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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (5): 1184-1196.doi: 10.3724/SP.J.1006.2023.21006

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-wide association study for agronomic traits in common wheat lines derived from wild emmer wheat

LIU Jia(), GONG Fang-Yi, LIU Ya-Xi, YAN Ze-Hong, ZHONG Xiao-Ying, CHEN Hou-Lin, HUANG Lin(), and WU Bi-Hua()   

  1. State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
  • Received:2022-01-25 Accepted:2022-09-05 Online:2023-05-12 Published:2022-09-28
  • Contact: *E-mail: wubihua2017@126.com; E-mail: lhuang@sicau.edu.cn
  • Supported by:
    International Science and Technology Innovation Cooperation Project of Sichuan Province(2021YFH0110);Major Science and Technology Project for Biological Breeding of Sichuan Province(2022ZDZX0014)

Abstract:

Wild emmer (Triticum dicoccoides ssp. dicoccoides) is the tetraploid progenitor of common wheat with wide genotypic variations, which is an important germplasm resource for common wheat improvement. In this study, the plant height, tiller number, spikelet number, heading date, anthesis date, and 1000-kernel weight of 161 introgression lines derived from wild emmer were phenotyped in four environments of different years and locations. We performed genome-wide association study (GWAS) of agronomic traits using 13,116 DArT markers to identify marker-trait associations (MTA) and candidate genes. A total of 147 stable markers associated with the tested 6 agronomic traits were identified. Among them, some MTAs were associated with both heading and anthesis date, and these MTAs were clustered on chromosome 2B. In addition, a total of 21 candidate genes related to the agronomic traits were deduced in introgression lines derived from wild emmer. Among them, the candidate gene associated with 1000-kernel weight on chromosome 7A maybe related to cyclin protein. These MTAs and candidate genes could provide the essential information for cloning genes related to excellent agronomic traits and further provide basis and guidance for comprehensive utilization of wild emmer for genetic improvement in common wheat background.

Key words: wild emmer wheat, common wheat, agronomic traits, wide hybridization, GWAS

Table S1

List of test materials"

