Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean

Prince, Silvas J; Song, Li; Qiu, Dan; Maldonado dos Santos, Joao V; Chai, Chenglin; Joshi, Trupti; Patil, Gunvant; Valliyodan, Babu; Vuong, Tri D; Murphy, Mackensie; Krampis, Konstantinos; Tucker, Dominic M; Biyashev, Ruslan; Dorrance, Anne E; Maroof, MA Saghai; Xu, Dong; Shannon, J Grover; Nguyen, Henry T

doi:10.1186/s12864-015-1334-6

Table 4 List of genes identified within each potential root QTL interval based on transcript abundance in microarray analyses

From: Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean

S. no	Affymetrix probe ID	Annotation based on expression profiling*	Gene ID	Gene details #	Root QTLs flanked
1	Gma.4222.1.S1_10	Probable carboxylesterase 6-like	Glyma06g46680	Alpha/beta hydrolase	Surface area, Total length
2	GmaAffx.77599.1.S1_7	Uncharacterized	Glyma06g46850	Histone-like CCAAT Transcription Factor	Surface area, Total length
3	GmaAffx.59884.1.S1_8	Kinesin-like protein KIF2C-like	Glyma07g09530	Kinesin like protein	Root length (1.0–1.5 mm)
3	GmaAffx.59884.1.S1_8	Kinesin-like protein KIF2C-like	Glyma09g32280	Kinesin like protein	Root thickness (0.5–1.0 mm)
4	Gma.8398.1.S1_11	Lipase 1-like	Glyma07g09860	Triglyceride lipase-cholesterol esterase
4	Gma.8398.1.S1_11	Lipase 1-like	Glyma09g31950	Triglyceride lipase-cholesterol esterase
5	Gma.1900.1.S1_3	DEAD-box ATP-dependent RNA helicase 20-like	Glyma07g11880	ATP-dependent RNA helicase
			Glyma08g20670
			Glyma07g01260
6	Gma.6648.1.S1_11	Apoptosis inhibitor 5-like	Glyma07g32480	Apoptosis Inhibitor 5-related	Tap root length
6	Gma.6648.1.S1_11	Apoptosis inhibitor 5-like	Glyma13g24090	Apoptosis Inhibitor 5-related
7	Gma.5451.1.S1_5	Uncharacterized	Glyma02g15190	Apoptosis-promoting RNA-binding protein
7	Gma.5451.1.S1_5	Uncharacterized	Glyma07g33300	Apoptosis-promoting RNA-binding protein
8	Gma.6807.1.S1_10	Cysteine synthase-like	Glyma15g41600	Cystathionine beta-synthase and related enzymes
9	Gma.9882.1.S1_10	Uncharacterized	Glyma15g42220	slow anion channel associated 1-like
10	Gma.4792.2.S1_5	Uncharacterized	Glyma04g42630	BTB domain transcription factor	Average diameter
10	Gma.4792.2.S1_5	Uncharacterized	Glyma06g12140	BTB domain transcription factor
11	Gma.15910.1.S1_10	Uncharacterized	Glyma11g26970	Nuclear distribution protein NUDC
11	Gma.15910.1.S1_10	Uncharacterized	Glyma18g07050	Nuclear distribution protein NUDC
	Gma.6807.1.S1_10	Cysteine synthase-like	Glyma15g41600	Cystathionine beta-synthase and related enzymes
12	GmaAffx.70452.1.S1_3	Calmodulin-binding transcription activator 2-like	Glyma08g19100	CAMTA Transcription factor	Root thickness (0.5–1.0 mm)
12	GmaAffx.70452.1.S1_3	Calmodulin-binding transcription activator 2-like	Glyma15g05900	CAMTA Transcription factor
13	GmaAffx.55124.1.S1_7	Metacaspase-1	Glyma08g19050	Metacaspase involved in regulation of apoptosis
14	Gma.16443.1.A1_2	Histone-lysine N-methyltransferase ASHH3-like	Glyma09g28430	Uncharacterized

*The full expression profiling data of mock control plants can be accessed from the NCBI database. (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11611).
# The gene annotation information was from SoyKB.

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ISSN: 1471-2164

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