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Table 6 Candidate resistance genes in Black Pod (BP) resistance QTL region

From: Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

UnigeneID

Blast Hit Description

Accession

Instances

Method

Term Description

gnl_UG_Tcc_S51555371

heat shock

EC:1.3.1.74

1

Blast2GO

2-alkenal reductase

  

GO:0000166

1

Blast2GO

nucleotide binding

  

GO:0006950

1

Blast2GO

response to stress

  

IPR019651

2

Interproscan

Glutamate dehydrogenase, NAD-specific

  

none

1

Interproscan

SignalP

gnl_UG_Tcc_S51563205

fructose-bisphosphatase precursor

EC:1.3.1.74

1

Blast2GO

2-alkenal reductase

  

EC:3.1.3.11

1

Blast2GO

fructose-bisphosphatase

  

GO:0005576

1

Blast2GO

extracellular region

  

GO:0005975

1

Blast2GO

carbohydrate metabolic process

  

GO:0006091

1

Blast2GO

generation of precursor metabolites and energy

  

GO:0006950

1

Blast2GO

response to stress

  

GO:0009536

1

Blast2GO

plastid

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

  

GO:0015979

1

Blast2GO

photosynthesis

  

GO:0016787

1

Blast2GO

hydrolase activity

gnl_UG_Tcc_S51573205

probable plasma membrane intrinsic protein 1c

GO:0005215

1

Blast2GO

transporter activity

  

GO:0005886

1

Blast2GO

plasma membrane

  

GO:0006810

1

Blast2GO

transport

  

GO:0006950

1

Blast2GO

response to stress

  

GO:0009536

1

Blast2GO

plastid

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

  

GO:0016020

1

Blast2GO

membrane

gnl_UG_Tcc_S51574569

at3g51780 orf3

GO:0000003

1

Blast2GO

reproduction

  

GO:0006950

1

Blast2GO

response to stress

  

GO:0008219

1

Blast2GO

cell death

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

  

GO:0009791

1

Blast2GO

post-embryonic development

  

IPR000626

2

Interproscan

Ubiquitin

  

IPR003103

3

Interproscan

Apoptosis regulator, Bcl-2 protein, BAG

  

IPR019955

2

Interproscan

Ubiquitin supergroup

gnl_UG_Tcc_S51576386

abc transporter family protein

EC:3.6.3.28

1

Blast2GO

phosphonate-transporting ATPase

  

GO:0000166

1

Blast2GO

nucleotide binding

  

GO:0005215

1

Blast2GO

transporter activity

  

GO:0006810

1

Blast2GO

transport

  

GO:0009607

1

Blast2GO

response to biotic stimulus

  

GO:0016020

1

Blast2GO

membrane

  

GO:0016787

1

Blast2GO

hydrolase activity

  

IPR013525

2

Interproscan

ABC-2 type transporter;GO:0016020

gnl_UG_Tcc_S51582115

at3g51780 orf3

GO:0000003

1

Blast2GO

reproduction

  

GO:0006950

1

Blast2GO

response to stress

  

GO:0008219

1

Blast2GO

cell death

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

  

GO:0009791

1

Blast2GO

post-embryonic development

gnl_UG_Tcc_S51583076

at5g01500 f7a7_20

GO:0005215

1

Blast2GO

transporter activity

  

GO:0005739

1

Blast2GO

mitochondrion

  

GO:0006091

1

Blast2GO

generation of precursor metabolites and energy

  

GO:0006810

1

Blast2GO

transport

  

GO:0009536

1

Blast2GO

plastid

  

GO:0009579

1

Blast2GO

thylakoid

  

GO:0009607

1

Blast2GO

response to biotic stimulus

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

  

GO:0015979

1

Blast2GO

photosynthesis

  

GO:0016020

1

Blast2GO

membrane

  

GO:0019538

1

Blast2GO

protein metabolic process

  

IPR018108

3

Interproscan

Mitochondrial substrate/solute carrier

  

IPR023395

3

Interproscan

Mitochondrial carrier domain

gnl_UG_Tcc_S51585933

pseudo response regulator

GO:0003677

1

Blast2GO

DNA binding

  

