Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (21): 4137-4149.doi: 10.3864/j.issn.0578-1752.2023.21.001

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

QTL Mapping and Molecular Marker Development of Traits Related to Grain Weight in Wheat

ZHANG ZeYuan1(), LI Yue2, ZHAO WenSha1, GU JingJing3, ZHANG AoYan1, ZHANG HaiLong1, SONG PengBo1, WU JianHui1, ZHANG ChuanLiang1, SONG QuanHao4, JIAN JunTao5, SUN DaoJie1(), WANG XingRong2()   

  1. 1 College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi
    2 Institute of Crop Science, Gansu Academy of Agricultural Sciences, Lanzhou 730000
    3 Luoyang Academy of Agriculture and Forestry Sciences, Luoyang 471023, Henan
    4 Zhumadian Academy of Agricultural Sciences, Zhumadian 463000, Henan
    5 Nanyang Academy of Agricultural Sciences, Nanyang 473000, Henan
  • Received:2023-03-28 Accepted:2023-04-20 Online:2023-11-01 Published:2023-11-06
  • Contact: SUN DaoJie, WANG XingRong

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Abstract:

【Objective】The yield of wheat, the second-highest-yielding food product in the world, has a major impact by grain weight. This research used materials from a recombinant inbred line (RIL) population derived from Heshangtou (HST) and Longchun 23 (LC23). Based on 55K SNP genotype data, QTL mapping was performed for traits related to grain weight of wheat, and co-segregation markers of major grain length QTL were developed and verified to provide reference for molecular marker assisted selection breeding.【Method】The wheat 55K SNP microarray was used to genotype parents and RIL populations, and a high density genetic linkage map was constructed, and its correlation with Chinese spring reference genome IWGSC RefSeq v1.0 was analyzed. QTL mapping of traits related to grain weight in multiple environments based on inclusive composite interval mapping method. The analysis of variance of major effect QTLs were performed to judge the additive interaction effect among different QTLs, and to analyse its effect on traits related to grain weight. At the same time, the corresponding kompetitive allele specific PCR marker was developed according to the closely linked SNP loci of major QTL for grain length, and verified in 242 wheat accessions worldwide.【Result】In this study, a high density genetic map of Heshangtou/Longchun 23 RIL population was constructed, with full length 4 543 cM, including 22 linkage groups, covering 21 chromosomes of wheat, and the average genetic distance was 1.7 cM. There was a significant correlation between genetic map and physical map, and the Pearson correlation coefficient were 0.77-0.99 (P<0.001). A total of 51 QTLs related to grain weight were detected, among them, 4 stable major QTLs were found in multi-environments (three or more environments) and distributed on 2D, 5A, 6B and 7D chromosomes. According to the physical interval and functional markers, it is inferred that stable major QTLs Qtkw.nwafu-2D.1 and Qtkw.nwafu-7D are photoperiod gene Ppd-D1 and flowering gene FT-D1, respectively. The analysis of variance shows that there is a significant interaction between them. The favorite alleles polymerization of Qtkw.nwafu-2D.1 and Qtkw.nwafu-7D can significantly increase thousand grain weight and grain width of wheat. In addition, the corresponding KASP molecular detection marker AX-111067709 was developed based on the co-segregated SNP of the major locus Qgl.nwafu-5A for grain length, which was significantly correlated with grain length and grain weight traits in a diversity panel comprising of 242 wheat accessions, and could increase grain length by 3.33% to 4.59% and grain weight 5.70% to 10.35% in different environments (P<0.001).【Conclusion】There are several genetic loci that affect traits linked to grain weight in Heshangtou (HST) and Longchun 23 (LC23), and Qtkw.nwafu-2D.1 and Qtkw.nwafu-7D dramatically increased thousand grain weight and grain width through additive interaction effects. Qgl.nwafu-5A is significantly correlated with grain weight and grain length, and its co-segregated molecular marker AX-11106770 can be used in molecular marker assisted selection breeding.

