) Far East conomon	13,218,638 bp	81,807	6.2	1,305 (1.6)
Intermediate types
4) Middle East and Indian momordica-dudaim-flexuosus	15,745,206 bp	132,792	8.4	13,826 (10.1)
C. melo subespecies melo
5) Group cantalupensis	13,982,666 bp	102,565	7.3	6,317 (6.2)
6) Group melo Europe-Asia inodorus-chandalak-ameri	4,430,082 bp	40,762	9.2	2,417 (5.9)
7) inodorus Spanish landraces	12,505,399 bp	79,551	6.4	3,210 (4.0)
8) inodorus group market class Piel de Sapo	8,680,064 bp	43,363	4.9	1,396 (3.2)

¹ Number of nucleotides sequenced at least 6 times used for SNP mining in each pool.
² Total number of SNPs detected within each pool (SNPs with two or more alleles within the corresponding group).
³ Total number of highly variable SNPs (those with a frequency of the major allele, MAF, <0.7). In parentheses the percentage over the total number of SNPs is indicated.

ISSN: 1471-2164