GO:0004871

1

Blast2GO

signal transducer activity

  

GO:0005634

1

Blast2GO

nucleus

  

GO:0005739

1

Blast2GO

mitochondrion

  

GO:0006350

1

Blast2GO

transcription

  

GO:0007165

1

Blast2GO

signal transduction

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

  

GO:0016301

1

Blast2GO

kinase activity

  

GO:0030528

1

Blast2GO

transcription regulator activity

gnl_UG_Tcc_S51595021

ammonium transporter

GO:0005215

1

Blast2GO

transporter activity

  

GO:0005886

1

Blast2GO

plasma membrane

  

GO:0006810

1

Blast2GO

transport

  

GO:0009607

1

Blast2GO

response to biotic stimulus

  

GO:0016020

1

Blast2GO

membrane

  

IPR001905

6

Interproscan

Ammonium transporter

gnl_UG_Tcc_S51598545

asymmetric leaves1 and rough

GO:0003700

1

Blast2GO

sequence-specific DNA binding transcription factor activity

  

GO:0005634

1

Blast2GO

nucleus

  

GO:0006350

1

Blast2GO

transcription

  

GO:0006950

1

Blast2GO

response to stress

  

GO:0007275

1

Blast2GO

multicellular organismal development

  

GO:0009607

1

Blast2GO

response to biotic stimulus

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

  

GO:0009653

1

Blast2GO

anatomical structure morphogenesis

  

GO:0009719

1

Blast2GO

response to endogenous stimulus

gnl_UG_Tcc_S51616674

3-oxo-5-alpha-steroid 4-dehydrogenase

EC:1.3.99.5

1

Blast2GO

3-oxo-5-alpha-steroid 4-dehydrogenase

  

GO:0005737

1

Blast2GO

cytoplasm

  

GO:0006629

1

Blast2GO

lipid metabolic process

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

  

GO:0016020

1

Blast2GO

membrane

gnl_UG_Tcc_S51619644

fungal defense

none

0

  

gnl_UG_Tcc_S51619902

sulfolipid synthase

GO:0006629

1

Blast2GO

lipid metabolic process

  

GO:0006950

1

Blast2GO

response to stress

  

GO:0007154

1

Blast2GO

cell communication

  

GO:0009536

1

Blast2GO

plastid

  

GO:0009991

1

Blast2GO

response to extracellular stimulus

  

GO:0016740

1

Blast2GO

transferase activity

gnl_UG_Tcc_S51633831

heat shock

EC:1.3.1.74

1

Blast2GO

2-alkenal reductase

  

GO:0000166

1

Blast2GO

nucleotide binding

  

GO:0006950

1

Blast2GO

response to stress

  

IPR019651

2

Interproscan

Glutamate dehydrogenase, NAD-specific

gnl_UG_Tcc_S51634817

thaumatin-like protein

GO:0005737

1

Blast2GO

cytoplasm

  

GO:0009607

1

Blast2GO

response to biotic stimulus

  

IPR001938

5

Interproscan

Thaumatin, pathogenesis-related

gnl_UG_Tcc_S51639853

gdp-mannose pyrophosphorylase

EC:2.7.7.13

1

Blast2GO

mannose-1-phosphate guanylyltransferase

  

EC:2.7.7.22

1

Blast2GO

mannose-1-phosphate guanylyltransferase (GDP)

  

GO:0005739

1

Blast2GO

mitochondrion

  

GO:0005975

1

Blast2GO

carbohydrate metabolic process

  

GO:0006950

1

Blast2GO

response to stress

  

GO:0009607

1

Blast2GO

response to biotic stimulus

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

  

GO:0009719

1

Blast2GO

response to endogenous stimulus

  

GO:0016740

1

Blast2GO

transferase activity

  

IPR001451

2

Interproscan

Bacterial transferase hexapeptide repeat

  

IPR011004

2

Interproscan

Trimeric LpxA-like

  

IPR018357

2

Interproscan

Hexapeptide transferase, conserved site

gnl_UG_Tcc_S51640638

at5g05440 k18i23_25

GO:0004872

1

Blast2GO

receptor activity

  

