Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts

Table 4 Summary of SNP effects in wild barley 454 transcripts

SNP effect	B1K2	B1K30	B1K	B1K2	B1K30	B1K	B1K2	B1K30	B1K
SNP effect	In all regions (#)			In genic region (%)			Mean per genic region
Synonymous	1,514	1,225	3,943	45.49	32.63	28.81	2.411	1.284	1.298
Non-synonymous	699	564	1,919	21.00	15.02	14.02	1.113	0.591	0.632
3′ UTR	816	1,546	6,570	24.52	41.18	48.01	1.299	1.621	2.163
5′ UTR	154	149	458	4.63	3.97	3.35	0.245	0.156	0.151
Non-synonymous start	1	2	2	0.03	0.05	0.01	0.002	0.002	0.001
Start lost	0	1	1	0.00	0.03	0.01		0.001	0.000
Stop gained	8	14	27	0.24	0.37	0.20	0.013	0.015	0.009
¹Splice site acceptor	2	3	10	0.06	0.08	0.07	0.003	0.003	0.003
²Splice site donor	3	6	13	0.09	0.16	0.09	0.005	0.006	0.004
Start gained	26	31	95	0.78	0.83	0.69	0.041	0.032	0.031
Intron	105	213	648	3.16	5.67	4.73
³Upstream	753	1,041	3,445				0.746	0.70	0.785
⁴Downstream	1,504	1,942	7,381				1.489	1.31	1.682
Intergenic	1,173	1,272	3,854				0.167	0.223	0.213
Summary – SNPs with/in:
⁵High/moderate impact	712	588	1,970				1.134	0.616	0.648
⁶Gene region	5,585	6,737	24,512
⁷Genic region	3,328	3,754	13,686
⁸CDS/exon regions	3,192	3,501	12,920
⁹Gene with genic SNPs	628	954	3,039

¹Splice site acceptor: variant hits a splice acceptor site (two bases before exon start, except for the first exon).
²Splice site donor: variant hits a Splice donor site (two bases after coding exon end, except for the last exon).
³Upstream: variant hits Upstream of a gene (within length of 5Kb).
⁴Downstream: variant hits Downstream of a gene (within length of 5Kb).
⁵High/Moderate SNPs effect: nsSNP CDS + Spice acceptor + splice donor + start lost + stop gained.
⁶Gene region: Upstream +5 UTR + Exon + Intron +3 UTR + Downstream.
⁷Genic region: 5 UTR + Exon + Intron +3 UTR.
⁸CDS/exon region: 5 UTR + Exon +3 UTR.
⁹Number of genes with SNPs affecting the UTRs, exon and intron.
SNP effects are based on mapping of 454 NR reads against chromosomal barley genome (Hv. 030312 v2.16).

ISSN: 1471-2164