材料名称Sample name 谱系Pedigree 亚群Subgroup
CN16 Female Parent Gp3
D1 Male Parent Gp3
BAd63-4 CN16×D1 Gp2
BAd64-5 CN16×D1 Gp2
BAd67-2 CN16×D1 Gp2
BAd68-2 CN16×D1 Gp2
BAd69-2 CN16×D1 Gp2
BAd70-2 CN16×D1 Gp2
BAd70-4 CN16×D1 Gp2
BAd71-2 CN16×D1 Gp2
BAd71-3 CN16×D1 Gp2
BAd73-2 CN16×D1 Gp2
BAd73-7 CN16×D1 Gp2
BAd74-2 CN16×D1 Gp2
BAd76-5 CN16×D1 Gp2
BAd79-5 CN16×D1 Gp2
BAd84-5 CN16×D1 Gp2
BAd89-1 CN16×D1 Gp2
BAd91-4 CN16×D1 Gp2
BAd93-5 CN16×D1 Gp2
BAd95-2 CN16×D1 Gp2
BAd95-4 CN16×D1 Gp2
BAd97-2 CN16×D1 Gp2
BAd99-5 CN16×D1 Gp2
BAd100-3 CN16×D1 Gp2
BAd104-2 CN16×D1 Gp2
BAd106-1 CN16×D1 Gp2
BAd106-4 CN16×D1 Gp2
BAd107-1 CN16×D1 Gp2
BAd107-4 CN16×D1 Gp2
BAd108-2 CN16×D1 Gp3
BAd109-2 CN16×D1 Gp2
BAd111-1 CN16×D1 Gp2
BAd112-6 CN16×D1 Gp2
BAd117-3 CN16×D1 Gp2
BAd119-3 CN16×D1 Gp2
BAd119-4 CN16×D1 Gp2
BAd122-3 CN16×D1 Gp2
BAd122-5 CN16×D1 Gp1
BAd123-2 CN16×D1 Gp2
BAd123-3 CN16×D1 Gp2
BAd124-4 CN16×D1 Gp2
BAd124-6 CN16×D1 Gp2
BAd125-2 CN16×D1 Gp2
BAd127-1 CN16×D1 Gp2
BAd128-2 CN16×D1 Gp2
BZn128-5 CN16×D1 Gp2
BAd128-6 CN16×D1 Gp2
BAd129-2 CN16×D1 Gp2
BAd129-4 CN16×D1 Gp2
BAd129-6 CN16×D1 Gp2
BZn130-3 CN16×D1 Gp2
BAd133-5 CN16×D1 Gp2
BAd134-3 CN16×D1 Gp2
BAd137-4 CN16×D1 Gp2
BAd137-5 CN16×D1 Gp2
BAd139-6 CN16×D1 Gp2
BAd141-6 CN16×D1 Gp1
BAd142-1 CN16×D1 Gp2
BAd142-4 CN16×D1 Gp2
BAd142-5 CN16×D1 Gp2
BAd142-6 CN16×D1 Gp2
BAd143-3 CN16×D1 Gp2
BAd144-1 CN16×D1 Gp2
BAd144-6 CN16×D1 Gp2
BAd145-3 CN16×D1 Gp2
BAd146-4 CN16×D1 Gp2
BAd147-2 CN16×D1 Gp1
BAd149-3 CN16×D1 Gp1
BAd152-7 CN16×D1 Gp1
BAd153-3 CN16×D1 Gp1
BAd156-2 CN16×D1 Gp1
BAd157-4 CN16×D1 Gp1
BAd159-3 CN16×D1 Gp1
BAd160-6 CN16×D1 Gp1
BAd161-5 CN16×D1 Gp1
BAd162-5 CN16×D1 Gp3
BAd163-2 CN16×D1 Gp1
BAd164-5 CN16×D1 Gp1
BFe164-6 CN16×D1 Gp1
BAd167-6 CN16×D1 Gp1
BAd168-3 CN16×D1 Gp1
BAd169-4 CN16×D1 Gp1
BAd170-1 CN16×D1 Gp1
BAd170-2 CN16×D1 Gp1
BAd170-4 CN16×D1 Gp1
BAd170-6 CN16×D1 Gp1
BAd173-5 CN16×D1 Gp1
BAd174-1 CN16×D1 Gp1
BAd174-6 CN16×D1 Gp1
BAd175-3 CN16×D1 Gp1
BAd175-6 CN16×D1 Gp1
