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Table 2 QTLs identified for CO frequency. Detailing for the QTL analysis; the population under analysis, phenotype, cross type and generation, chromosome, position (cM), logarithm of odds (LOD) score, % variation explained, additive effect, flanking markers including QTL region length and gene number, top marker from QTL scan and annotation of identified candidate genes in the region

From: Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

Population/phenotype

Cross

BC.gen

F.gen

Chr

Pos cM

LOD

%var

Add eff

Flanking markers

Top marker

Candidate genes plus annotation

Parent with increasing effect

CSxP

CO-Phenotype

RIself

NA

NA

6A

11.84

3.637

6.037

− 4.502

AX-95155001

AX-94507146

6,740,223-21,438,976 bp

TraesCS6A01G013800-TraesCS6A01G040900 (including 267 genes)

AX-94901219 11.84 cM

6D: 13,554,815 bp; TraesCS6D01G032100; Pre-mRNA-processing protein 40A

Marker at 11.84 cM on 6A: 14,609,435 bp

TraesCS6A01G026300.2 Holliday junction ATP-dependent DNA helicase RuvB (13,063,092 bp)

TraesCS6A01G037500.1 Holliday junction ATP-dependent DNA helicase RuvA (18,534,777 bp)

Chinese Spring

CSxP

GC-Phenotype

RIself

NA

NA

2A

161

2.513

4.212

− 14.73

AX-94616756

AX-94639168

51,940,072-70,183,206 bp

TraesCS2A01G098600-TraesCS2A01G119800

(including 207 genes)

AX-94419084

57,999,746 bp

TraesCS2A01G103300 (56,942,731 bp)

ATP-dependent RNA helicase DeaD; DNA helicase, ATP-dependent, RecQ type

Chinese Spring

PxCIM47

GC-Phenotype

RIself

0

5

2B

0

6.041

6.623

0.519

AX-94768203

AX-9454604547,425,660-64,988,255 bpTraesCS2B01G084900-

TraesCS2B01G104200

(including 189 genes)

AX-9476820364,988,255 bp

TraesCS2B01G103300 (64,091,671 bp)

ATP-dependent DNA helicase PIF2

CIM47

PxWat94

GC-Phenotype

RIself

0

4

4B

191

2.591

10.461

− 0.838

AX-94840592

AX-95186017

3,513,381-4,996,179 bp

TraesCS4B01G005000-TraesCS4B01G007500

(including 26 genes)

AX-94840592

4,996,179 bp

TraesCS4B01G006700 Protein HIRA (4,526,708 bp)

Paragon

PxBaj

GC-Phenotype

RIself

0

4

5A

304.6

3.802

9.898

1.24

AX-95240942

AX-94480416464,478,676-487,684,559 bp

TraesCS5A01G249800-TraesCS5A01G277700

(including 273 genes)

AX-94758045472,344,060 bp

TraesCS5A01G257000 (472,343,789-472,347,557 bp)

WPP domain-interacting protein 1

TraesCS5A01G260500 (474,537,170 bp) Regulator of chromosome condensation (RCC1)

TraesCS5A01G381700LC (472,221,190-472,221,614 bp)

BURP domain protein RD22-similar to C-PH1 for homologous chromosome pairing

Baj