Theoretical and Applied Genetics

Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars

Minghui Wang1, Ning Jiang1, 2, Tianye Jia1, Lindsey Leach3, James Cockram4, Robbie Waugh2, Luke Ramsay2, Bill Thomas2, Zewei Luo1, †

1School of Biosciences, The University of Birmingham, Edgbaston, BirminghamB15 2TT, UK

2 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK

3BioSS Unit,Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

4John Bingham Laboratory, National Institute of Agricultural Botany, Cambridge CB3 0LE, UK

Author for correspondence:

Professor Zewei Luo

E-mail:

Table S2Descriptionof (a) BLUP and (b)DUStraits.

a.

# / Trait / Traitdescription
1 / Yield.F* / Yield improvement after using fungicidesto protect against disease
2 / TKW* / Weight of 1000 cleaned and graded seed
3 / SpecW* / Specific Weight - equivalent volumetric weight of grain
4 / GrainN* / Percentage of nitrogen in dry grain
5 / MaltN* / Percentage of nitrogen in dry malted grain
6 / SolN* / Percentage of nitrogen solubilised in malt extract
7 / Viscosity* / Wort viscosity - viscosity of hot water malt extract
8 / GE4ml* / Grain germination a month after watering 72 hours in 4ml of water
9 / Dorm4ml* / Grain germination shortly after watering 72 hours in 4ml of water
10 / Dorm8ml* / Grain germination shortly after watering 72 hours in 8ml of water

b.

# / Trait / Trait description
1 / Aleurone layer colour* / none to strong
2 / Auricles anthocyanin colouration* / present or absent
3 / Auricle anthocyanin intensity / absent to very strong
4 / Awns anthocyanin colouration* / presence or absence
5 / Awns tip anthocyanin intensity / absent to very strong
6 / Awn length* / short to long
7 / Awn margin speculation / absent, reduced, present
8 / Collar type / recurrent - platform - cup
9 / Ear attitude / erect to recurved
10 / Ear emergence time / very early to very late
11 / Ear glaucosity* / absent to very strong
12 / Ear density / very lax to very dense
13 / Ear length / very short to very long
14 / Ear row number* / two-row, six-row
15 / Ear shape / tapering - parallel - fusiform
16 / Flag leaf sheath glaucosity / absent to very strong
17 / Grain furrow hair* / absent, sharkskin, present
18 / Grain husk / absent or present
19 / Grain inner lateral nerve spiculation* / absent to very strong
20 / Grain rachilla hair type* / short or long
21 / Plant growth habit* / erect to prostrate
22 / Leaf sheaths hairiness* / present or absent
23 / Lemma nerves anthocyanin colouration* / absent to very strong
24 / Plant height / very short to very tall
25 / Rachis first segment curvature / absent to very strong
26 / Rachis first segment length / short to long
27 / Recurved leaf frequency / absent to very high
28 / Seasonal type / winter or spring
29 / Sterile spikelet attitude* / parallel to divergent
30 / Sterile spikelets development* / none or full
31 / Median spikelet glume and awn length / short to long
32 / Sterile spikelet tip shape / pointed, rounded, squared

*Significantly associated with winter and spring seasonal growth types (P value threshold 0.05/41 = 1.2×10-3) byusing chi-square test for binary traits, Mann-Whitney test for ordinal traits and Student t test for quantitative traits.