Key words: wheat, thousand-grain weight, QTL, KASP marker, molecular marker-assisted selection breeding

Table 1

Phenotypic analysis of HST/LC23 population"

性状
Traits		 环境
Environment		 亲本Parents 平均值±标准差
Mean ± SD		 最小值
Min		 最大值
Max		 w检验
w-test		 P 遗传力
H2
和尚头HST 陇春LC23
千粒重
TKW (g)		 E1 46.77 39.56** 43.22±6.74 23.85 59.74 0.97 0.24 0.81
E2 45.81 39.00** 41.64±5.85 24.09 54.73 0.97 0.07
E3 48.03 39.32** 43.94±5.53 26.32 57.71 0.97 0.07
E4 47.93 46.82 42.02±6.87 23.36 60.69 0.98 0.75
BLUP 46.33 41.47** 42.75±4.04 30.53 52.94 0.98 0.32
粒长
GL (mm)		 E1 7.26 6.69** 6.99±0.58 4.95 8.92 0.99 0.98 0.58
E2 6.53 6.10** 6.36±0.28 5.52 7.19 0.98 0.63
E3 7.47 7.09** 8.03±0.93 5.59 10.29 0.96 0.00
E4 6.41 6.02** 6.20±0.56 4.38 7.39 0.84 0.00
BLUP 6.91 6.65 ** 6.91±0.24 6.29 7.71 0.98 0.72
粒宽
GW (mm)		 E1 3.31 3.07 3.15±0.31 2.10 3.99 0.98 0.63 0.56
E2 3.01 2.88 2.95±0.15 2.41 3.34 0.96 0.01
E3 3.64 3.42* 3.79±0.42 2.46 4.87 0.96 0.00
E4 3.22 3.21 3.01±0.30 1.97 3.53 0.85 0.00
BLUP 3.27 3.18 3.23±0.11 2.85 3.55 0.97 0.29
籽粒长宽比
LWR		 E1 2.19 2.18 2.22±0.15 1.88 2.98 0.96 0.00 0.84
E2 2.17 2.12* 2.16±0.13 1.89 2.53 0.96 0.00
E3 2.05 2.07 2.12±0.13 1.77 2.61 0.98 0.52
E4 1.99 1.88** 2.06±0.14 1.72 2.69 0.97 0.31
BLUP 2.11 2.08** 2.14±0.09 1.88 2.47 0.98 0.63

Fig. 1

Correlation analysis of traits related to grain weight The same as below"

Table 2

Statistics of marker distribution on genetic map of HST/LC23 RIL population"

染色体
Chromosome		 连锁群
Linkage
group		 遗传长度
Genetic length
(cM)		 Bin标记数量
No. of Bin		 标记数量
No. of marker		 Bin标记密度
Bin density
(Bin/cM)		 最大遗传距离
Max genetic distance (cM)
1A LG1A 165.15 161 1059 1.03 9.21
1B LG1B 198.34 153 1388 1.30 14.02
1D LG1D 133.99 46 377 2.91 19.57
2A LD2A 211.24 140 937 1.51 15.13
2B LG2B 237.42 175 1295 1.36 11.76
2D LG2D 286.16 109 464 2.63 20.80
3A LG3A 259.25 174 1008 1.49 14.16
3B LG3B 249.84 165 1331 1.51 15.08
3D LG3D 251.05 94 638 2.67 18.11
4A LG4A 209.20 108 641 1.94 11.16
4B LG4B 122.92 69 256 1.78 13.47
4D LG4D 180.03 112 442 1.61 18.11
5A LG5A 247.18 174 816 1.42 22.91
5B LG5B 247.07 172 760 1.44 10.86
5D LG5D 305.92 91 293 3.36 17.21
6A LG6A 183.40 101 727 1.82 17.92
6B LG6B 160.84 138 953 1.17 17.20
6D LG6D 215.15 90 713 2.39 31.82
7A LG7A.1 217.90 148 1104 1.47 10.74
LG7A.2 15.94 19 82 0.84 3.30
7B LG7B 206.74 151 901 1.37 14.96
7D LG7D 238.28 82 344 2.91 15.93
A基因组 A genome 1509.26 1025 6374 1.47 22.91
B基因组 B genome 1423.17 1023 6884 1.39 17.20
D基因组 D genome 1610.57 624 3271 2.58 31.82
总计 Total 4543.00 2672 16529 1.70 31.82

Fig. 2

Collinearity analysis of genetic map and physical map The red scatter point indicates collinearity, and the black histogram indicates the recombination rate of Bin markers on the reference genome. **: P<0.01, ***: P<0.001"

Table 3

Partial QTLs of traits related to grain weight"