BAd175-7 CN16×D1 Gp1
BAd176-4 CN16×D1 Gp1
BAd177-2 CN16×D1 Gp1
BAd177-6 CN16×D1 Gp1
BAd178-2 CN16×D1 Gp1
BAd178-6 CN16×D1 Gp1
BAd179-4 CN16×D1 Gp1
BAd180-3 CN16×D1 Gp1
BAd180-5 CN16×D1 Gp1
BAd181-1 CN16×D1 Gp1
BAd182-3 CN16×D1 Gp1
BAd182-5 CN16×D1 Gp1
BAd183-3 CN16×D1 Gp1
BAd183-4 CN16×D1 Gp1
BAd184-1 CN16×D1 Gp2
BAd185-1 CN16×D1 Gp1
AdA116-(1) BAd116-1×MM46 Gp3
AdA116-(3) BAd116-1×MM46 Gp3
AdA116-(4) BAd116-1×MM46 Gp3
AdA116-(5) BAd116-1×MM46 Gp3
AdA116-(6) BAd116-1×MM46 Gp3
AdA116-⑩ BAd116-1×MM46 Gp3
AdA180-1 BAd180-1×CM50 Gp3
AdA180-2 BAd180-1×CM50 Gp3
AdA180-3 BAd180-1×CM50 Gp3
AdA168-1 BAd168-1×KCM2 Gp3
AdA168-2 BAd168-1×KCM2 Gp3
AdA168-4 BAd168-1×KCM2 Gp3
AdA168-5 BAd168-1×KCM2 Gp3
AdA168-6 BAd168-1×KCM2 Gp3
AdA168-9 BAd168-1×KCM2 Gp3
AdA168-(1) BAd168-1×KCM2 Gp3
AdA168-(10) BAd168-1×KCM2 Gp3
AdA168-(11) BAd168-1×KCM2 Gp3
AdA168-(12) BAd168-1×KCM2 Gp3
AdA168-(14) BAd168-1×KCM2 Gp3
AdA168-(15) BAd168-1×KCM2 Gp3
AdA168-(16) BAd168-1×KCM2 Gp3
AdA168-(17) BAd168-1×KCM2 Gp3
AdA168-(18) BAd168-1×KCM2 Gp3
AdA168-(19) BAd168-1×KCM2 Gp3
AdA168-(2) BAd168-1×KCM2 Gp3
AdA168-(20) BAd168-1×KCM2 Gp3
AdA168-(21) BAd168-1×KCM2 Gp3
AdA168-(3) BAd168-1×KCM2 Gp3
AdA168-(4) BAd168-1×KCM2 Gp3
AdA168-(5) BAd168-1×KCM2 Gp3
AdA168-(6) BAd168-1×KCM2 Gp3
AdA168-(7) BAd168-1×KCM2 Gp3
AdA168-(8) BAd168-1×KCM2 Gp3
AdA95-1 BAd95-1×MM46 Gp3
AdA95-2 BAd95-1×MM46 Gp3
AdA95-3 BAd95-1×MM46 Gp3
AdA95-4 BAd95-1×MM46 Gp2
AdA95-5 BAd95-1×MM46 Gp3
AdA79-1 BAd79-1×MM46 Gp3
AdA79-2 BAd79-1×MM46 Gp3
AdA79-3 BAd79-1×MM46 Gp3
AdA79-4 BAd79-1×MM46 Gp3
AdA79-5 BAd79-1×MM46 Gp3
AdA73-1 BAd73-7×(YB58863×CY18) Gp2
AdA73-10 BAd73-7×(YB58863×CY18) Gp2
AdA73-11 BAd73-7×(YB58863×CY18) Gp2
AdA73-2 BAd73-7×(YB58863×CY18) Gp2
AdA73-3 BAd73-7×(YB58863×CY18) Gp2
AdA73-6 BAd73-7×(YB58863×CY18) Gp2
AdA73-8 BAd73-7×(YB58863×CY18) Gp2
AdA73-9 BAd73-7×(YB58863×CY18) Gp2
AdA73-(2) BAd73-7×(YB58863×CY18) Gp2
AdA73-(3) BAd73-7×(YB58863×CY18) Gp2
AdA73-(4) BAd73-7×(YB58863×CY18) Gp2

