Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip Soybean Genome Array: optimizing analysis by masking biased probes.
BACKGROUND
Common bean (Phaseolus vulgaris L.) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. This suggests that the GeneChip(R) Soybean Genome Array (soybean GeneChip) may be used for gene expression studies using common bean.


RESULTS
To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and accuracy of measuring differential gene expression in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and accuracy of measuring differential gene expression. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR (qRT-PCR) analysis of 20 randomly selected genes and purine-ureide pathway genes demonstrated an increased accuracy of measuring differential gene expression after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The sequence divergence pattern analysis suggested that the genes for basic cellular functions and metabolism were highly conserved between soybean and common bean. Additionally, our results show that some classes of genes, particularly those associated with environmental adaptation, are highly divergent.


CONCLUSIONS
The soybean GeneChip is a suitable cross-species platform for transcript profiling in common bean when used in combination with the masking protocol described. In addition to transcript profiling, CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.
Yang
S Samuel
SS
USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA. sam.yang@ars.usda.gov
Valdés-López
Oswaldo
O
Xu
Wayne W
WW
Bucciarelli
Bruna
B
Gronwald
John W
JW
Hernández
Georgina
G
Vance
Carroll P
CP
D055028:Comparative Genomic Hybridization; D018744:DNA, Plant / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005810:Multigene Family; D015341:Nucleic Acid Probes; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D027805:Phaseolus / Q000235:genetics*; D025341:Principal Component Analysis; D018749:RNA, Plant / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics
D018744:DNA, Plant; D015341:Nucleic Acid Probes; D018749:RNA, Plant
Plant Physiol. 2007 Feb;143(2):825-37
17220366
Plant Physiol. 2004 Mar;134(3):960-8
15020760
BMC Genomics. 2007 Apr 03;8:89
17407579
Nucleic Acids Res. 2003 Feb 15;31(4):e15
12582260
Nat Protoc. 2008;3(6):1101-8
18546601
Plant Physiol. 2002 Mar;128(3):793-802
11891236
J Struct Funct Genomics. 2000;1(1):1-7
12836675
Plant J. 1999 Nov;20(3):317-32
10571892
Plant J. 2003 Apr;34(1):125-34
12662315
Curr Opin Plant Biol. 2001 Oct;4(5):447-56
11597504
Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):13030-5
14557539
Plant Mol Biol. 2006 Jan;60(1):107-24
16463103
Theor Appl Genet. 1993 Aug;86(7):797-810
24193874
Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2957-62
14976249
Plant Physiol. 2005 Apr;137(4):1211-27
15824284
Nature. 2010 Jan 14;463(7278):178-83
20075913
Genome. 1995 Oct;38(5):928-37
18470218
Plant J. 2004 Jan;37(2):269-81
14690510
Science. 2002 Apr 12;296(5566):340-3
11951044
New Phytol. 2006;170(2):239-60
16608451
Curr Opin Plant Biol. 2000 Oct;3(5):423-34
11019812
Plant Mol Biol. 1999 Nov;41(5):577-85
10645718
Annu Rev Phytopathol. 2001;39:285-312
11701867
Proteomics. 2002 Dec;2(12):1715-23
12469341
Plant J. 2004 Mar;37(6):914-39
14996223
Science. 2003 Jun 13;300(5626):1742-5
12805547
PLoS One. 2008 Sep 25;3(9):e3279
18815615
Plant Methods. 2005 Nov 09;1(1):10
16280083
PLoS Biol. 2004 May;2(5):E132
15138501
Mol Biol Evol. 2004 Jul;21(7):1308-17
15034135
Syst Biol. 2005 Aug;54(4):575-94
16085576
J Exp Bot. 2005 Nov;56(421):2885-95
16216847
Annu Rev Genet. 2007;41:465-507
17678444
Plant Physiol. 2003 Mar;131(3):900-10
12644643
Trends Plant Sci. 2005 Feb;10(2):63-70
15708343
Plant Cell Environ. 2008 Dec;31(12):1834-43
18771575
Nucleic Acids Res. 2004 Jul 01;32(11):e93
15247326
BMC Genomics. 2010 May 24;11:323
20497574
Bioinformatics. 2006 Dec 1;22(23):2958-9
17046975
Prog Nucleic Acid Res Mol Biol. 1992;42:259-87
1574589
Mol Biol Evol. 2003 Jul;20(7):1070-6
12777520
Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):9894-9
12907700
BMC Genomics. 2006 May 10;7:113
16686947
BMC Bioinformatics. 2006 Dec 18;7:535
17176458
Genetics. 2003 Feb;163(2):723-33
12618409
J Hered. 2002 Mar-Apr;93(2):148-52
12140276
Nature. 2001 May 3;411(6833):41-2
11333967
Plant J. 2004 Jan;37(2):251-68
14690509
Development. 2001 May;128(9):1539-46
11290293
Genetics. 1992 Jul;131(3):733-40
1352759
Genome Res. 2004 Jul;14(7):1310-4
15231746
Nature. 2001 Jun 14;411(6839):843-7
11459067
BMC Bioinformatics. 2004 Oct 26;5:165
15507140
Nature. 2001 Jun 14;411(6839):826-33
11459065