GO:0005634

1

Blast2GO

nucleus

  

GO:0005737

1

Blast2GO

cytoplasm

  

GO:0007165

1

Blast2GO

signal transduction

  

GO:0008289

1

Blast2GO

lipid binding

  

GO:0009719

1

Blast2GO

response to endogenous stimulus

gnl_UG_Tcc_S51641476

dna binding protein

EC:2.7.11.17

1

Blast2GO

calcium/calmodulin-dependent protein kinase

  

GO:0003677

1

Blast2GO

DNA binding

  

GO:0004518

1

Blast2GO

nuclease activity

  

GO:0006464

1

Blast2GO

protein modification process

  

GO:0006950

1

Blast2GO

response to stress

  

GO:0009536

1

Blast2GO

plastid

  

GO:0016301

1

Blast2GO

kinase activity

gnl_UG_Tcc_S51660381

heat shock

EC:1.3.1.74

1

Blast2GO

2-alkenal reductase

  

GO:0000166

1

Blast2GO

nucleotide binding

  

GO:0006950

1

Blast2GO

response to stress

  

IPR001023

2

Interproscan

Heat shock protein Hsp70

gnl_UG_Tcc_S51662116

ca2+ antiporter cation exchanger

GO:0005215

1

Blast2GO

transporter activity

  

GO:0005773

1

Blast2GO

vacuole

  

GO:0006810

1

Blast2GO

transport

  

GO:0006950

1

Blast2GO

response to stress

  

GO:0009607

1

Blast2GO

response to biotic stimulus

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

  

GO:0016020

1

Blast2GO

membrane

  

GO:0019725

1

Blast2GO

cellular homeostasis

  

IPR004837

3

Interproscan

Sodium/calcium exchanger membrane region

gnl_UG_Tcc_S51666712

white-brown-complex abc transporter family

EC:3.6.3.28

1

Blast2GO

phosphonate-transporting ATPase

  

GO:0000166

1

Blast2GO

nucleotide binding

  

GO:0005215

1

Blast2GO

transporter activity

  

GO:0006810

1

Blast2GO

transport

  

GO:0009607

1

Blast2GO

response to biotic stimulus

  

GO:0016020

1

Blast2GO

membrane

  

GO:0016787

1

Blast2GO

hydrolase activity

  

IPR003439

3

Interproscan

ABC transporter-like

  

IPR017871

3

Interproscan

ABC transporter, conserved site

gnl_UG_Tcc_S51667842

sodium-and lithium-tolerant 1

GO:0006950

1

Blast2GO

response to stress

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

gnl_UG_Tcc_S51688650

type i small heat shock protein kda isoform

GO:0005737

1

Blast2GO

cytoplasm

  

GO:0006950

1

Blast2GO

response to stress

  

IPR002068

3

Interproscan

Heat shock protein Hsp20

  

IPR008978

2

Interproscan

HSP20-like chaperone

gnl_UG_Tcc_S51695094

at3g53990 f5k20_290

GO:0006950

1

Blast2GO

response to stress

  

GO:0009628

1

Blast2GO

response to abiotic stimulus

gnl_UG_Tcc_S51700457

pyruvate decarboxylase-1

EC:4.1.1.1

1

Blast2GO

pyruvate decarboxylase

  

GO:0006950

1

Blast2GO

response to stress

  

GO:0016020

1

Blast2GO

membrane

  

GO:0016740

1

Blast2GO

transferase activity

  

IPR012001

2

Interproscan

Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain

  1. The following bold terms were used for candidate gene selection: response to abiotic stimulus(GO:0009628); response to biotic stimulus(GO:0009607); response to endogenous stimulus(GO:0009719); response to extracellular stimulus(GO:0009991); response to stress(GO:0006950).
  2. The following terms were omitted due to low information content: biological_process(GO:0008150); biosynthetic process(GO:0009058); binding(GO:0005488); catalytic activity(GO:0003824);cellular process(GO:0009987); DNA metabolic process(GO:0006259); metabolic process(GO:0008152). protein binding(GO:0005515).
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BMC Genomics

ISSN: 1471-2164

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