Table 1

Variation for agronomic traits in introgression lines derived from wild emmer D1 and their parents"

性状
Trait
环境
Environment
亲本Parents 渗入系群体Introgression lines
CN16 D1 均值±标准差
Mean±SD
范围
Range
变异系数
CV (%)
株高
Plant height (cm)
2015温江WJ 85.10 a±0.80 92.20 a±1.40 99.03 a±10.23 77.20-123.30 10.33
2015崇州CZ 79.73 c±2.95 116.53 a±8.05 97.35 b±9.79 70.40-118.50 10.06
2016温江WJ 87.60 b±2.27 120.37 a±2.60 94.42 b±9.66 74.30-117.80 10.23
2016崇州CZ 81.60 b±8.01 117.97 a±5.20 90.88 b±10.32 68.10-117.50 11.36
分蘖数
Tiller number
2015温江WJ 8.00 b±1.00 21.33 a±0.58 7.74 b±1.23 4.60-11.30 15.89
2015崇州CZ 7.60 b±2.69 19.87 a±1.10 8.54 b±1.40 5.50-12.50 16.39
2016温江WJ 8.33 ab±1.33 9.53 a±3.56 7.51 b±1.40 4.30-12.70 18.64
2016崇州CZ 10.67 b±2.02 24.13 a±3.64 9.54 b±1.74 6.10-15.90 18.24
小穗数
Spikelet number
2015温江WJ 19.03 b±0.95 20.97 a±1.15 19.74 ab±1.35 16.30-24.10 6.84
2015崇州CZ 17.07 b±2.69 20.47 a±0.46 19.33 a±1.22 16.30-23.30 6.31
2016温江WJ 18.40 a±1.22 19.27 a±1.97 19.40 a±1.08 15.90-22.30 5.57
2016崇州CZ 21.13 a±0.61 19.80 a±1.04 19.98 a±1.11 16.70-23.50 5.56
抽穗期
Heading date (d)
2015温江WJ 134.00 b±7.00 160.33 a±0.58 135.75 b±3.47 127.30-145.30 2.56
2015崇州CZ 124.00 b±0.00 152.00 a±0.00 128.60 b±4.42 121.30-142.30 3.44
2016温江WJ 142.67 b±0.58 165.00 a±0.00 145.18 b±3.22 135.70-152.30 2.22
2016崇州CZ 137.33 b±1.15 164.33 a±0.58 137.61 b±3.16 129.70-151.00 2.30
开花期
Anthesis date (d)
2015温江WJ 143.67 c±2.08 166.00 a±0.00 147.96 b±2.68 140.70-153.70 1.81
2015崇州CZ 136.67 b±1.15 158.00 a±0.00 140.31 b±2.98 133.00-150.30 2.12
2016温江WJ 154.67 b±0.58 169.00 a±0.00 156.67 b±2.45 149.00-161.70 1.56
2016崇州CZ 145.67 b±2.08 170.33 a±0.58 147.68 b±3.01 142.00-160.70 2.04
千粒重
1000-kernel weight (g)
2015温江WJ 43.19 a±4.99 19.21 b±4.39 46.08 a±4.64 30.70-57.00 10.07
2015崇州CZ 49.33 a±1.54 15.00 b±0.67 52.90 a±4.35 37.08-64.63 8.22
2016温江WJ 49.22 a±1.84 32.80 b±1.61 49.88 a±4.28 33.93-60.11 8.58
2016崇州CZ 42.70 b±4.97 31.63 c±0.71 49.06 a±4.52 35.00-60.88 9.21