性状
Trait		 QTL 环境
Environment		 左侧标记
Left marker		 右侧标记
Right marker		 物理位置
Physical interval (Mb)		 LOD 贡献率
PVE (%)		 加性效应1)
Add
千粒重TKW Qtkw.nwafu-2A E1\E2 AX-169336957 AX-109601471 94.16—136.56 3.47—7.93 5.22—7.42 1.45—2.12
Qtkw.nwafu-2D.1 E1\E2\E4\BLUP AX-111696354 AX-109755068 28.09—47.89 4.33—11.89 7.19—12.92 -2.44—-1.42
Qtkw.nwafu-2D.2 E4\BLUP AX-110373068 AX-109710757 148.29—197.50 3.58—4.16 5.69—5.80 -1.75—-1.01
Qtkw.nwafu-7D E1\E2\E3\E4\BLUP AX-110826147 AX-111618969 65.50—75.23 4.63—10.71 7.53—13.26 1.55—2.46
粒长
GL		 Qgl.nwafu-2A.1 E2\BLUP AX-109402024 AX-169336957 86.97—94.16 3.88—6.74 3.74—8.05 0.06—0.09
Qgl.nwafu-4B E3\BLUP AX-110076607 AX-109852046 11.43—12.82 4.03—5.6 6.14—8.06 0.08—0.28
Qgl.nwafu-5A E1\E2\E3\BLUP AX-111067709 AX-110670888 0.65—0.75 3.93—59.43 4.56—17.86 0.09—0.81
Qgl.nwafu-6B E2\BLUP AX-110927266 AX-110464369 135.98—173.59 5.06—7.10 5.10—8.78 -0.10—-0.07
粒宽
GW		 Qgw.nwafu-2D.1 E2\E3\BLUP AX-111096297 AX-109755068 32.97—47.89 4.41—10.14 7.28—12.36 -0.12—-0.04
Qgw.nwafu-4B E1\BLUP AX-110076607 AX-94699353 11.43—19.76 3.93—4.10 5.50—7.91 0.03—0.10
Qgw.nwafu-5A.1 E3\BLUP AX-111067709 AX-110670888 0.65—0.75 4.06—5.17 5.97—6.57 0.03—0.12
Qgw.nwafu-7D.2 E2\E4\BLUP AX-111843581 AX-111618969 67.45—75.23 4.76—16.00 7.85—20.13 0.05—0.10
籽粒长
宽比LWR		 Qlwr.nwafu-2A E3\E4\BLUP AX-109287352 AX-111258161 613.88—626.08 4.54—7.01 5.41—11.90 0.02—0.05
Qlwr.nwafu-2D E1\E2\BLUP AX-109422526 AX-109755068 35.02—47.89 8.32—12.93 7.68—14.51 0.03—0.06
Qlwr.nwafu-4A E1\E2\BLUP AX-110629864 AX-111561234 72.00—129.02 5.53—9.57 5.75—8.11 -0.04—-0.03
Qlwr.nwafu-4D E3\BLUP AX-110015970 AX-109181699 33.04—35.23 3.30—4.90 2.54—8.16 -0.04—-0.02
Qlwr.nwafu-6B.2 E1\E2\E3\BLUP AX-110603992 AX-95659567 455.92—559.34 4.40—9.13 4.87—10.48 -0.04—-0.03
Qlwr.nwafu-7D E1\E2\BLUP AX-109866327 AX-111618969 61.80—75.23 4.12—12.57 4.67—12.16 -0.05—-0.03

Fig. 3

Distribution of QTLs related to grain weight on chromosomes"

Table 4

Analysis of variance of Qtkw.nwafu-2D.1 and Qtkw.nwafu-7D under different environments"

源Source 自由度df 千粒重TKW 粒宽GW 粒长GL 籽粒长宽比LWR
Qtkw.nwafu-2D.1 (2D) 1 76.83*** 39.88*** 3.80 61.42***
Qtkw.nwafu-7D (7D) 1 71.32*** 44.50*** 1.62 96.21***
环境Environment (E) 4 2.27 195.79*** 205.2*** 35.32***
2D×7D 1 26.75*** 11.51** 0.33 26.98***
2D×E 4 1.74 4.59** 4.21** 1.41
7D×E 4 0.73 0.74 0.06 1.52
2D×7D×E 4 0.817 1.81 1.10 0.86
误差Error 813 30.21 0.08 0.35 0.01

Fig. 4

Polymerization additive effect of Qtkw.nwafu-2D.1 and Qtkw.nwafu-7D +: Allele of the corresponding flanking marker derived from the lines of HST; -: Allele of the corresponding flanking marker derived from the lines of LC23. Different lowercase letters indicate significant differences"

Fig. 5

Significance test of grain length of 242 wheat materials (AX-111067709) a: Yangling; b: Nanyang; c: Luoyang"

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