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Table 3 The most important genomic regions and candidate genes derived from the window-based single-breed FST analyses

From: Genomic diversity and signatures of selection in meat and fancy rabbit breeds based on high-density marker data

Traits

OCU:positiona

Candidate gene

Breed (method: FST value)b

Previous studiesc

Coat colour and structure

1:127,563,000–127,668,085

TYR**

Burgundy Fawn (M1: 0.79; M2*: 0.62), Italian White (M1: 0.49; M2*: 0.50), Italian Spotted (M1: 0.54)

[15, 16]

4:5,435,027–5,439,803

ASIP**

Giant Grey (M1*: 0.49; M2: 0.53), Belgian Hare (M2*: 0.63)

[13]

8:79,700,292–79,724,918

EDNRB**

Rhinelander (M1: 0.64; M2: 0.63)

[78]

9:37,191,805–37,434,390

MITF

Giant White (M1*: 0.44; M2: 0.54)

–

14:80,045,788–80,094,927

LIPH**

Rex (M1*: 0.45; M2: 0.56)

[18]

15:17,113,617–17,196,501

EDNRA**

Italian White (M1: 0.54; M2: 0.60), Thuringian (M2: 0.71)

–

17:78,036,010–78,397,189

OCA2**

Checkered Giant (M1: 0.62; M2: 0.57)

–

Un0267:152,309–153,232

MC1R

Rhinelander (M2: 0.60)

[12]

Body size

2:8,357,629–8,403,513, 2:8,404,807–8,620,864

NCAPG**, LCORL**

Dwarf Lop (M2: 0.62), Ermine (M2: 0.72)

[19]

13:36,771,716–36,779,306

MEX3A**

Coloured Dwarf (M1: 0.69; M2: 0.61), Ermine (M1*: 0.70; M2*: 0.61)

–

13:36,843,459–36,895,416

ARHGEF2**

Coloured Dwarf (M1: 0.69; M2: 0.61), Ermine (M1*: 0.70; M2*: 0.61)

–

13:37,616,687–37,631,494

DCST1**

Coloured Dwarf (M1: 0.69; M2:0.61), Ermine (M1*: 0.70; M2*: 0.61)

–

13:37,644,467–37,654,971

ZBTB7B**

Coloured Dwarf (M1: 0.69; M2: 0.61), Ermine (M1*: 0.70; M2*: 0.61)

–

13: 38,651,582–38,702,056

GATAD2B**

Coloured Dwarf (M1: 0.55; M2: 0.55)

–

13:61,054,286–61,261,797

COL11A1

Coloured Dwarf (M1*: 0.44), Ermine (M1*: 0.61)

[19]

18: 66,434,580–66,630,682

GRK5**

Dwarf Lop (M2: 0.63)

–

Un0251:72,110–94,586

COL2A1

Dwarf Lop (M2: 0.57)

–

  1. Additional information for this table is in Additional file 1: Table S17
  2. FST values from both methods were reported (M1 and M2); in case for which the relevant identified gene was based only on one method (M1 or M2), the method is indicated
  3. OCU: Oryctolagus cuniculus chromosome
  4. aPosition of the candidate gene, in basepairs, on the O. cuniculus reference genome (OryCun2.0)
  5. bMethod used in the single breed approach: M1 or M2. FST value of the window including the candidate gene
  6. cCandidate genes previously reported in other studies in rabbit
  7. *Top 70 windows; all other FST results are from the top 14 windows containing the reported candidate gene
  8. **Relevant genes have been identified based on FST window-based analysis and single marker-based analysis (see Additional file 3: Tables S15 and S16)
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Genetics Selection Evolution

ISSN: 1297-9686