Fig. 1

Frequency distributions of agronomic traits values under all environments in the introgression lines derived from wild emmer D1 The solid arrow indicates the parent wild emmer wheat D1, and the dotted arrow indicates the parent common wheat CN16. WJ: Wenjiang; CZ: Chongzhou."

Table 2

Pearson correlation coefficients of agronomic traits in introgression lines derived from wild emmer D1 based on BLUP data"

性状
Trait
株高
Plant height
分蘖数
Tiller number
小穗数
Spikelet number
抽穗期
Heading date
开花期
Anthesis date
分蘖数 Tiller number 0.162*
小穗数 Spikelet number -0.351** -0.342**
抽穗期 Heading date -0.051 0.130 0.311**
开花期 Anthesis date -0.046 0.124 0.209** 0.938**
千粒重 1000-kernel weight 0.300** -0.059 -0.169* 0.088 0.098

Table 3

In the introgression lines derived from wild emmer D1, GWAS of the investigated agronomic traits in detected by both the models"

性状
Trait
模型
Model
显著MTA
No. sig.a
显著P均值
Average
-log10 (P)
显著P值范围
Range -log10 (P)
表型变异
解释率均值
Average PVE (%)
表型变异
解释率均值范围
Range PVE (%)
稳定
标记数
No. of shared b
株高
Plant height
MLM 25 3.31 3.04-3.80 8.21 7.31-10.32 14
GLM 1162 4.34 3.00-12.58 5.42 3.48-15.26
分蘖数
Tiller number
MLM 59 3.29 3.00-3.75 7.73 6.99-9.69 55
GLM 932 4.21 3.00-9.57 9.72 6.38-21.60
小穗数
Spikelet number
MLM 6 3.33 3.01-3.62 8.07 6.95-8.81 5
GLM 1566 4.35 3.00-11.17 8.43 5.38-21.18
抽穗期
Heading date
MLM 188 3.48 3.00-4.72 8.64 6.91-13.62 39
GLM 529 4.27 3.00-7.27 8.16 5.36-14.93
开花期
Anthesis date
MLM 26 3.38 3.00-3.98 8.34 6.88-10.38 19
GLM 630 4.00 3.00-7.16 8.15 5.70-15.63
千粒重
1000-kernel weight
MLM 45 3.29 3.01-3.78 10.66 9.48-12.98 15
GLM 357 3.85 3.00-6.55 8.46 6.15-15.43

Table S2

Significant and stable MTAs for agronomic traits identified by MLM and GLM"

性状
Trait
性状关联标记
MTA
染色体
Chromosome
位置
Position (cM)
混合线性模型MLM 一般线性模型GLM
显著P
-log10(P)
表型变异解释率
PVE (%)
显著P
-log10(P)
表型变异解释率
PVE (%)
株高
PH
1767955 1A 134.66 3.05 7.58 6.24 7.82
1268900 1B 68.58 3.48 8.72 3.51 4.26
1073712 1B 205.80 3.53 8.51 5.09 6.46
12776744 2A 125.28 3.04 7.34 6.04 7.52
1013390 2B 169.52 3.10 7.38 3.55 4.54
1067538 2B 169.52 3.15 7.43 3.95 5.04
1130621 3A 76.65 3.11 7.64 6.46 8.24
982324 3A 95.54 3.54 8.91 11.24 14.57
6041358 3A 95.54 3.42 8.26 12.58 15.26
3021986 6D 123.58 3.58 8.96 9.07 12.24
1666084 6D 125.74 3.73 9.39 11.25 14.23
1296920 6D 140.67 3.29 8.06 6.17 7.87
2292535 7A 19.26 3.30 8.59 3.26 4.22
1687570 7B 82.30 3.25 7.96 4.46 5.40
分蘖数
TN
5411823 1B 104.00 3.32 7.56 3.12 6.66
12743876 1B 396.15 3.14 7.19 3.09 6.69
1405940 2B 76.70 3.45 8.16 4.47 10.65
1090835 2B 94.77 3.70 9.69 3.99 9.49
7884146 2B 94.77 3.75 8.76 4.25 9.46
1252801 2B 95.78 3.30 7.99 3.86 9.37
2366453 2B 113.20 3.41 8.08 3.96 9.45
1684342 2B 114.33 3.57 8.36 3.93 8.85
1165797 2B 115.46 3.15 7.09 3.21 6.87
3022409 2B 117.77 3.01 7.51 3.76 8.83
1114669 2B 118.39 3.32 7.56 3.12 6.66
1160144 2B 119.70 3.21 7.27 3.48 7.55
分蘖数TN 987712 2B 120.12 3.25 7.70 3.43 7.93
1091031 2B 120.12 3.21 7.79 3.51 8.40
4004990 2B 120.12 3.32 7.56 3.12 6.66
1234254 2B 120.63 3.17 7.34 3.23 7.55
1102098 2B 134.76 3.25 7.80 3.73 8.98
1110856 2B 135.57 3.29 8.05 3.90 9.19
1054964 2B 137.11 3.16 7.51 3.44 7.93
1096265 2B 137.11 3.32 7.56 3.12 6.66
12768537 2B 137.20 3.20 7.22 3.55 7.73
1160910 2B 138.41 3.32 7.56 3.12 6.66
978979 2B 139.32 3.31 7.76 3.31 7.59
1100798 2B 139.32 3.41 8.45 4.14 9.99
1203705 2B 139.32 3.14 7.16 3.43 7.87
3064449 2B 139.32 3.07 7.42 3.23 7.54
1093009 2B 139.77 3.32 8.16 3.65 8.57
3023277 2B 144.20 3.49 8.56 5.32 13.27
2288916 2B 147.13 3.11 7.65 3.53 8.33
1130961 2B 147.49 3.30 7.51 3.17 6.84
1068936 2B 147.53 3.00 7.21 3.39 8.04
7906177 2B 148.21 3.30 7.52 3.20 6.90
1093839 2B 149.44 3.07 7.51 3.60 8.65
2356896 2B 149.44 3.18 7.56 3.86 9.19
3021490 2B 150.67 3.25 7.43 3.07 6.68
3034249 2B 151.10 3.01 7.29 3.52 8.38
979343 2B 151.35 3.29 7.74 3.77 8.67
12832697 2B 151.35 3.38 7.75 3.16 6.88
1234491 2B 151.77 3.40 7.81 3.41 7.42
10992880 2B 152.04 3.40 7.80 3.19 6.96
1150153 2B 154.34 3.32 7.56 3.12 6.66
1086699 2D 258.12 3.62 8.48 3.32 7.34
1318969 3B 132.24 3.23 7.54 3.29 7.35
1160384 3B 222.96 3.35 7.77 4.41 10.08
4992374 4A 58.58 3.16 7.17 3.27 7.06
1145045 4B 149.69 3.49 8.04 9.57 21.60
1217208 4B 149.69 3.49 8.04 9.57 21.60
2275152 4D 143.79 3.30 7.80 3.77 8.87
1860396 6A 46.40 3.14 7.06 5.07 11.59
5567513 6A 70.00 3.32 7.56 3.12 6.66
1225584 6B 64.10 3.17 7.71 3.90 9.33
12774898 7A 1.18 3.31 7.54 3.22 6.97
12854634 7A 285.84 3.36 7.75 3.39 7.36
分蘖数
TN
1200976 7D 125.99 3.67 9.20 6.09 14.36
999801 7D 126.44 3.06 7.61 4.60 11.20
小穗数
SN
1289016 3A 105.69 3.01 7.07 9.10 17.03
1082521 4A 215.47 3.34 8.22 4.68 9.36
1145238 7B 21.79 3.62 8.72 3.55 6.61
1111098 7D 216.22 3.59 8.81 11.17 21.18
1264045 7D 216.25 3.38 8.63 9.51 19.20
抽穗期
HD
1233288 1A 363.51 4.06 10.43 4.79 9.29
12768537 2B 137.20 3.01 6.92 7.00 13.17
2290258 2B 138.25 4.72 13.62 5.46 10.40
3024538 2B 138.78 4.63 12.67 5.44 11.19
1108320 2B 139.63 3.79 10.21 5.57 11.28
1037539 2B 146.47 4.44 11.96 4.81 9.57
1130961 2B 147.49 3.02 6.96 7.22 13.58
1158396 2B 148.12 4.72 12.12 3.14 5.92
2280469 2B 148.12 3.63 8.79 3.24 5.90
1128165 2B 148.62 3.52 8.50 6.10 11.47
3025235 2B 148.62 3.70 8.96 3.99 7.62
1107369 2B 149.05 3.98 10.19 5.72 11.31
1254240 2B 149.78 3.01 6.95 4.21 7.82
2303763 2B 149.78 3.02 6.97 4.21 7.85
3021490 2B 150.67 3.01 6.99 7.00 13.34
3023438 2B 150.97 3.01 6.94 3.93 7.34
1116554 2B 152.10 3.63 8.81 5.30 10.16
1233376 2B 152.10 3.80 9.38 5.92 11.37
1234002 2B 152.10 3.05 7.06 5.41 10.20
1111821 2B 152.97 3.65 8.87 5.20 10.16
1096366 2B 155.58 4.60 11.75 4.41 8.26
2259939 2B 155.58 3.03 7.04 5.33 10.19
1233381 2B 155.87 4.64 11.81 4.06 7.65
3023927 2B 171.58 4.16 10.36 3.91 7.48
1020733 2B 201.12 3.06 7.52 4.44 8.62
2246033 2D 137.48 4.14 12.27 3.87 7.16
2338436 2D 137.48 4.15 11.43 4.47 8.63
5324411 2D 258.12 3.29 7.93 4.64 9.22
1111555 4D 127.39 3.74 9.23 5.51 11.22
1254583 5D 232.48 3.77 9.44 5.65 11.38
1256190 5D 232.48 4.44 11.67 6.58 12.71
1255241 5D 233.53 3.90 9.73 6.44 12.63
1106873 5D 238.83 3.53 8.54 7.02 14.19
1255155 6A 18.29 3.50 9.03 3.67 7.10
抽穗期
HD
2293190 6A 19.44 3.54 9.61 4.29 8.23
1121033 6B 86.89 3.35 8.25 3.40 6.22
1036713 7A 38.12 3.06 8.61 3.18 5.85
12854634 7A 285.84 3.00 6.91 7.13 13.43
1263147 7B 205.56 3.56 9.14 3.70 7.12
开花期
AD
2290258 2B 138.25 3.28 8.73 5.53 11.47
3024538 2B 138.78 3.74 9.78 5.62 12.37
1108320 2B 139.63 3.59 9.24 5.77 12.57
1037539 2B 146.47 3.02 8.06 4.96 10.64
1130961 2B 147.49 3.00 6.89 5.95 11.94
1120608 2B 148.62 3.27 7.84 3.44 6.83
1128165 2B 148.62 3.98 9.87 5.53 11.10
1254240 2B 149.78 3.32 7.83 3.73 7.34
2303763 2B 149.78 3.32 7.86 3.73 7.38
3021490 2B 150.67 3.00 6.88 5.76 11.71
3023438 2B 150.97 3.32 7.83 3.52 6.95
3958642 2B 152.80 3.30 7.70 3.35 6.42
1096366 2B 155.58 3.64 8.87 5.27 10.65
2259939 2B 155.58 3.17 7.44 4.85 9.87
1233381 2B 155.87 3.62 8.75 4.10 8.26
5325220 2D 248.14 3.09 7.70 3.78 7.67
1113976 3B 156.41 3.57 8.88 4.30 9.19
1101163 4B 148.56 3.08 7.29 3.08 5.96
1092921 7D 112.92 3.76 9.60 3.06 6.21
千粒重
TKW
1070490 3B 94.94 3.42 11.68 4.60 10.62
1241817 3B 94.94 3.26 10.91 3.77 8.35
1251709 3B 94.94 3.21 10.00 3.97 8.40
1265489 3B 94.94 3.53 11.20 4.10 8.64
3033937 3B 94.94 3.68 12.04 4.39 9.76
3954514 3B 94.94 3.75 12.09 4.29 9.24
3026622 3B 95.15 3.78 12.98 4.54 10.31
1101250 3B 95.66 3.59 11.95 4.91 10.93
1102583 3B 99.31 3.78 12.20 4.87 10.47
2352813 3B 102.94 3.28 10.22 4.04 8.42
1119949 3B 103.13 3.29 10.25 4.02 8.44
1298772 5A 68.92 3.68 12.11 3.18 6.67
1219440 6A 54.76 3.37 10.84 5.65 12.39
1141591 7A 293.14 3.25 10.29 4.00 8.91
1164130 7D 218.19 3.34 10.76 4.49 9.70

Fig. 2

Manhattan plots of genome-wide association scan for agronomic traits in the introgression lines derived from wild emmer D1 based on the mixed linear models A: chromosomes carrying significant MTA detected by MLM, the red line indicates the -log10 (P) threshold of 3.00; B: the black line indicates the expected values in Quantile-Quantile plots."

Fig. 3

Manhattan plots of genome-wide association scan for agronomic traits in the introgression lines derived from wild emmer D1 based on the general linear model A: chromosomes carrying significant MTA detected by GLM, the red lines indicate the -log10 (P) threshold of 3.00; B: the black lines indicate the expected values in Quantile-Quantile plots."

Table 4

List of significant MTAs from wild emmer A and B genomes"

关联标记
MTA
染色体
Chromosome
位置
Position (cM)
关联性状
Trait
1767955 1A 134.66 株高 Plant height
1268900 1B 68.58 株高 Plant height
12776744 2A 125.28 株高 Plant height
1130621 3A 76.65 株高 Plant height
6041358 3A 95.54 株高 Plant height
1687570 7B 82.30 株高Plant height
5411823 1B 104.00 分蘖数 Tiller number
12743876 1B 396.15 分蘖数 Tiller number
7884146 2B 94.77 分蘖数 Tiller number
1684342 2B 114.33 分蘖数 Tiller number
1165797 2B 115.46 分蘖数 Tiller number
1114669 2B 118.39 分蘖数 Tiller number
1160144 2B 119.70 分蘖数 Tiller number
4004990 2B 120.12 分蘖数 Tiller number
1096265 2B 137.11 分蘖数 Tiller number
12768537 2B 137.20 分蘖数/抽穗期Tiller number/Heading date
1160910 2B 138.41 分蘖数 Tiller number
1130961 2B 147.49 分蘖数/抽穗期/开花期Tiller number/Heading date/Anthesis date
7906177 2B 148.21 分蘖数 Tiller number
3021490 2B 150.67 分蘖数/抽穗期/开花期Tiller number/Heading date/Anthesis date
12832697 2B 151.35 分蘖数 Tiller number
1234491 2B 151.77 分蘖数 Tiller number
10992880 2B 152.04 分蘖数 Tiller number
1150153 2B 154.34 分蘖数 Tiller number
4992374 4A 58.58 分蘖数 Tiller number
1145045 4B 149.69 分蘖数 Tiller number
1217208 4B 149.69 分蘖数 Tiller number
1860396 6A 46.40 分蘖数 Tiller number
5567513 6A 70.00 分蘖数 Tiller number
12774898 7A 1.18 分蘖数 Tiller number
12854634 7A 285.84 分蘖数/抽穗期Tiller number/Heading date
1082521 4A 215.47 小穗数 Spikelet number
1128165 2B 148.62 抽穗期/开花期Heading date/Anthesis date
1254240 2B 149.78 抽穗期/开花期Heading date/Anthesis date
2303763 2B 149.78 抽穗期/开花期Heading date/Anthesis date
3023438 2B 150.97 抽穗期/开花期Heading date/Anthesis date
1233376 2B 152.10 抽穗期 Heading date
1234002 2B 152.10 抽穗期 Heading date
1111821 2B 152.97 抽穗期 Heading date
1096366 2B 155.58 抽穗期 Heading date
2259939 2B 155.58 抽穗期/开花期Heading date/Anthesis date
1120608 2B 148.62 开花期 Anthesis date
3958642 2B 152.80 开花期 Anthesis date
1298772 5A 68.92 千粒重 1000-kernel weight
1141591 7A 293.14 千粒重 1000-kernel weight

Table S3

List of candidate genes for agronomic traits in the introgression lines derived from wild emmer"

性状
Trait
性状关联标记
MTA
染色体
Chr.
中国春小麦基因组 野生二粒小麦基因组
基因Gene 基因描述Gene Description 基因Gene 基因描述Gene Description
株高
PH
1767955 1A \ \ TRIDC1AG013630.1 Auxin-responsive protein IAA15
982324 3A \ \ TRIDC3AG049250.1 Auxin efflux carrier family protein
1666084 6D TraesCS6D01G271900.1 Calcium sensing receptor \ \
2292535 7A TraesCS7A01G019400.1 Pectin lyase-like superfamily protein TRIDC7AG001740.1 Pectin lyase-like superfamily protein
分蘖数
TN
1090835 2B TraesCS2B01G110300.1 DnaJ TRIDC2BG013350.1 Heat shock protein DnaJ with tetratricopeptide repeat
1100798 2B \ \ TRIDC2BG033050.1 Glucose-6-phosphate/phosphate translocator 2
999801 7D TraesCS7D01G168700LC.1 Glycine-rich cell wall structural protein 2 \ \
小穗数
SN
1289016 3A TraesCS3A01G370300.1 Amino acid transporter TRIDC3AG053230.1 Transmembrane amino acid transporter family protein
1264045 7D TraesCS7D01G522800LC Polynucleotidyl transferase \ \
抽穗期
HD
2290258 2B TraesCS2B01G266000.1 Sugar/inositol transporter TRIDC2BG038220.1 calcium dependent protein kinase 1
1037539 2B \ \ TRIDC2BG058610.3 kinesin-like protein 1
3021490 2B TraesCS2B01G080900 Leucine-rich repeat receptor-like protein kinase family protein TRIDC2BG071280.1 Disease resistance protein RGA2
2259939 2B TraesCS2B01G517800 FBD-associated F-box protein \ \
1111555 4D TraesCS4D01G313400.1 Ethylene-responsive transcription factor \ \
开花期
AD
2290258 2B TraesCS2B01G266000.1 Sugar/inositol transporter TRIDC2BG038220.1 calcium dependent protein kinase 1
1037539 2B \ \ TRIDC2BG058610.3 kinesin-like protein 1
开花期
AD
3021490 2B TraesCS2B01G080900 Leucine-rich repeat receptor-like protein kinase family protein TRIDC2BG071280.1 Disease resistance protein RGA2
2259939 2B TraesCS2B01G517800 FBD-associated F-box protein
1092921 7D TraesCS7D01G107200.1 MADS-box transcription factor
千粒重
TKW
1141591 7A \ \ TRIDC7AG076170.1 Cyclin B2
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